Olivar: automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens

Tiled amplicon sequencing has served as an essential tool for tracking the spread and evolution of pathogens. Over 2 million complete SARS-CoV-2 genomes are now publicly available, most sequenced and assembled via tiled amplicon sequencing. While computational tools for tiled amplicon design exist, they require downstream manual optimization both computationally and experimentally, which is slow and costly. Here we present Olivar, a first step towards a fully automated, variant-aware design of tiled amplicons for pathogen genomes. Olivar converts each nucleotide of the target genome into a numeric risk score, capturing undesired sequence features that should be avoided. In a direct comparison with PrimalScheme, we show that Olivar has fewer SNPs overlapping with primers and predicted PCR byproducts. We also compared Olivar head-to-head with ARTIC v4.1, the most widely used primer set for SARS-CoV-2 sequencing, and show Olivar yields similar read mapping rates (~90%) and better coverage to the manually designed ARTIC v4.1 amplicons. We also evaluated Olivar on real wastewater samples and found that Olivar had up to 3-fold higher mapping rates while retaining similar coverage. In summary, Olivar automates and accelerates the generation of tiled amplicons, even in situations of high mutation frequency and/or density. Olivar is available as a web application at https://olivar.rice.edu. Olivar can also be installed locally as a command line tool with Bioconda. Source code, installation guide and usage are available at https://github.com/treangenlab/Olivar.

[Clinical efficacy of the treatment of bilateral gluteal muscle contracture by inside-out iliotibial band release under arthroscopy in the supine position]

Objective: To investigate the clinical efficacy of bilateral gluteal muscle contracture treated with inside-out iliotibial band release under arthroscopy in the supine position. Methods: A prospective non-randomized controlled trial. Forty-six patients admitted to the Department of Sports Medicine, Senior Department of Orthopedics, the Fourth Medical Center of PLA General Hospital from April 2021 to August 2022 for bilateral gluteal muscle contracture and proposed surgical treatment were enrolled. The subjects were divided into two groups according to the preferred surgical protocols of the patients: the supine position group was treated with inside-out iliotibial band release under arthroscopy in the supine position, and the operation in lateral position group was carried out with outside-in iliotibial band release under arthroscopy in the lateral position. The total duration of non-surgical operations and the total duration of surgical operations were recorded for all patients. The gluteal muscle contracture disability scale within 3 days before surgery and at least 2 months after surgery were compared between the two groups, and the occurrence of complications between the two groups was compared too. Results: There were 26 cases in the supine position group, 11 males and 15 females with a mean age of (31.8±7.3) years; and there were 20 cases in the lateral position group, 7 males and 13 females with a mean age of (30.6±6.3) years. The differences in gender, age, body mass index (BMI) and postoperative follow-up time between the two groups were not statistically significant (all P>0.05). The total duration of non-surgical operations was shorter in the supine position group than in the lateral position group [(47.9±10.4) min vs (63.9±7.5) min, P<0.001]. There was no statistically significant difference in the total duration of surgical operations between the supine position group and the lateral position group [31.0(27.0, 43.5) min vs 33.0(24.8, 38.0) min, P>0.05]. The postoperative gluteal muscle contracture disability scales were significantly improved in both the supine position and lateral position groups when compared with those before the operation [93.0 (85.0, 98.0) vs 61.0 (50.5, 66.8), P<0.001 and 88.5±6.9 vs 63.6±9.6, P<0.001, respectively]. There was no statistically significant difference in the gluteal muscle contracture disability scale between the supine position and lateral position groups before and 2 months after surgery [59.3±11.9 vs 63.6±9.6 and 93.0 (85.0, 98.0) vs 89.5(84.0, 94.8), both P>0.05, respectively]. Two patients in each group developed subcutaneous hematoma after surgery, and all of them resolved within 2 weeks after surgery, the difference in complication incidence rate was not statistically significant (P>0.05). No postoperative complications such as fat liquefaction in the operated area, infection, decreased hip abductor muscle strength or nerve injury in the lower extremity were observed in both groups. Conclusion: The treatment of bilateral gluteal muscle contracture by inside-out iliotibial band release under arthroscopy in the supine position can effectively improve clinical efficiency, with definite efficacy, and it is an operative program worth promoting.

[Outcomes of fluoroscopy-free hip arthroscopy technique in the treatment of femoroacetabular impingement syndrome]

Objective: To evaluate the effect of fluoroscopy-free technique in the arthroscopic treatment of femoroacetabular impingement syndrome (FAIS). Methods: A retrospective cohort study. Clinical data of FAI patients treated with hip arthroscopy in the No.4 Medical Center, PLA General Hospital from October 2018 to December 2021 were retrospectively analyzed. The patients were divided into two groups according to the surgical procedure: the fluoroscopy group and the fluoroscopy-free group. The operation time and modified Harris hip score (mHHS), international hip outcome tool (iHOT12) and visual analogue scale (VAS) of hip joint pain before and after the operation were observed and compared between the two groups. And the incidence of surgical complications in the two groups were compared too. Results: A total of 460 patients (213 males and 247 females) [aged (32.6±8.3) years (15-67 years)] with valid follow-up were included in this study. There were 275 cases in the fluoroscopy-free group and 185 cases in the fluoroscopy group. The operation time was shorter in the fluoroscopy-free group when compared with that in the fluoroscopy group, and the difference was statistically significant [(93.36±12.54) min vs (115.62±6.03) min, P<0.001]. In both groups, the VAS scores decreased and the mHHS scores and iHOT12 scores improved significantly at the last follow-up when compared with those before the operation (all P<0.001); however, there was no significant difference in the scores between the two groups (all P>0.05). The complication rate in the fluoroscopy-free group was 10.18% (28/275), and it was 10.81%(20/185) in the fluoroscopy group (P=0.829). Conclusion: Fluoroscopy-free hip arthroscopy technique for FAI can avoid radiation and shorten the operation time, but it does not increase the incidence of complications with reliable clinical outcomes.

Abstract PR003: Apoptotic DNase DFFB mediates stress-induced mutagenesis

It was recently discovered that actively proliferating and post-mitotic normal human tissues acquire somatic mutations at the same rate. This indicates that somatic mutagenesis is primarily independent of cell proliferation and therefore cannot be based on DNA replication errors. Furthermore, the mutagenic mechanisms which contribute to ubiquitous mutational signatures such as SBS5 remain unknown. It has been hypothesized that tissues accumulate mutations through unknown physiologic processes which contribute to DNA damage but the molecular details remain unknown. These observations have revealed our lack of understanding of the fundamental processes of mutagenesis. Stress-induced mutagenesis has been previously characterized in bacteria which respond to stress by transiently increasing the rate of mutagenesis to promote the emergence of resistance mutations. This phenomenon was recently discovered in human cancer cells but the mechanism is unknown. Here, we present our discovery that cancer cells under drug stress undergo sublethal apoptotic signaling resulting in activation of apoptotic DNase DFFB. DFFB, which canonically acts to fragment chromosomal DNA during apoptosis, induces DNA strand breaks in surviving cancer cells resulting in error prone repair and mutagenesis. In the context of targeted therapy-treated cancer, we found that DFFB is required for acquired resistance to emerge in multiple tumor types. We also found that CD8 T cells induce a similar process in targeted tumor cells which survive. Therefore, sublethal apoptotic signaling may be a general phenomenon which promotes mutagenesis in human cancer. Based on these observations and prior literature showing sublethal apoptotic signaling occurs in normal cells in response to various stress stimuli, we propose that this mechanism may be a previously unknown fundamental mutagenic process which contributes not only to acquired resistance in cancer but also to tumor initiation, aging and other conditions.

Citation Format: August F. Williams, David A.G. Gervasio, Claire E. Turkal, Mehrshad Hairani, Michael X. Wang, Anna E. Stuhlfire, Ariel H. West, Brandon E. Mauch, Michelle H. Paw, Cooper P. Lathrop, Sophie H. Harris, Jennifer L. Page, Matthew J. Hangauer. Apoptotic DNase DFFB mediates stress-induced mutagenesis [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr PR003.

Visualization of Chiral Electronic Structure and Anomalous Optical Response in a Material with Chiral Charge Density Waves

Chiral materials have attracted significant research interests as they exhibit intriguing physical properties, such as chiral optical response, spin-momentum locking, and chiral induced spin selectivity. Recently, layered transition metal dichalcogenide 1T-TaS_{2} has been found to host a chiral charge density wave (CDW) order. Nevertheless, the physical consequences of the chiral order, for example, in electronic structures and the optical properties, are yet to be explored. Here, we report the spectroscopic visualization of an emergent chiral electronic band structure in the CDW phase, characterized by windmill-shaped Fermi surfaces. We uncover a remarkable chirality-dependent circularly polarized Raman response due to the salient in-plane chiral symmetry of CDW, although the ordinary circular dichroism vanishes. Chiral Fermi surfaces and anomalous Raman responses coincide with the CDW transition, proving their lattice origin. Our Letter paves a path to manipulate the chiral electronic and optical properties in two-dimensional materials and explore applications in polarization optics and spintronics.

Genetic resiliency associated with dominant lethal TPM1 mutation causing atrial septal defect with high heritability

Analysis of large-scale human genomic data has yielded unexplained mutations known to cause severe disease in healthy individuals. Here, we report the unexpected recovery of a rare dominant lethal mutation in TPM1, a sarcomeric actin-binding protein, in eight individuals with large atrial septal defect (ASD) in a five-generation pedigree. Mice with Tpm1 mutation exhibit early embryonic lethality with disrupted myofibril assembly and no heartbeat. However, patient-induced pluripotent-stem-cell-derived cardiomyocytes show normal beating with mild myofilament defect, indicating disease suppression. A variant in TLN2, another myofilament actin-binding protein, is identified as a candidate suppressor. Mouse CRISPR knock-in (KI) of both the TLN2 and TPM1 variants rescues heart beating, with near-term fetuses exhibiting large ASD. Thus, the role of TPM1 in ASD pathogenesis unfolds with suppression of its embryonic lethality by protective TLN2 variant. These findings provide evidence that genetic resiliency can arise with genetic suppression of a deleterious mutation.

[Chromosomal karyotypes and C-band analysis of Triatoma rubrofasciata in China]

OBJECTIVE

To investigate the karyotypes and C bands of Triatoma rubrofasciata in China, so as to understand its chromosome number, morphology and C-band staining of T. rubrofasciata.

METHODS

The testis specimens were sampled from male T. rubrofasciata collected from Shunde City, Guangdong Province, prepared into slides of metaphase chromosomes and subjected to Giemsa staining and C-band staining. The morphology of metaphase chromosomes and the location of heterochromatin were observed using microscopy, and the long arm and short arm of each chromosome and total chromosome length were recorded to analyze the karyotypes and C bands of T. rubrofasciata.

RESULTS

The male T. rubrofasciata presented a chromosome number of 2n = 25, including 22 autosomes and 3 sex chromosomes. The relative length of chromosomes ranged from 3.59% to 12.76%, the arm ratio was 1.06 to 1.24, and the centromere index was 44.76% to 48.47%. All chromosomes were metacentric chromosomes and the karyotype formula was 2n = 22 metacentric + X₁X₂Y, and the C bands varied on different chromosomes. No heterochromatin was found in the X chromosome, and the overall staining appeared pale, while heterochromatin was detected in all regions of the Y chromosome, and the overall staining appeared dark. In addition, heterochromatin was present in both ends of the autosome.

CONCLUSIONS

The male T. rubrofasciata presents a chromosome number of 2n = 25 in China, and the karyotype formula is 2n = 22 metacentric + X₁X₂Y. C-banding shows dark staining of the Y chromosome, pale staining of the X chromosome, and dark staining of both ends of the autosome. Our data may provide insights into the investigation on the origin, evolution and gene mapping of T. rubrofasciata in China.

A deep learning model for predicting next-generation sequencing depth from DNA sequence

Targeted high-throughput DNA sequencing is a primary approach for genomics and molecular diagnostics, and more recently as a readout for DNA information storage. Oligonucleotide probes used to enrich gene loci of interest have different hybridization kinetics, resulting in non-uniform coverage that increases sequencing costs and decreases sequencing sensitivities. Here, we present a deep learning model (DLM) for predicting Next-Generation Sequencing (NGS) depth from DNA probe sequences. Our DLM includes a bidirectional recurrent neural network that takes as input both DNA nucleotide identities as well as the calculated probability of the nucleotide being unpaired. We apply our DLM to three different NGS panels: a 39,145-plex panel for human single nucleotide polymorphisms (SNP), a 2000-plex panel for human long non-coding RNA (lncRNA), and a 7373-plex panel targeting non-human sequences for DNA information storage. In cross-validation, our DLM predicts sequencing depth to within a factor of 3 with 93% accuracy for the SNP panel, and 99% accuracy for the non-human panel. In independent testing, the DLM predicts the lncRNA panel with 89% accuracy when trained on the SNP panel. The same model is also effective at predicting the measured single-plex kinetic rate constants of DNA hybridization and strand displacement.

DNA probes used in next generation sequencing (NGS) have variable hybridisation kinetics, resulting in non-uniform coverage. Here, the authors develop a deep learning model to predict NGS depth using DNA probe sequences and apply to human and non-human sequencing panels.

Common deletion variants causing protocadherin-α deficiency contribute to the complex genetics of BAV and left-sided congenital heart disease

Bicuspid aortic valve (BAV) with ~1%-2% prevalence is the most common congenital heart defect (CHD). It frequently results in valve disease and aorta dilation and is a major cause of adult cardiac surgery. BAV is genetically linked to rare left-heart obstructions (left ventricular outflow tract obstructions [LVOTOs]), including hypoplastic left heart syndrome (HLHS) and coarctation of the aorta (CoA). Mouse and human studies indicate LVOTO is genetically heterogeneous with a complex genetic etiology. Homozygous mutation in the Pcdha protocadherin gene cluster in mice can cause BAV, and also HLHS and other LVOTO phenotypes when accompanied by a second mutation. Here we show two common deletion copy number variants (delCNVs) within the PCDHA gene cluster are associated with LVOTO. Analysis of 1,218 white individuals with LVOTO versus 463 disease-free local control individuals yielded odds ratios (ORs) at 1.47 (95% confidence interval [CI], 1.13-1.92; p = 4.2 × 10-3) for LVOTO, 1.47 (95% CI, 1.10-1.97; p = 0.01) for BAV, 6.13 (95% CI, 2.75-13.7; p = 9.7 × 10-6) for CoA, and 1.49 (95% CI, 1.07-2.08; p = 0.019) for HLHS. Increased OR was observed for all LVOTO phenotypes in homozygous or compound heterozygous PCDHA delCNV genotype comparison versus wild type. Analysis of an independent white cohort (381 affected individuals, 1,352 control individuals) replicated the PCDHA delCNV association with LVOTO. Generalizability of these findings is suggested by similar observations in Black and Chinese individuals with LVOTO. Analysis of Pcdha mutant mice showed reduced PCDHA expression at regions of cell-cell contact in aortic smooth muscle and cushion mesenchyme, suggesting potential mechanisms for BAV pathogenesis and aortopathy. Together, these findings indicate common variants causing PCDHA deficiency play a significant role in the genetic etiology of common and rare LVOTO-CHD.

MifS, a DctB family histidine kinase, is a specific regulator of α-ketoglutarate response in Pseudomonas aeruginosa PAO1

The C5-dicarboxylate α-ketoglutarate (α-KG) is a preferred nutrient source for the opportunistic pathogen Pseudomonas aeruginosa. However, very little is known about how P. aeruginosa detects and responds to α-KG in the environment. Our laboratory has previously shown that the MifS/MifR two-component signal transduction system regulates α-KG assimilation in P. aeruginosa PAO1. In an effort to better understand how this bacterium detects α-KG, we characterized the MifS sensor histidine kinase. In this study we show that although MifS is a homologue of the C4-dicarboxylate sensor DctB, it specifically responds to the C5-dicarboxylate α-KG. MifS activity increased >10-fold in the presence of α-KG, while the related C5-dicarboxylate glutarate caused only a 2-fold increase in activity. All other dicarboxylates tested did not show any significant effect on MifS activity. Homology modelling of the MifS sensor domain revealed a substrate binding pocket for α-KG. Using protein modelling and mutational analysis, we identified nine residues that are important for α-KG response, including one residue that determines the substrate specificity of MifS. Further, we found that MifS has a novel cytoplasmic linker domain that is required for α-KG response and is probably involved in signal transduction from the sensor domain to the cytoplasmic transmitter domain. Until this study, DctB family histidine kinases were known to only respond to C4-dicarboxylates. Our work shows that MifS is a novel member of the DctB family histidine kinase that specifically responds to α-KG.

[Correlation analysis between decreased cerebral perfusion measured from arterial spin labeling and cerebrovascular events in patients with bilateral moyamoya angiography]

Objective: To explore the correlation between decreased cerebral perfusion measured from arterial spin labeling and cerebrovascular events in patients with bilateral moyamoya angiography (MMA). Methods: Twenty-seven consecutive cases with bilateral MMA, who were admitted to the neurosurgery department of Nanjing Drum Tower Hospital from April to November 2020, were included in this retrospective study. Among them, 10 were males and 17 were females, aged 35-66 (55±9) years. These patients all presented with unilateral cerebral hemisphere cerebral infarction or cerebral hemorrhage. The Wilcoxon paired signed-rank test was used to qualitatively analyze the differences in the Arterial Transit Artifact (ATA) of the bilateral cerebral hemispheres. The mean gray value, the kurtosis and skewness of gray distribution curve of bilateral cerebral hemispheres on cerebral blood flow (CBF) images with post labeling delay (PLD) of 1.5 s and 2.5 s were quantitative calculated. The relationship between ASL and cerebrovascular event was determined using binary logistics regression analysis. Results: No significant difference was observed in ATA between bilateral hemispheres on CBF images with PLDs of 1.5 s and 2.5 s (P>0.05). On the CBF images with a PLD of 1.5 s, the mean gray value of the cerebral hemisphere on the lesion side (17.50±5.88) was markly lower than that on the non-lesion side (20.80±5.51) (P<0.001), the kurtosis and skewness of gray distribution were significantly different between bilateral cerebral hemispheres (P<0.05);On the CBF images with a PLD of 2.5 s, the mean gray value and the skewness of the gray distribution on the lesion side of the cerebral hemisphere were statistically different from those on the non-lesion side (P<0.05), while the difference in kurtosis was not statistically significant between bilateral cerebral hemispheres (P>0.05). Multivariate regression analysis showed that the reduction of gray value on the side of the lesion was independently associated to the occurrence of the cerebrovascular events (OR_PLD1.5=0.192, 95%CI:0.047-0.783;OR_PLD2.5=0.175, 95%CI:0.050-0.615). Conclusion: The decreased perfusion detected by ASL is independently associated with cerebrovascular events in patients with MMA.

[A cross-sectional study on psychological needs of family members of critically ill inpatients in semi-closed wards and analysis of influence factors]

Objective: To analyze and discuss the psychological needs of family members of critically ill burn inpatients in semi-closed wards and their related influence factors. Methods: A cross-sectional survey was conducted among the 82 burn patients, who met the inclusion criteria and were admitted to the Department of Burns and Plastic Surgery of Ruijin Hospital of Shanghai Jiao Tong University School of Medicine from October 2018 to April 2019, and their family members. A general condition questionnaire of 15 indexes was applied to investigate the general data of burn patients and their family members including cause of burn, gender, age, total burn area, burn depth, burn severity, burn site, and type of medical insurance of patients, kinship with the patients, gender, age, experience of accompanying in intensive care isolation wards, occupation, education level, and monthly income of their family members. The Critical Care Family Needs Inventory (CCFNI) was used to assess each item, each factor, and total scores of the family members of patients including 5 factors and 45 items such as support scale (SS), comfort scale (CS), information scale (IS), proximity scale (PS), assurance scale (AS). CCFNI was used to assess the total scores of patients and their family members after classification according to the general data, the data were statistically analyzed with one-way analysis of variance or independent sample t test. Indicators with statistical significance in the above analysis were selected for multiple linear regression analysis to screen the independent influence factors of psychological needs of patients' family members. CCFNI was used to assess each dimension scores of patients and their family members after classification according to the aforementioned selected independent influence factors including age and burn area of patients, gender, educational level, and experience of accompanying in intensive care isolation wards of their family members, and the data were statistically analyzed with one-way analysis of variance or independent sample t test. Results: A total of 82 questionnaires were sent out in this study, and 80 were effectively received, with s a recovery rate of 97.6%. In 80 patients, there were 45 males and 35 females; 35 cases (43.75%) were ≤14 years; most of the patients had flame and thermal burns; 33 patients (41.25%), 21 patients (26.25%), and 26 patients (32.50%) had moderate, severe, and extremely severe burns, respectively; and only 3 patients (3.75%) had no health insurance. In 80 family members of patients, 34 (42.50%) were males and 46 (57.50%) were females; 62.50% in the family members of patients were concentrated between 18 and 45 years old; and 12 family members of patients had experience of accompanying in intensive care isolation wards, accounting for 15.00%. The total CCFNI score of the family members was (141±14) points, and the scores of AS, PS, IS, CS, and SS were (3.77±0.23), (3.43±0.37), (3.53±0.34), (2.50±0.59), and (2.69±0.45) points, respectively. The top five items of the psychological needs of family members of patients were concentrated in three factors (AS, PS, and IS), and the item "ensuring that patients receive the best treatment" ranked the first, with a score of (3.99±0.11) points. There were significant differences on the CCFNI total scores of patients with different age, total burns area, and severity of burns and of their family members with different gender, education level, and whether or not experience of accompanying in intensive care isolation unit (F=4.378, 5.481, 5.913, t=4.027, 14.339, 7.265, P<0.05 or P<0.01). Multiple linear regression analysis showed that the patient's age (≤14, 15-45 years) and total burn area (11%-30%, 31%-49%, ≥50% TBSA) and the patient's family members' gender, educational level, experience of accompanying in intensive care isolation unit could affect the psychological needs of family members of patients (t=3.133, 2.260, 2.297, 2.433, 3.015, 2.200, 2.102, 2.463, P<0.05 or P<0.01). There was statistically significant difference in AS score of the patients' family members with different age (F=4.390, P<0.05). There were significant differences in both IS and AS scores of the patients' family members of patients with different burn area (F=5.042, 3.131, P<0.05 or P<0.01). The AS score of the patients' family members with experience of accompanying in intensive care isolation unit was significantly lower than those without (t=-1.040, P<0.05). The SS score of the patients' family members with college education or above was significantly higher than those with high school (technical secondary school) or below (t=0.657, P<0.05). The IS score of the patients' family members with college education or above was significantly lower than those with high school (technical secondary school) or below (t=-1.438, P<0.05). The SS score of male family members of patients was significantly lower than those of female patients (t=4.149, P<0.05). Conclusions: The family members of burn patients in semi-closed ward have the most urgent need to ensure the patients receive the best treatment. Patients' age, total burn area, and their family members' gender, education level, experience of accompanying in intensive care isolation unit are the main factors affecting the psychological needs of family members of patients.

Altered resting-state functional connectivity between subregions in the thalamus and cortex in migraine without aura

BACKGROUND AND PURPOSE

Migraine is a complex and disabling neurological disorder, the exact neurological mechanisms of which remain unclear. The thalamus is considered to be the hub of the central processing and integration of nociceptive information, as well as the modulation of these processes.

METHODS

A total of 48 migraineurs without aura (MWoAs) during the interictal phase and 48 age- and sex-matched healthy controls underwent resting-state functional magnetic resonance imaging scans. We utilized masked independent component analysis and seed-based functional connectivity (FC) to investigate whether MWoAs exhibited abnormal FC between subregions in the thalamus and the cortex regions.

RESULTS

The MWoAs showed significantly weaker FC between the anterior dorsal thalamic nucleus and left precuneus. Additionally, MWoAs exhibited significantly reduced FC between the ventral posterior nucleus (VPN) and left precuneus, right inferior parietal lobule (R-IPL) and right middle frontal gyrus. Furthermore, the FC Z-scores between the VPN and R-IPL were negatively correlated with pain intensity in MWoAs. The disease duration of patients was negatively correlated with the FC Z-scores between the VPN and R-IPL.

CONCLUSION

These altered thalamocortical connectivity patterns may contribute to multisensory integration abnormalities, deficits in pain attention, cognitive evaluation and pain modulation. Pain sensitivity and disease duration are closely tied to abnormal FC between the VPN and R-IPL. Remarkably, recurrent headache attacks might contribute to this maladaptive functional plasticity closely related to pain intensity.

[Efficacy and safety of intranasal dexmedetomidine premedication for children undergoing CT or magnetic resonance imaging: a systematic review and meta-analysis]

Objective: To review the efficacy and safety in children receiving intranasal dexmedetomidine premedication before CT or magnetic resonance imaging (MRI). Methods: A literature search (search terms included "dexmedetomidine" "intranasal drug administration" "children" "CT" and "MRI") was conducted using Embase, PubMed, the Cochrane Library, ClinicalTrials.gov, CNKI, Wanfang, VIP database and Chinese Biomedical Literature Database (searched from inception to March 18, 2019). Randomized controlled trials of children receiving intranasal dexmedetomidine versus chloral hydrate, ketamine or midazolam premedication before CT or MRI were included. The Cochrane Reviewers' Handbook 5.1.0 was used to evaluate the quality of the enrolled studies. The primary outcomes were sedation success rate and sedation induction time. The secondary outcomes included respiratory depression, heart rate, systolic blood pressure and blood oxygen saturation. Statistical analyses were performed using the Review Manager 5.3 software. Results: A total of 1 167 participants in 9 randomized controlled trials were included. The results of meta-analysis showed that intranasal dexmedetomidine premedication provided higher sedation success rate than oral chloral hydrate (relative risk (RR) =1.13, 95% confidence interval (CI) 1.02 to 1.26, P=0.020). There was no significant difference between intranasal dexmedetomidine and midazolam. In addition, the sedation induction time of intranasal dexmedetomidine group was significantly shorter than that in the oral chloral hydrate group (weighted mean difference -1.49, 95% CI -2.87 to -0.11; P=0.030), but showed no significant difference as compared with that of intranasal ketamine or midazolam. The patients treated with intranasal dexmedetomidine also showed significantly lower heart rate (RR=4.78, 95%CI 1.85-12.35, P=0.001) and less respiratory depression (RR=0.28, 95%CI 0.09-0.87, P=0.030). There were no intergroup differences in systolic blood pressure and blood oxygen saturation. Conclusions: Intranasal dexmedetomidine provided more effective sedation and higher safety in children undergoing CT or MRI. As this meta-analysis is limited by the small sample size, further high-quality randomized controlled trials are needed.

Greatly enhanced performance of AlGaN-based deep ultraviolet light emitting diodes by introducing a polarization modulated electron blocking layer

Carrier transport in AlGaN-based deep ultraviolet (DUV) light emitting diodes (LEDs) with the wavelength of 273 nm has been investigated by introducing polarization modulated electron blocking layer (EBL) that adopts an Al composition and thickness graded multiple quantum barriers (MQB) structure. The experimental result shows that the maximum light output power and external quantum efficiency for the proposed structure at the current of 250 mA are 9.6 mW and 1.03% respectively, severally increasing by 405% and 249% compared to traditional one, meanwhile, the efficiency droop at 250 mA is also dramatically reduced from 42.2% to 16.6%. Further simulation analysis indicates that this graded MQB-EBL enhances the potential barrier height for electrons and meanwhile reduces that for holes, hence effectively suppresses the electron leakage, and at the same time significantly improves the hole injection efficiency. As a result, the whole performance of the LED with the proposed MQB-EBL is dramatically improved.

Impact of whole egg intake on blood pressure, lipids and lipoproteins in middle-aged and older population: A systematic review and meta-analysis of randomized controlled trials

BACKGROUND AND AIM

Effects of whole egg consumption on cardiovascular diseases (CVD) risk in the middle-aged and older population remain unclear due to inconsistent findings from observational and randomized controlled trials (RCTs). This meta-analysis aimed to assess the impacts of whole egg and egg category (whole eggs versus egg substitutes) intake quantity on CVD risk factors from systematically searched RCTs. Egg substitutes were hypothesized to have minimal effects of the blood lipid and lipoprotein profile as they are void of dietary cholesterol.

METHODS AND RESULTS

As many as 434 studies identified from PubMed, Cochrane Library, CINAHL and Medline (Ovid) databases were screened and data were extracted from 8 selected RCTs. Quality of the selected studies were assessed and the overall effect sizes of weighted mean differences (WMD) were calculated using a random effects model. Non-differential effects in blood pressures, lipids and lipoproteins were observed when >4 whole eggs/week compared to ≤4 whole eggs/week were consumed. Intake of >4 whole eggs/week compared to equivalent amounts of egg substitutes caused greater elevations in blood total cholesterol (WMD: 0.198 mmol/L; 95% CIs: 0.056, 0.339), HDL cholesterol (WMD: 0.068 mmol/L; 95% CIs: 0.006, 0.130) and LDL cholesterol (WMD: 0.171 mmol/L; 95% CIs: 0.028, 0.315) but did not differentially affect triglycerides concentration.

CONCLUSION

Overall, the results support the notion that quantity of whole egg intake does not affect CVD risk factors and consuming egg substitutes may also be beneficial compared to whole eggs on lowering CVD risk in the middle-aged and older population.

[Anxiety and depression in patients with idiopathic tinnitus and its relative factors analysis]

Objective: To investigate the psychological status of anxiety and depression in patients with idiopathic tinnitus, and to analyze its relative factors. Method: One hundred and sixty seven patients with idiopathic tinnitus were assessed by Self-Rating Anxiety Scale(SAS),Self-Rating Depression Scale(SDS) and general condition questionnaire. Patients with anxiety or depression were reassessed after corresponding treatment for 6 weeks. Result: Fifty-five patients(32.93%) were in anxiety state and 43 patients(25.75%) were in depression state. Twenty-seven patients(16.17%) were in both anxiety and depression state. The multivariate logistic regression analysis found that the incidence of anxiety and depression in patients with idiopathic tinnitus were related to sleep disorders, course of disease and THI score(P<0.05). Treatment scores(SAS and SDS) were statistically significantly different between pre- and post-treatment(P<0.01). Conclusion: The anxiety and depression state is highly prevalent in idiopathic tinnitus patients and is related to course of disease, severity of tinnitus and sleep disorders. In clinical practice, we should pay close attention to the psychological status of patients with idiopathic tinnitus, and take timely psychological intervention.

Discrete Superconducting Phases in FeSe-Derived Superconductors

A general feature of unconventional superconductors is the existence of a superconducting dome in the phase diagram. Here we report a series of discrete superconducting phases in the simplest iron-based superconductor, FeSe thin flakes, by continuously tuning the carrier concentration through the intercalation of Li and Na ions with a solid ionic gating technique. Such discrete superconducting phases are robust against the substitution of 20% S for Se, but they are vulnerable to the substitution of 2% Cu for Fe, highlighting the importance of the iron site being intact. The superconducting phase diagram for FeSe derivatives is given, which is distinct from that of other unconventional superconductors.

[Interleukin-1β and C-reactive protein level in plasma and gingival crevicular fluid in adolescents with diabetes mellitus]

OBJECTIVE

Cytokines produced by various cells are strong local mediators of inflammation. Interleukin-1beta (IL-1β) and C-reactive protein (CRP) play essential roles in the development and progression of diabetes mellitus (DM). Thus periodontal diseases could be related to DM via the same mediators of inflammation. To evaluate plasma and gingival crevicular fluid (GCF) levels of IL-1β and CRP in adolescents with DM to further investigate whether DM has an impact on the levels of inflammation factors at an early stage, and to analyze the risk of developing periodontal diseases in adolescents with DM.

METHODS

A total of 121 adolescents aged from ten to sixteen years were enrolled, 41 adolescents diagnosed with diabetes mellitus were collected in the DM group, and 80 nondiabetic adolescents as the control group. The periodontal indices of each individual were recorded, including plaque index (PLI), modified bleeding index (mBI), probing depth (PD) and attachment loss (AL). GCF and intravenous blood samples were collected, and CRP and IL-1β levels were detected by enzyme-linked immunosorbent assay (ELISA).

RESULTS

(1) PLI of DM group and control group were 1.23±0.05 and 0.95±0.04 separately, with significant difference (P=0.001). DM group and control group had mBI of 0.80±0.08 and 0.51±0.06 separately, with significant difference (P=0.003). Attachment loss was found in none of the subjects. PDs of DM group and control group were (2.37±0.51) mm and (2.31±0.05) mm separately, and there was no significant difference. (2) CRP in GCF was only detectable in partial of the individuals, with a detectable rate of 22.9% (11/48) in total. The detectable rate of CRP in GCF was significantly higher in DM group (38.5%) than that in control group (4.5%, P=0.006). The plasma level of CRP in DM group [0.23 (0.15, 1.89) mg/L] was higher than that in control group [0.19 (0.12, 4.18) mg/L], but without significance (P=0.776). (3) The plasma levels of IL-1β in DM group and control group were (14.11±0.57) ng/L and (14.71±0.50) ng/L separately, but there was no significance (P=0.456). GCF levels of IL-1β in DM group and control group were (12.91±1.95) μg/L and (17.68±3.07) μg/L, without significant difference (P=0.185).

CONCLUSION

Periodontitis was not observed in adolescents with DM at an early stage. However, the rising levels of periodontal indices and CRP in GCF, might indicate that adolescents with DM have a higher risk of developing periodontal diseases in the future.

[Study of bioequiavailability of paclitaxel for Injection (Albumin Bound) and abraxane and the efficacy of extension treatments in patients with metastatic breast cancer]

Objective: To compare the bioequiavailability of paclitaxel for injection (albumin bound) (PAB) and reference listed drug abraxane in the patients with metastatic breast cancer, and to investigate the safety and efficacy in the extension treatments of PAB. Methods: This study was random, two cycles, self-crossover control study in the bioequiavailability stage. PAB was the investigational drug T and Abraxane was the reference drug R. Patients were randomly assigned to two cycles therapy of either R→T or T→R(260 mg/m(2)/21d). Non-PD patients entered in the extension treatments of the investigational drug PAB(260 mg/m(2)/21d) until the disease progression or the intolerance toxicity. Results: From Mar 1, 2016 to May 24, 2016, we enrolled 40 patients. The blood concentration-time curve and the parameters of pharmacokinetics indicated the two drugs were the bioequivalent drug products in the initial two cycles crossover-therapy.The incidence of adverse drug reactions were 89.7% vs 97.4% in investigational drug vs reference drug and grade 3/4 toxicities were 20.5% vs 21.1%(P=1.000). Patients received a median of 7 treatment cycles(range 1-23) and a median of 260mg/m(2) actual drug dose (range 220-260 mg/m(2)). Seven patients (17.5%) had dose reductions because of toxicities (260 mg/m(2) reduce to 220 mg/m(2)). Twenty-two patients (55%) discontinued treatment prematurely because of toxicity.Overall response rates (ORR) were 40% (95% CI, 24.8%-55.2%). For patients who received PAB as first-line vs non-first-line therapy, the ORR were 43.8% vs 25%. For patients who taxane-naïve vs taxane-pretreated, the ORR were 45.5% vs 37.9%. Median PFS was 49 weeks(95% CI, 30weeks-NA). Conclusion: The paclitaxel for injection (albumin bound) (PAB) and reference listed drug abraxane are the bioequivalent drug products.The toxicity and efficacy of the PAB are similar with abraxane.The more therapy chances for Chinese patients will come by the research and development of domestic drugs.

[Anxiety and depression in patients with sudden sensorineural hearing loss and its influencing factors]

Objective:To evaluate the psychological status of anxiety and depression in patients with sudden sensorineural hearing loss, and to analyze the factors that affect the occurrence of anxiety and depression. Method:A total of 198 patients with moderate and severe sudden sensorineural hearing loss were enrolled. The patients were tested by general condition questionnaire and hospital anxiety and depression scale (HADS). Patients who developed anxiety and depression were tested again using the HADS at 1 week after completion of the treatment. Result:The incidence of anxiety was 27.27% in patients with moderate and severe sudden sensorineural hearing loss, and the incidence of depression was 25.25%. The scores of anxiety and depression were statistically significant (P<0.05). The multivariate logistic regression analysis showed that the status of anxiety and depression was accompanied by symptoms and other diseases (P<0.05). There was a significant difference between the effective group, the significant efficacy group and the cured group (P<0.05). The difference between the scores before and after treatment was compared. Differences in the ineffective group compared with the other three groups, and the cured group compared with the other three groups of anxiety, depression were statistically significant. Conclusion:The problem of anxiety and depression in patients with moderate and severe sudden sensorineural hearing loss is relatively prominent, and the symptoms of anxiety and depression are obviously affected by the symptoms and other diseases. After treatment, anxiety and depression status changes significantly. In clinical practice, anxiety and depression and its influencing factors should be taken into account for the treatment of the patients with severe sudden sensorineural hearing loss.

[The features of c/oVEMP in patient with unilateral Meniere's disease]

Objective:To evaluate the difference in c/oVEMPs between patients with MD and normal controls.Method:Twenty-two patients with unilateral MD and 21 healthy subjects (as normal controls) were prospectively examined with c/oVEMPs. The results were compared between these two groups. MD group were divided into two groups according to the pure tone average threshold: group1 PTA≤40 dBnHL,group2 PTA>40 dBnHL,and then compared their results. A commercially available software package SPSS 19.0 was used for statistical analysis.Result:The latency and amplitude of cVEMP and oVEMP in the affected side and contralateral side of the MD group were no significant difference. Compared with normal controls,the latency of P1 and N1 was prolonged,the amplitude was decreased in the MD group's cVEMP. The amplitude was decreased in the MD group's oVEMP,but the latency was not prolonged. Group 2's extraction rate of cVEMP was significantly lower than group 1.Conclusion:An increased occurrence of abnormal c/oVEMP recordings appeared in MD patients,possibly as a result of hydrops of the otolith. The saccular dysfunction may be more common than utricular dysfunction. Furthermore,that otolith damage is gradually increasing with the aggravation of cochlear injury in MD.

Monitoring thioredoxin redox with a genetically encoded red fluorescent biosensor

Thioredoxin (Trx) is one of the two major thiol antioxidants, playing essential roles in redox homeostasis and signaling. Despite its importance, there is a lack of methods for monitoring Trx redox dynamics in live cells, hindering a better understanding of physiological and pathological roles of the Trx redox system. In this work, we developed the first genetically encoded fluorescent biosensor for Trx redox by engineering a redox relay between the active-site cysteines of human Trx1 and rxRFP1, a redox-sensitive red fluorescent protein. We used the resultant biosensor-TrxRFP1-to selectively monitor perturbations of Trx redox in various mammalian cell lines. We subcellularly localized TrxRFP1 to image compartmentalized Trx redox changes. We further combined TrxRFP1 with a green fluorescent Grx1-roGFP2 biosensor to simultaneously monitor Trx and glutathione redox dynamics in live cells in response to chemical and physiologically relevant stimuli.

Nanolock-Nanopore Facilitated Digital Diagnostics of Cancer Driver Mutation in Tumor Tissue

Cancer driver mutations are clinically significant biomarkers. In precision medicine, accurate detection of these oncogenic changes in patients would enable early diagnostics of cancer, individually tailored targeted therapy, and precise monitoring of treatment response. Here we investigated a novel nanolock-nanopore method for single-molecule detection of a serine/threonine protein kinase gene BRAF V600E mutation in tumor tissues of thyroid cancer patients. The method lies in a noncovalent, mutation sequence-specific nanolock. We found that the nanolock formed on the mutant allele/probe duplex can separate the duplex dehybridization procedure into two sequential steps in the nanopore. Remarkably, this stepwise unzipping kinetics can produce a unique nanopore electric marker, with which a single DNA molecule of the cancer mutant allele can be unmistakably identified in various backgrounds of the normal wild-type allele. The single-molecule sensitivity for mutant allele enables both binary diagnostics and quantitative analysis of mutation occurrence. In the current configuration, the method can detect the BRAF V600E mutant DNA lower than 1% in the tumor tissues. The nanolock-nanopore method can be adapted to detect a broad spectrum of both transversion and transition DNA mutations, with applications from diagnostics to targeted therapy.

Molecular and pathological evaluation of cryopreserved colorectal cancerous tissues: Effects of freezing method and cryoprotection

BACKGROUND

Snap freezing and RNAlater stabilization are methods that were wildly used in biospecimen depositories to preserve cancer tissues. Both methods have its own limitations. An ideal method for preservation of diseased tissues should permit the broader uses of stored tissue samples, including not just for molecular diagnostic analysis, histopathological evaluation, but also for the recovery of functional live cells and tissues as well as the regeneration of patient-derived xenograft (PDX) models for the drug screening study.

MATERIALS AND METHODS

This study investigated molecular and pathological evaluation of cryopreserved colorectal cancer tissues, with an emphasis on effects of freezing method and cryoprotection. Global gene expression analysis with microarrays and histological examination of tissue samples were performed to compare tissue specimens after snap freezing, cryoprotectant permeation and subsequent cryopreservation.

RESULTS

Compared with the fresh tissue samples (immediately stabilized in RNAlater after collection), samples preserved by snap freezing exhibited the largest number of differentially-expressed genes. Some genes relate to neuron, drug addiction and drug binding, but the rest of differentially-expressed genes were functionally dispersive. Cryoprotectant permeation into tissue samples and subsequent cryopreservation via a rate-controlled freezing resulted in much less differentially expressed genes. Histological structures of tissue specimens were both well preserved by snap freezing and cryoproservation.

CONCLUSION

Snap freezing may not be as reliable as commonly considered. The pilot study demonstrates the feasibility of using cryopreservation to retain viable diseased tissues for multiple applications.

[Research on spatiotemporal spread of avian influenza A(H7N9) virus based on discrete geographic information]

Objective: To establish a dynamic spatiotemporal spread modes of influenza A (H7N9) virus by using discrete geographic information and explore the spatiotemporal transmission of the virus. Methods: The gene sequences of H7N9 virus isolated from human in China, which were available from Global Initiative on Sharing Avian Influenza Data (GISAID), were used in alignment by using software BioEdit 7.0. Spatiotemporal spread model of H7N9 virus was established in a Bayesian statistical framework by using software BEAST 1.8.2. The symmetric substitution model and Bayesian stochastic search variable selection (BSSVS) were used to infer and verify the historical transmission route of H7N9 virus. Finally the spatiotemporal transmission route was presented by Google Earth software. Results: The transmission of avian influenza A (H7N9) virus originated in Shanghai and Hangzhou, and can be dated back to October 2012. In March and April 2013, it began to spread to the neighboring provinces. The transmission speed up in August and September and affected more than ten geographic positions within 3 months. Conclusion: Based on gene sequences and spatial geographic information, the transmission route of H7N9 virus was traced, which would support the avian influenza prevention and control as well as avian influenza virus tracing.

[Comparison of anxiety and depression state among patients with different type of benign paroxysmal positional vertigo]

Objective:To investigate and analyze the state of anxiety and depression among patients with different type of benign paroxysmal positional vertigo(BPPV).Method:Patients with four types of BPPV were enrolled in our study,which named as posterior semicircular canals BPPV(PC-BPPV),anterior semicircular canals BPPV(AC-BPPV), horizontal semicircular canals BPPV(HC-BPPV), multiple canals BPPV(MC-BPPV).Thorough otological and neuro-otological examinations were performed on all cases,and their states of anxiety and depression were assessed by hospital anxiety and depression scale(HADS).Result:The incidence of anxiety and depression of all cases divided into four types BPPV (PC-BPP, AC-BPPV, HC-BPPV, MC-BPPV) were 36.45%, 22.78%, 28.57%, 63.16% respectively in our study .The differences among the four groups were statistically significant(P< 0.05).That were higher in these cases with PC-BPPV or MC-BPPV than those with AC-BPPV or HC-BPPV.The HADS aggregate scores of the pre-repositioning were statistically significant(P< 0.05). And the patients with PC-BPPV or MC-BPPV were higher than the other two groups.The HADS aggregate scores of the post-repositioning were statistically significant(P<0.05). And the cases with PC-BPPV or MC-BPPV were higher than the other two groups. The post-repositioning scores were compared with the pre-repositioning scores, and the difference was significant(P< 0.05).Conclusion:Among all cases with the four different types of BPPV,anxiety and depression psychological mood is more common in patients with PC-BPPV or MC-BPPV.Mood disorders affect the reset recovery after treatment,and reduce the therapeutic effect.We should pay more attention to psychological state of the patients with BPPV during treatment.And early psychological intervention can improve treatment effect.

[Study on bimodal stimulation for aural rehabilitationdevelopmentin infants with a unilateral cochlear implant]

Objective:To evaluated the aural rehabilitation development of the bimodal stimulation in deaf infants with a unilateral cochlear implant. Method:The 36 infants, suffering from severe-to-profound bilateral sensorineural hearing loss with residual hearing on at least one side, assigned into two groups randomly:18 wore only the cochlear implant(unilateral A group),while the other 18 used the CI and a contralateral hearing aid at the same time(bimodal group).The aural rehabilitation development was evaluated by sound field test and speech rehabilitation tests(including vowels, consonants, tones, monosyllables, disyllables, tri-syllables and selected hearing) after rehabilitation lasting 3 month(T1),6 month(T2)and 12 month(T3)respectively. Result:At time T1，free-field hearing threshold of 500 Hz of unilateral A group was statistically higher than bimodal group. Free-field hearing thresholds of 500 Hz and 1 000 Hz of unilateral A group were statistically higher than bimodal group attime T2（P<0.05）.At time T1, vowels, consonants, tones ,monosyllables, and disyllables rehabilitation scores of unilateral A group were statistically higher than bimodal group（P<0.05）.At time T2,there were no statistically significant differences between two groups（P>0.05）.However,consonants, tones,disyllables, tri-syllables and selected hearing rehabilitation scores of bimodal group were statistically higher than unilateral group（P<0.05）. Conclusion:The cochlear implant infants with bimodal stimulation have better aural rehabilitation development with the process of aural rehabilitation gradually.Therefore, it is essential to make full use of the advantages of binaural hearing and to choose the appropriate aural rehabilitation mode for every deaf infant.

Expression of anti-SRP19 antibody in muscle tissues from patients with autoimmune necrotizing myopathy

This study aimed to investigate the role of anti-SRP19 antibody in muscle tissues of patients with autoimmune necrotizing myopathy. Immunohistochemistry staining was used to determine the expression of anti-SRP19 antibodies in muscle tissues of autoimmune necrotizing myopathy patients. Results demonstrated that anti-SRP19 antibody was expressed in 71.4% (20/28) of muscle tissue specimens from patients with autoimmune necrotizing myopathy. Anti-SRP19 antibody expression was mainly localized in cytoplasm of necrotic muscle fibers surrounding the small blood vessels and interstitial cells. There were no significant differences in the age, course of disease, muscle, and creatine kinase levels between patients with positive or negative expression of anti-SRP19 antibodies. The expression levels of anti-SRP19, serum anti-nuclear antibodies, as well as anti-Ro-52, anti- SSA, anti-Sm, and anti-Jo-1 antibodies were not significantly different among groups. This study demonstrates that anti-SRP19 antibody is highly expressed in muscle tissues of patients with autoimmune necrotizing myopathy, and suggests that this protein may be involved in the origin and progression of the disease.

[Mental health research for new nurse during the standardized training period]

Objective: To explore the mental health status for new nurse during the standardization training period and provide scientific basis for managers to formulate corresponding measures. Methods: Using eysenck personality questionnaire (EPQ) and symptom self-assessment scale (SCL-90) , understanding social support scale (PSSS) , trait coping style questionnaire (TCSQ) and other standardized psychological assessment tools and self designed general situation questionnaire, 141 nurses in our hospital before rotary department and 1 year later accepted the questionnaire survey while the control group accepted the same questionnaire. Results: Compared with before rotary department and the control group, the forced, anxiety and interpersonal sensitivity factor increased significantly in SCL-90 for rotary nurse and the differences were significant statistical significance (P<0.05) ; Pearson correlation analysis showed rotary nurse SCL-90 forcing factor scores and EPQ-E dimension scores, TCSQ negative coping scores were positively correlated (P<0.05; r₁=0.537; r₂=0.407; r₃=0.701) , and were negatively correlated with EPQ-E dimension scores, PSSS scores and TCSQ active responding score (P<0.05; r₁=-0.621; r₂=-0.671; r₃=-0.312) ; Anxiety was positively correlated with EPQ-N, PSSS scores and TCSQ negative responding score (P<0.05; r₁=0.607; r₂=0.409; r₃=0.764) , was negatively correlated with EPQ-E dimension scores, PSSS scores and TCSQ positive responding score (P<0.05; r₁=-0.569; r₂=-0.723; r₃= -0.418) ; Interpersonal sensitivity factor score was positively correlated with EPQ-N, P dimension scores and TCSQ negative coping scores (P<0.05; r₁=0.611; r₂=0.687; r₃=0.773) , was negatively correlated with EPQ-E dimension scores, PSSS scores and TCSQ active responding score (P<0.05; r₁=-0.506; r₂=-0.693; r₃=-0.307) . Conclusion: Rotary nurse mental health status was significantly lower than non-rotary nurse.Insufficient social support, negative coping style and instability personality characteristics are the main risk factors to affect the rotation nurses mental health.

[The value of area curve ratio electrocochleography in diagnosisof Meniere's disease during different periods]

Objective:To evaluate the value of summating potential /action potential (SP/AP) area curve ratio in diagnosis of Meniere s disease(MD) during acute attacks and quiescence phase.Method:The normal control group and the MD group during acute attacks and quiescence phase received electrocochleography(EcochG)examination.The SP/AP amplitude and area curve ratios were measured respectively(to derive the SP/AP amplitude and area curve ratio),with normal SP/AP amplitude and area curve ratios of EcochG were identified,and analysed the results of EcochG in MD acute attacks and MD quiescence phase and the normal control group.Result:The upper limit of normal for SP/AP amplitude and area curve ratio were respectively 0.40 and 1.78.The SP/AP area curve ratio positive rate during acute attacks was 95.56% and SP/AP amplitude ratio was 71.77%.SP/AP area curve ratio positive rate during quiescence phase was 55.56% and amplitude ratio was 33.33%.The results showed that there were significant different between the two markers(P<0.05).The positive rate which during the period of acute attacks was higher than that quiescence phase period,The positive rate of the SP/AP amplitude and area curve ratios between acute attacks and quiescence phase were significant different(P<0.05).By the F rest,the SP/AP area curve ratio parameters in MD acute attacks and MD quiescence phase and the normal control group were compared,and the difference was significant(F=111.10,P<0.05).There were significant different between the two groups among three(P<0.05).The SP/AP area curve ratio parameters among the MD acute attacks and MD quiescence phase and the normal control group were significant different(F=65.68,P<0.05).There were significant different between the two groups among three(P<0.05).Conclusion:It can increase the positive rate when undergo the EcochG examination during acute attacks of Meniere's disease,while the SP/AP area curve measures are more sensitive than SP/AP amplitude ratio in diagnosis of Meniere's disease.

[The normative values of vestibular evoked myogenic potentialin different age-groups]

Objective:To obtain the normative values of vestibular evoked myogenic potential(VEMP),i.e.the threshold,latency,latency-interval,amplitude of healthy population in Tianjin medical university General hospital.These values will help clinical diagnosis.Method:Seventy-five healthy individuals (39 males and 36 females,age from 21 to 70 years)were enrolled in this study.They were divided into 3 groups according to age:group 1(21-30 years),group 2(>30-50 years),group 3(>50-70 years).oVEMP and cVEMP were performed and the normative values were obtained.SPSS 19.0 was used to analyze the data.Result:The response rate was 77.3% and 85.3% of oVEMP and cVEMP respectively in all subjects.The values of oVEMP:in group 1 response rate was 100%,amplitude was(8.29±1.25)μV and threshold value was(83.65±4.10) dBnHL.In group 2 response rate was 85.4%,amplitude was(6.32±1.21)μV and threshold value was(89.24±4.18) dBnHL.In group 3 response rate was 46%,amplitude was(4.26±1.20) μV,threshold value was(95.13±4.21) dBnHL.The values of cVEMP: in group 1 response rate was 100%,amplitude was(108.87±19.10)μV and threshold value was(84.54±4.35) dBnHL.In group 2 response rate was 83.3%,amplitude was(84.10±20.02)μV and threshold value was (90.33±4.29)dBnHL.In group 3 response rate was 72.0%,amplitude was(64.18±19.22)μV and threshold value was (95.19±4.30)dBnHL.The statistical analysis show significant difference in oVEMP/cVEMP response rate,threshold and amplitude among different age-groups(P<0.05).No significant difference was found in N1,P1 latency and latency-interval among different age-groups(P>0.05).Conclusion:The normative values of VEMP of healthy population in Tianjin medical university General hospital were obtained in this research.These VEMP data were used for the diagnosis of related diseases.

Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling

Protein structure prediction and modeling provide a tool for understanding protein functions by computationally constructing protein structures from amino acid sequences and analyzing them. With help from protein prediction tools and web servers, users can obtain the three-dimensional protein structure models and gain knowledge of functions from the proteins. In this chapter, we will provide several examples of such studies. As an example, structure modeling methods were used to investigate the relation between mutation-caused misfolding of protein and human diseases including epilepsy and leukemia. Protein structure prediction and modeling were also applied in nucleotide-gated channels and their interaction interfaces to investigate their roles in brain and heart cells. In molecular mechanism studies of plants, rice salinity tolerance mechanism was studied via structure modeling on crucial proteins identified by systems biology analysis; trait-associated protein-protein interactions were modeled, which sheds some light on the roles of mutations in soybean oil/protein content. In the age of precision medicine, we believe protein structure prediction and modeling will play more and more important roles in investigating biomedical mechanism of diseases and drug design.

Effect of CYP3A5 gene polymorphisms on tacrolimus concentration/dosage ratio in adult liver transplant patients

We examined the influence of the cytochrome P450 3A5 (CYP3A5) genes in both donors and recipients on the concentration-dosage ratio (C/D) of tacrolimus in Chinese liver transplant patients. Fifty-one adult liver transplant patients who received tacrolimus were included in this study. The CYP3A5 polymorphism in donors and recipients was determined at the time of transplantation, and tacrolimus-based immunosuppressive therapy was started based on each patient's genetic constitution. The relationship between the C/D of tacrolimus for 3 months after surgery and the CYP3A5 genotype was analyzed. A stepwise regression model was used to analyze the relationship between C/D of tacrolimus and genotype, time course, age, and liver weight in liver transplant patients. Three months after liver transplantation, C/D was both affected by the CYP3A5 genotype of both the donors and the recipients. The C/D of tacrolimus in patients with the CYP3A5*1 allele or carrying CYP3A5*1 allele in the liver was lower than that in CYP3A5*3/*3 patients with the CYP3A5*3/*3 genotype in the liver (P < 0.01). The CYP3A5*1 genotype in donors as well as in patients both contributes to interindividual variation in the C/D of tacrolimus in adult liver transplantation.

Expanding the Genetic Code for a Dinitrophenyl Hapten

Haptens, such as dinitrophenyl (DNP) are small molecules that induce strong immune responses when attached to proteins or peptides and, as such, have been exploited for diverse applications. We engineered a Methanosarcina barkeri pyrrolysyl-tRNA synthetase (mbPylRS) to genetically encode a DNP-containing unnatural amino acid, N(6) -(2-(2,4-dinitrophenyl)acetyl)lysine (DnpK). Although this moiety was unstable in Escherichia coli, we found that its stability was enhanced in mammalian HEK 293T cells and was able to induce selective interactions with anti-DNP antibodies. The capability of genetically introducing DNP into proteins is expected to find broad applications in biosensing, immunology, and therapeutics.

A case-control study on the risk factors of urinary calculus in Uyghur children in the Kashi region

The incidence of urinary calculus (UC) is very high in Uyghur children in the Kashi region of Xinjiang, China, which seriously affects the growth and life quality of these children. This study was aimed at investigating the risk factors of UC in Uyghur children in Kashi region. One hundred fifteen Uyghur children (age <7 years) with UC who were treated in First People's Hospital in Kashi were enrolled in the case group. A 1:1 case-control study with a questionnaire was performed. The results showed that, among the 115 UC patients, there were more boys (71.3%) than girls (28.7%), and most cases had an onset age of 1-3 years (75.7%). A lower than primary school education in the mother, drinking unboiled water, water intake <500 mL/day, and eating too much sweets were risk factors [odds ratio (OR) = 2.385, 9.160, 3.263, and 8.945, respectively], whereas vegetable intake and exposure to summer sunshine of <2 h/day were protective factors against UC onset (OR = 0.154 and 0.344, respectively). Analysis of UC-related factors in 99 cases of <3-year-old children revealed that breastfeeding was also a protective factor (OR = 0.007), whereas frequent cow's milk intake within 5 months (OR = 2.414) and frequent "panada" intake (OR = 2.529) were risk factors. The occurrence of UC in Uyghur children in the Kashi region is mainly affected by maternal educational background, quality of drinking water, water intake volume, and dietary pattern. Furthermore, geography may also have a role.

Flame-enhanced laser-induced breakdown spectroscopy

Flame-enhanced laser-induced breakdown spectroscopy (LIBS) was investigated to improve the sensitivity of LIBS. It was realized by generating laser-induced plasmas in the blue outer envelope of a neutral oxy-acetylene flame. Fast imaging and temporally resolved spectroscopy of the plasmas were carried out. Enhanced intensity of up to 4 times and narrowed full width at half maximum (FWHM) down to 60% for emission lines were observed. Electron temperatures and densities were calculated to investigate the flame effects on plasma evolution. These calculated electron temperatures and densities showed that high-temperature and low-density plasmas were achieved before 4 µs in the flame environment, which has the potential to improve LIBS sensitivity and spectral resolution.

Designing DNA interstrand lock for locus-specific methylation detection in a nanopore

DNA methylation is an important epigenetic regulation of gene transcription. Locus-specific DNA methylation can be used as biomarkers in various diseases including cancer. Many methods have been developed for genome-wide methylation analysis, but molecular diagnotics needs simple tools to determine methylation states at individual CpG sites in a gene fragment. In this report, we utilized the nanopore single-molecule sensor to investigate a base-pair specific metal ion/nucleic acids interaction, and explored its potential application in locus-specific DNA methylation analysis. We identified that divalent Mercury ion (Hg²⁺) can selectively bind a uracil-thymine mismatch (U-T) in a dsDNA. The Hg²⁺ binding creates a reversible interstrand lock, called MercuLock, which enhances the hybridization strength by two orders of magnitude. Such MercuLock cannot be formed in a 5-methylcytosine-thymine mismatch (mC-T). By nanopore detection of dsDNA stability, single bases of uracil and 5-methylcytosine can be distinguished. Since uracil is converted from cytosine by bisulfite treatment, cytosine and 5′-methylcytosine can be discriminated. We have demonstrated the methylation analysis of multiple CpGs in a p16 gene CpG island. This single-molecule assay may have potential in detection of epigenetic cancer biomarkers in biofluids, with an ultimate goal for early diagnosis of cancer.

Occult pulmonary mucosa-associated lymphoid tissue lymphoma presenting as catastrophic antiphospholipid antibody syndrome

Catastrophic antiphospholipid antibody syndrome (CAPS) is characterized by fulminant thrombosis of the arterial and venous beds of multiple organ systems over a relatively short period of time and with a high mortality rate. Mucosa-associated lymphoid tissue (MALT) lymphoma of the lung has never been reported as a causative or precipitating factor for CAPS in the CAPS registry database. The present study describes a rare case of pulmonary MALT lymphoma of the lung that presented as CAPS. A 19-year-old Hispanic female presented with shortness of breath and abdominal pain. Computed tomography (CT) scans of the chest and abdomen revealed multiple portal vein thromboses and bilateral pulmonary nodules. Within one week of presentation, the patient developed a straight sinus thrombosis and upper extremity deep vein thrombosis, which led to shortness of breath. A biopsy of the lung nodule revealed MALT lymphoma. The present case illustrates a rarely reported pulmonary MALT lymphoma presenting as CAPS in a young female. The patient was successfully treated with 90 mg/m² bendamustine on days one and two and rituximab 375 mg/m² on day one of each 28-day cycle. Complete remission of the lung nodules was observed following three cycles of treatment, as visualized by positron emission tomography (PET)/CT scan. Fondaparinux was identified as a feasible anticoagulation drug of choice for this case. At seven months post-treatment, the patient continues to be stable with no further evidence of thrombosis and is currently undergoing rituximab maintenance therapy every six months for two years. A repeat lupus anticoagulant antibody assay turned and remained negative during the clinical follow-up period. A prompt diagnosis and early aggressive treatment is potentially curative and may dramatically decrease the mortality risk. Future studies should explore the role of rituximab in the management of CAPS-associated B-cell lymphoid malignancies.

Detection of miRNAs with a nanopore single-molecule counter

miRNAs are short noncoding RNA molecules that are important in regulating gene expression. Due to the correlation of their expression levels and various diseases, miRNAs are being investigated as potential biomarkers for molecular diagnostics. The fast-growing miRNA exploration demands rapid, accurate, low-cost miRNA detection technologies. This article will focus on two platforms of nanopore single-molecule approach that can quantitatively measure miRNA levels in samples from tissue and cancer patient plasma. Both nanopore methods are sensitive and specific, and do not need labeling, enzymatic reaction or amplification. In the next 5 years, the nanopore-based miRNA techniques will be improved and validated for noninvasive and early diagnosis of diseases.

First Report of Wilt on Alfalfa in China Caused by Verticillium nigrescens

Alfalfa (Medicago sativa Linn.), widely grown throughout the world, is an important perennial forage crop. It is high in protein and digestible fiber and is an excellent source of several vitamins (A, D, E, and K) and minerals for beef cattle, horses, sheep, goats, and even humans (2). Wilt symptoms on alfalfa were observed during a disease survey in Yangling, Shaanxi, China in 2009. Symptoms included discoloration, shortened internode, and plant death. However, the vascular tissue of diseased alfalfa plants did not exhibit discoloration and typical "V" symptoms of Verticillium albo-atrum infection. Eleven fungal isolates were obtained from diseased alfalfa plants in Yangling by a tissue isolation method (1). Isolates were cultured on Czapek Dox Agar (CDA; pH 7.2) slants at 22 ± 1°C in darkness. Colonies on CDA plates were whitish and cream-white when viewed from the underside, later becoming dark gray due to the formation of gray or dark brown chlamydospores in single or in short chains. DNA was extracted from each isolate and the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (rDNA) was amplified and sequenced using primers ITS-1F and ITS4. The 11 isolates were divided into five groups based on their in vitro morphological characters. A single isolate from each of the five groups was chosen for ITS sequencing. All five isolates had the same ITS sequence (GenBank Accession No. AB551216). On the basis of the ITS sequence and morphology (4), these isolates were identified as V. nigrescens Pethyhr. (recently renamed as Gibellulopsis nigrescens). Five representative isolates were used to fulfill Koch's postulates. Alfalfa seeds (cv. Cossack) were surface sterilized with 75% ethanol for 5 min, allowed to dry, and planted into cow dung compost that had been autoclaved at 160°C for 2 h. Plants were cultivated under controlled greenhouse conditions at 23 to 25°C with a photoperiod of 14 h. Inoculum was prepared by comminuting 15-day-old cultures and sterile deionized water into a suspension of mycelial fragments and conidia (10⁵ to 10⁶ CFU/ml) in a blender. Seedlings (four-leaf stage) were inoculated by immersing roots in the inoculum suspension for 60 min (3). Each isolate was inoculated onto 30 seedlings, six in each pot; another 30 seedlings were soaked with sterile deionized water for 60 min as a control. After 20 days in the greenhouse, all inoculated plants exhibited wilt symptoms similar to the original wilt symptoms observed on diseased alfalfa plants. In contrast, none of the control plants showed wilt symptoms. The pathogen was reisolated from all diseased plants and confirmed to the original ones. To our knowledge, this is the first report of V. nigrescens infecting M. sativa in China, indicating V. nigrescens as one possible important pathogen of alfalfa. References: (1) O. D. Dhingra and J. B. Sinclair. Basic Plant Pathology Methods. CRC Press, Boca Raton, FL, 1995. (2) D. Jasjeet et al. J. Adv. Sci. Res. 2:50, 2011. (3) H. A. Melouk and C. E. Horner. Phytopathology 64:1267, 1974. (4) R. Zare et al. Nova Hedwigia 85:463, 2007.

Plasma microRNAs as novel biomarkers for early detection of lung cancer

A diagnosis of lung cancer at its early stages is vital for improving the survival rate of patients. MicroRNAs (miRNAs), a family of 19- to 25-nucleotide non-coding small RNAs, are frequently dysregulated in lung cancer. The objective of this study was to investigate the potential of circulating miRNAs for early detection of lung cancer. We searched the published literature for the miRNA microarray data of primary lung cancer and selected 15 miRNAs that were most frequently up-regulated in lung cancer tissues. Total plasma RNA including miRNAs was isolated, polyadenylated and reverse-transcribed into cDNAs. The levels of miRNAs were determined by real-time RT-PCR in 74 lung cancer patients and 68 age-matched cancer-free controls. We found that the levels of miR-155, miR-197, and miR-182 in the plasma of lung cancer including stage I patients were significantly elevated compared with controls (P<0.001). The combination of these 3 miRNAs yielded 81.33% sensitivity and 86.76% specificity in discriminating lung cancer patients from controls. The levels of miR-155 and miR-197 were higher in the plasma from lung cancer patients with metastasis than in those without metastasis (P<0.05) and were significantly decreased in responsive patients during chemotherapy (P<0.001). These results indicate that miR-155, miR-197, and miR-182 can be potential non-invasive biomarkers for early detection of lung cancer.