A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species

Chinese indicine cattle harbor a much higher genetic diversity compared with other domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi sequencing data from 10 Chinese indicine cattle across southern China, we assembled 20 high-quality partially phased genomes and integrated them into a multiassembly graph containing 148.5 Mb (5.6%) of novel sequence. We identified 156,009 high-confidence nonredundant structural variants (SVs) and 206 SV hotspots spanning ∼195 Mb of gene-rich sequence. We detected 34,249 archaic introgressed fragments in Chinese indicine cattle covering 1.93 Gb (73.3%) of the genome. We inferred an average of 3.8%, 3.2%, 1.4%, and 0.5% of introgressed sequence originating, respectively, from banteng-like, kouprey-like, gayal-like, and gaur-like Bos species, as well as 0.6% of unknown origin. Introgression from multiple donors might have contributed to the genetic diversity of Chinese indicine cattle. Altogether, this study highlights the contribution of interspecies introgression to the genomic architecture of an important livestock population and shows how exotic genomic elements can contribute to the genetic variation available for selection.

Exploring the Impact of Ampelopsis Grossedentata Flavonoids on Growth Performance, Ruminal Microbiota, and Plasma Physiology and Biochemistry of Kids

This study was conducted to evaluate the influences of supplementing Ampelopsis grossedentata flavonoids (AGF) on the rumen bacterial microbiome, plasma physiology and biochemistry, and growth performance of goats. Twenty-four Nubian kids were randomly allocated to three dietary treatments: the control (CON, basal diet), the 1.0 g/kg AGF treatment (AGF), and the 12.5 mg/kg monensin treatment (MN). This trial consisted of 10 days for adaptation and 90 days for data and sample collection. The results reveal that Bacteroidetes, Firmicutes, and Proteobacteria are the dominant phyla in kids' rumen. Compared with the CON group, the alpha diversity in the MN and AGF groups significantly increased (p < 0.01). Beta-diversity shows that rumen microbial composition is more similar in the MN and AGF groups. LEfSe analysis shows that Prevotella_1 in the AGF group were significantly higher than those in the MN and CON group. The high-density lipoprotein cholesterol and glucose levels in the AGF group were significantly higher than those in the CON group (p < 0.05), whereas the low-density lipoprotein cholesterol, glutamic-pyruvic transaminase, and alkaline phosphatase levels exhibited the opposite trend. The average daily gains in the AGF and MN groups significantly increased, while the feed-to-gain ratios were significantly decreased (p < 0.05). The results suggest that adding AGF to the diet improves microbial composition and has important implications for studying juvenile livestock growth and improving economic benefits.

Measurement of the J/ψ Polarization with Respect to the Event Plane in Pb-Pb Collisions at the LHC

We study the polarization of inclusive J/ψ produced in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV at the LHC in the dimuon channel, via the measurement of the angular distribution of its decay products. We perform the study in the rapidity region 2.5 Collapse

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First Measurement of Antideuteron Number Fluctuations at Energies Available at the Large Hadron Collider

The first measurement of event-by-event antideuteron number fluctuations in high energy heavy-ion collisions is presented. The measurements are carried out at midrapidity (|η|<0.8) as a function of collision centrality in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV using the ALICE detector. A significant negative correlation between the produced antiprotons and antideuterons is observed in all collision centralities. The results are compared with a state-of-the-art coalescence calculation. While it describes the ratio of higher order cumulants of the antideuteron multiplicity distribution, it fails to describe quantitatively the magnitude of the correlation between antiproton and antideuteron production. On the other hand, thermal-statistical model calculations describe all the measured observables within uncertainties only for correlation volumes that are different with respect to those describing proton yields and a similar measurement of net-proton number fluctuations.

Enhanced Deuteron Coalescence Probability in Jets

The transverse-momentum (p_{T}) spectra and coalescence parameters B_{2} of (anti)deuterons are measured in p-p collisions at sqrt[s]=13  TeV for the first time in and out of jets. In this measurement, the direction of the leading particle with the highest p_{T} in the event (p_{T}^{lead}>5  GeV/c) is used as an approximation for the jet axis. The event is consequently divided into three azimuthal regions, and the jet signal is obtained as the difference between the toward region, that contains jet fragmentation products in addition to the underlying event (UE), and the transverse region, which is dominated by the UE. The coalescence parameter in the jet is found to be approximately a factor of 10 larger than that in the underlying event. This experimental observation is consistent with the coalescence picture and can be attributed to the smaller average phase-space distance between nucleons in the jet cone as compared with the underlying event. The results presented in this Letter are compared to predictions from a simple nucleon coalescence model, where the phase-space distributions of nucleons are generated using pythia8 with the Monash 2013 tuning, and to predictions from a deuteron production model based on ordinary nuclear reactions with parametrized energy-dependent cross sections tuned on data. The latter model is implemented in pythia8.3. Both models reproduce the observed large difference between in-jet and out-of-jet coalescence parameters, although the almost flat trend of the B_{2}^{Jet} is not reproduced by the models, which instead give a decreasing trend.

[Analysis of therapeutic mechanism of Liushen Wan against colitis-associated colorectal cancer based on network pharmacology and validation in mice]

OBJECTIVE

To explore the therapeutic mechanism of Liushen Wan (LSW) against colitis-associated colorectal cancer (CAC) by network pharmacology.

METHODS

TCMSP, BATMAN-TCM, CNKI, PubMed, Genecards, OMIM, and TTD databases were used to obtain the related targets of LSW and CAC. The common targets of LSW and CAC were obtained using Venny online website. The PPI network was constructed using Cytoscape 3.8.2 to screen the core targets of LSW in the treatment of CAC. GO and KEGG enrichment analysis were conducted using DAVID database. The therapeutic effect of LSW on CAC was evaluated in a C57BL/6J mouse model of AOM/DSS-induced CAC by observing the changes in body weight, disease activity index, colon length, and size and number of the tumor. HE staining and RT-qPCR were used to analyze the effect of LSW on inflammatory mediators. Immunohistochemistry and TUNEL staining were used to evaluate the effect of LSW on the proliferation and apoptosis of AOM/DSS-treated colon tumor cells. Immunohistochemistry and Western blotting were used to detect the effects of LSW on the expression of TLR4 proteins in CAC mice.

RESULTS

Network pharmacology analysis identified 69 common targets of LSW and CAC, and 33 hub targets were screened in the PPI network. KEGG pathway enrichment analysis suggested that the effect of LSW on CAC was mediated by the Toll-like receptor signaling pathway. In the mouse model of AOM/DSS-induced CAC, LSW significantly inhibited colitis-associated tumorigenesis, reduced tumor number and tumor load (P < 0.05), obviously improved histopathological changes in the colon, downregulated the mRNA levels of proinflammatory cytokines, and inhibited the proliferation (P < 0.01) and promoted apoptosis of colon tumor cells (P < 0.001). LSW also significantly decreased TLR4 protein expression in the colon tissue (P < 0.05).

CONCLUSION

LSW can inhibit CAC in mice possibly by regulating the expression of TLR4 to reduce intestinal inflammation, inhibit colon tumor cell proliferation and promote their apoptosis.

Aerosol generation with the use of positive pressure ventilation via supraglottic airway devices: an observational study

The amount of aerosol generation associated with the use of positive pressure ventilation via a supraglottic airway device has not been quantified. We conducted a two-group, two-centre, prospective cohort study in which we recruited 21 low-risk adult patients scheduled for elective surgery under general anaesthesia with second-generation supraglottic airway devices. An optical particle sizer and an isokinetic sampling probe were used to record particle concentrations per second at different size distributions (0.3-10 μm) during use as well as baseline levels during two common activities (conversation and coughing). There was a median (IQR [range]) peak increase of 2.8 (1.5-4.5 [1-28.1]) and 4.1 (2.0-7.1 [1-18.2]) times background concentrations during SAD insertion and removal. Most of the particles generated during supraglottic airway insertion (85.0%) and removal (85.3%) were < 3 μm diameter. Median (IQR [range]) aerosol concentration generated by insertion (1.1 (0.6-5.1 [0.2-22.3]) particles.cm^-3 ) and removal (2.1 (0.5-3.0 [0.1-18.9]) particles.cm^-3 ) of SADs were significantly lower than those produced during continuous talking (44.5 (28.3-70.5 [2.0-134.5]) particles.cm^-3 ) and coughing (141.0 (98.3-202.8 [4.0-296.5]) particles.cm^-3 ) (p < 0.001). The aerosol levels produced were similar with the two devices. The proportion of easily inhaled and small particles (<1 μm) produced during insertion (57.5%) and removal (57.5%) was much lower than during talking (99.1%) and coughing (99.6%). These results suggest that the use of supraglottic airway devices in low-risk patients, even with positive pressure ventilation, generates fewer aerosols than speaking and coughing in awake patients.

[Clinical effects of free anterolateral thigh perforator flap pedicled with descending genicular artery in repairing wounds after lower leg limb-sparing surgery]

Objective: To explore the clinical effects of free anterolateral thigh perforator flap pedicled with descending genicular artery in repairing wounds after lower leg limb-sparing surgery. Methods: A retrospective observational study was conducted. From January 2019 to June 2021, 12 patients with wounds after lower leg limb-sparing surgery who met the inclusion criteria were admitted to Suzhou Ruihua Orthopedic Hospital, including 6 males and 6 females, aged 17 to 74 years, with original wound area ranging from 17 cm×9 cm to 40 cm×15 cm. Five patients had infection in wounds. The wounds were all repaired by free anterolateral thigh perforator flap from contralateral thigh, with area of 18 cm×10 cm to 37 cm×9 cm. The artery of flap was anastomosed with the descending genicular artery, and the wounds in donor areas were sutured directly. Seven patients were transplanted with split-thickness skin grafts from the contralateral thigh to cover the remaining wounds that can not be covered by flap and the wounds in donor areas were covered with gauze. During the operation, the types of perforating branch carried by flap and the types of arteries and veins in recipient areas were recorded. The survival and occurrence of vascular crisis of flap, the survival of skin graft, the wound healing in donor and recipient areas, and the length of hospital stay after flap transplant surgery were recorded. During follow-up, the color and texture of flap, reinfection in lower leg, and fracture healing were recorded. At the last follow-up, the limb salvage function of patients was evaluated according to the functional evaluation criteria of Chen Zhongwei's amputated limb replantation. Results: The types of perforating branches carried by flaps were as follows: 6 cases of only carrying the descending branch of the lateral circumflex femoral artery, 3 cases of only carrying the oblique branch of the lateral circumflex femoral artery, and 3 cases of carrying the descending branch of the lateral circumflex femoral artery and oblique branch of the lateral circumflex femoral artery after internal pressurization anastomosis. The types of arteries in the recipient area of flap were as follows: one case of main trunk of the descending genicular artery, 8 cases of the saphenous branch of the descending genicular artery, and 3 cases of the articular branch of the descending genicular artery. The types of veins in the recipient area of flap were as follows: 8 cases of one accompanying vein of the descending genicular artery and one branch of the great saphenous vein, and 4 cases of two branches of the great saphenous vein. All the flaps survived without vascular crisis, and all the skin grafts also survived. The wounds in the donor and recipient areas were all healed. The length of hospital stay of patient after flap transplant surgery ranged from 13 to 79 days. During the follow-up of 6 to 23 months, the color and texture of flap were both good, with no infection in lower leg wound. Internal or external fixation were removed after fracture healing in 5 patients, and bone graft internal fixation was performed in 7 patients whose fractures were not healed after surgery and all the incisions healed without infection. At the last follow-up, the limb salvage effect of patients was evaluated as followings: excellent in 7 patients, good in 4 patients, and fair in one patient. Conclusions: Free anterolateral thigh flap pedicled with descending genicular artery can effectively repair the wounds after lower leg limb-sparing surgery and control infection with short length of hospital stay, while not increasing the risk of secondary injury of distal limb vessels. Thus, it can obtain satisfactory limb salvage effect which is worthy of clinical promotion.

A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes

Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, discovering 130.3 Mb nonreference sequences, from which 588 genes were annotated. A total of 149,158 biallelic insertions/deletions, 6531 divergent alleles, and 14,707 multiallelic variations with precise breakpoints were discovered. The SV spectrum is characterized by an excess of derived insertions compared to deletions (94,422 vs. 33,571), suggesting recent active LINE expansions in sheep. Nearly half of the SVs display low to moderate linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified 865 population-stratified SVs including 122 SVs possibly derived in the domestication process among 690 individuals from sheep breeds worldwide. A novel 168-bp insertion in the 5′ untranslated region (5′ UTR) ofHOXB13is found at high frequency in long-tailed sheep. Further genome-wide association study and gene expression analyses suggest that this mutation is causative for the long-tail trait. In summary, we have developed a panel of high-quality de novo assemblies and present a catalog of structural variations in sheep. Our data capture abundant candidate functional variations that were previously unexplored and provide a fundamental resource for understanding trait biology in sheep.

Surgical treatment of tethered cord syndrome showed promising outcome in young children with short duration

OBJECTIVE

Aside from the severity, surgical interventions for the treatment of neurological dysfunctions remain controversial. This study aimed to find factors predicting the benefits of tethered cord syndrome (TCS) surgery.

PATIENTS AND METHODS

80 children with TCS were included and followed up for pre- and post-operative factors along with neurophysiological analysis. Outcomes were assessed by univariate and multivariate analysis.

RESULTS

Surgical treatment not only improved preoperative signs and symptoms in 79% of TCS patients but it showed to be an efficient procedure for the occurrence of future neurological defects. Univariate analysis also revealed that surgical intervention in TCS children (age <1 year) can modulate filar lipoma location and cutaneous abnormalities three months after surgery. Neurophysiological assessment revealed only 5.0% of surgical complications in TCS patients. Two patients had cerebrospinal fluid leakage, and two cases of CNS infection were detected.

CONCLUSIONS

Surgical intervention is highly recommended for the prevention of neurological deficits in children with TCS. Electrophysiological monitoring revealed rare complications following the surgery.

The Joint Effect of Body Mass Index and Serum Lipid Levels on Incident Dementia among Community-Dwelling Older Adults

OBJECTIVES

This study aimed to explore the joint effect of body mass index (BMI) and serum lipids levels on incident dementia.

METHODS

We prospectively followed up with 1,627 dementia-free community residents aged ≥60 for 5.7 years on average. At baseline, weight, and height were measured, and total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C) were detected in serum. Demographic characteristics were collected through questionnaires. Dementia was based on consensus diagnosis of neurologists and neuropsychologists using DSM-IV criteria. Additive Cox proportional model was used to assess the exposure-response relationship between BMI and serum lipid levels and dementia risk. Interactions and further classifications of BMI and serum lipid levels were further presented by bivariate surface models and decision-tree models.

RESULTS

The joint effects of TC with BMI, TG with BMI, and LDL-C with BMI on the risk of incident dementia shared a similar pattern, different from their independent exposure-response curves. The joint effect of HDL-C with BMI showed an S-surface but without statistical significance. Participants with TC<5.4 mmol/L and BMI<21 kg/m2 (Hazard Ratio(HR) 1.93, 95% Confidence Interval (CI) 1.05-3.53), TC<5.4 mmol/L and BMI≥21 kg/m2 (HR 1.73, 95% CI 1.09-2.72), and TC≥5.4 mmol/L and BMI<21 kg/m2 (HR 4.02, 95% CI 2.10-7.71) were identified to have the increased risk of incident dementia compared to those with TC≥5.4 mmol/L and BMI≥21 kg/m2. Participants with TG<1.7 mmol/L and BMI<21 kg/m2 had an increased risk of incident dementia compared to those with TG≥1.7 mmol/L and BMI≥21 kg/m2 (HR 1.98, 95%CI 1.17-3.3). Participants with LDL-C≥3.3 mmol/L and BMI<21 kg/m2 were identified to have an increased risk of incident dementia compared to those with LDL-C≥3.3 mmol/L and BMI≥21 kg/m2 (HR 3.33, 95%CI 1.64-6.78).

CONCLUSIONS

Our study showed that low BMI combined with low or high levels of serum lipids may increase the risk of dementia among older adults. This finding suggests the potential impacts of these two metabolic indexes on the risk of dementia.

Association between maternal oxygenation and brain growth in fetuses with left-sided cardiac obstructive lesions

OBJECTIVE

Impaired brain growth has been observed in fetuses with left-sided obstructive lesions (LSOL). Maternal oxygenation (MO) can alter fetal cerebral oxygenation and vascular reactivity. Our aim was to observe whether brain growth improves during MO in fetuses with LSOL.

METHODS

Forty-six fetuses with LSOL and 23 control fetuses were enrolled in this prospective longitudinal study. Fetuses with LSOL were subgrouped into those with MO (LSOL-MO, n = 23) and those without MO (LSOL-nMO, n = 23). Fetal head circumference (HC) and total intracranial volume (TIV) were evaluated serially at 4-week intervals. Brain biometry and growth were analyzed using linear mixed models adjusted for gestational age and sex. Spearman's correlation coefficients were calculated to identify baseline characteristics predictive of brain growth in the LSOL-MO group.

RESULTS

Duration of MO therapy had significant interaction effects on cerebral biometry in fetuses with LSOL. TIV increased more rapidly after 8 weeks of oxygen exposure and HC was larger after 16 weeks of oxygen exposure in the LSOL-MO group compared with the LSOL-nMO group (P &lt; 0.001). The change in TIV at the final time- point relative to the initial timepoint in the LSOL-MO group correlated negatively with the baseline pulsatility index of the middle cerebral artery (r = -0.58, P = 0.003) and baseline myocardial performance index of the left ventricle (r = -0.68, P &lt; 0.001).

CONCLUSIONS

TIV and HC increased faster in fetuses with LSOL which had MO compared with those that did not. Lower cerebral vascular resistance and preserved left heart function at baseline may predict greater cerebral biometric growth during MO. Additional research, including larger serial studies, is needed to confirm these preliminary findings and evaluate the clinical application of MO in this population. © 2022 International Society of Ultrasound in Obstetrics and Gynecology.

Hypertriton Production in p-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

The study of nuclei and antinuclei production has proven to be a powerful tool to investigate the formation mechanism of loosely bound states in high-energy hadronic collisions. The first measurement of the production of _{Λ}^{3}H in p-Pb collisions at sqrt[s_{NN}]=5.02  TeV is presented in this Letter. Its production yield measured in the rapidity interval -1<y<0 for the 40% highest-multiplicity p-Pb collisions is dN/dy=[6.3±1.8(stat)±1.2(syst)]×10^{-7}. The measurement is compared with the expectations of statistical hadronization and coalescence models, which describe the nucleosynthesis in hadronic collisions. These two models predict very different yields of the hypertriton in charged particle multiplicity environments relevant to small collision systems such as p-Pb, and therefore the measurement of dN/dy is crucial to distinguish between them. The precision of this measurement leads to the exclusion with a significance larger than 6.9σ of some configurations of the statistical hadronization model, thus constraining the theory behind the production of loosely bound states at hadron colliders.

AB0228 THE CONNECTION BETWEEN NUTRITIONAL STATUS AND DISEASE ACTIVITY IN RHEUMATOID ARTHRITIS

Background

Nutritional status is closely associated with a person’s physical condition. As for patients with autoimmune disease, nutritional status may affect the balance of immune system, which successively affects disease activity.

Objectives

The prognostic nutritional index (PNI), nutritional risk index (NRI), controlling nutritional status (CONUT) score and body mass index (BMI) are four widely used nutritional indices [1]. This study aimed to investigate the relationship between nutritional status and disease activity of rheumatoid arthritis (RA).

Methods

168 RA patients and 50 healthy volunteers were retrospectively enrolled. According to the disease activity score using 28 joint counts-erythrocyte sedimentation rate (DAS28-ESR), the cohort of RA patients was divided into the lower disease activity groups (DAS28-ESR≤3.2) and the higher disease activity groups (DAS28-ESR>3.2). We recorded clinical assessment and laboratory data for further analysis. Spearman’s correlation, receiver operation characteristic (ROC) curves, binary logistic regression analysis were carried out.

Results

Compared to the higher disease activity group, the lower disease activity group had low-level total protein (TP), ESR and CRP (all P<0.05), while high-level albumin and PNI (all P<0.05). PNI and NRI were negatively correlated with DAS28-ESR (r=-0.395, and r=-0.200, all P<0.05), while CONUT score was positively correlated with DAS28-ESR (r=0.324, P<0.05). ROC curve illustrated that area under the curve (AUC) of PNI for RA patients with higher disease activity was superior to NRI, CONUT score and BMI. The AUC of PNI was 0.693.

Figure 1.

The diagnostic value of variables for disease activity in rheumatoid arthritis using ROC curve

Table 1.

The correlation between nutritional indices and disease activity score using 28 joint counts-erythrocyte sedimentation rate (DAS28-ESR)

PNINRICONUT scoreBMIrP valuerP valuerP valuerP valueNeutrophil(×109/L)-0.0610.4340.0450.5680.0250.7570.0790.313Monocyte(×109/L)0.1830.1630.1450.064-0.1040.1930.1520.052Lymphocyte(×109/L)0.4720.0000.2010.010-0.4360.0000.2080.007ESR (mm/h)-0.5610.000-0.2580.0010.3930.000-0.1820.020CRP (mg/L)-0.5200.000-0.0770.3260.3910.0000.0030.967RF(IU/ml)-0.2240.004-0.1160.1510.2600.001-0.0820.306CCP(IU/ml)-0.1390.088-0.2010.0140.1950.018-0.1880.022DAS28-ESR-0.3950.000-0.2000.0110.3240.000-0.1420.072

Conclusion

PNI may become a manageable marker for detector disease activity of RA patients.

References

[1]Ahn, S.S., et al., Comparison of the Clinical Implications among Five Different Nutritional Indices in Patients with Lupus Nephritis. Nutrients, 2019. 11(7).

Disclosure of Interests

None declared