Characterization of thermoluminescence kinetic parameters of beta irradiated B doped Ca5(PO4)3OH powder obtained from eggshell

In this study, we have synthesized B doped Ca5(PO4)3OH (HAP) by a sonication chemical method. The thermoluminescence (TL) properties of the family of synthesized samples (B doped Ca5(PO4)3OH (HAP) were investigated using an IRSL-TL 565 nm filter. This gave the highest TL intensity of each phosphor after 2 Gy β-irradiation. Three TL glow peaks of B doped Ca5(PO4)3OH (HAP) are centered at around 84, 208 and 324 °C (with a heating rate of 2 °Cs-1). The trapping parameters such as activation energy (E), order of kinetics (b), frequency factor (s) were calculated by using initial rise (IR), various heating rates (VHR) and computerized glow curve deconvolution (CGCD) method. The response of TL glow curves remained constant within ±5% deviation from the initial value after 9 cycles of reuse; but only at tenth cycle the deviation goes up to 6%.

UniProt: the universal protein knowledgebase in 2021

The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.

Abstract 5235: In vitro validation of drug-target interactions revealed in silico by Comprehensive Resource of Biomedical Relations with Network Representations and Deep Learning (CROssBAR) in HCC

Computational methods are more commonly employed for our understanding of cellular signaling mechanisms with the aim to develop cures for diseases including cancer. Identification of disease specific targeted drugs requires systems level analysis of cellular networks. Our research group developed a comprehensive resource, called CROssBAR, which connects various biological data sources in order to provide a well-connected resource with a focus on drug discovery and precision medicine. CROssBAR aims to predict and reveal novel drug-target interactions using deep learning algorithms. CROssBAR predictions were validated on hepatocellular carcinoma cells which is the 5th most prevalent and 3th deadliest cancer worldwide. We have selected 2 new small molecule kinase inhibitors Lenvatinib, Sunitinib along with Sorafenib and Regorafenib which are currently used in clinics. CROssBAR identifies novel and known gene targets for Lenvatinib, Sunitinib in comparison with Sorafenib and Regorafenib. Genes from SAPK/JNK and PI3K/Akt pathway that were not previously associated with hepatocellular carcinoma therapeutics were determined. All selected small molecules were bioactive on Huh7 and Mahlavu cells by SRB assay. Cell death was characterized by Annexin V which was due to G1/S cell cycle arrest. Further analysis of proteins involved in the SAPK/JNK, PI3K/Akt pathways and apoptotic markers such as PARP and Caspases were examined with immunoblotting upon treatment. As a result, cellular stress mechanisms activated PI3K/Akt and SAPK/JNK pathways which caused programmed cell death in HCC. With our deep learning approach, we were able to demonstrate a correlation between Lenvatinib and Sunitinib and their novel targets in HCC. Our validation results have illustrated that the comprehensive CROssBAR tool developed by our research group achieved in vitro significant predictions of new drugs and their targets against HCC that were not previously reported. Hence with this study we were able to demonstrate the use and validity of the CROssBAR tool along with new targets for primary liver cancer therapeutics.

Citation Format: Esra Nalbat, Ahmet Sureyya Rifaioglu, Tunca Dogan, Maria Jesus Martin, Rengul Cetin-Atalay, Volkan Atalay. In vitro validation of drug-target interactions revealed in silico by Comprehensive Resource of Biomedical Relations with Network Representations and Deep Learning (CROssBAR) in HCC [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5235.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

BACKGROUND

The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.

RESULTS

Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.

CONCLUSION

We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.

P3838Evaluation of echocardiographic determinants of interatrial block in patients with essential hypertension

Introduction

Interatrial block (IAB), defined as a conduction delay between the right and left atrium, is manifested on the electrocardiogram as a prolonged P-wave duration. Large number of studies recently have been published regarding the prevalence of IAB and its associations with cardiovascular events. It has been previously reported that myocardial fibrosis may cause conduction delays in hypertensive patients. In this study, we aimed to investigate the echocardiographic determinants of IAB in patients with hypertension.

Methods

This study enrolled a total of 220 patients [male: 93 (42.3%), mean age: 61.8±7.8 years] with hypertension. Patients with atrial fibrillation were excluded. IAB was defined as P wave duration of ≥120 ms with or without presence of notching. Routinely obtained 12-lead electrocardiography recordings were examined, and patients were divided into two groups as those with and without IAB. All patients were evaluated by transthoracic echocardiography.

Results

Electrocardiography revealed IAB in 70 patients. The baseline demographic characteristics of the patients with and without IAB were similar in both groups. Left atrial diameter (LAD), interventricular septal thickness, posterior wall thickness, left ventricular mass, left ventricular mass index, and the prevalence of left ventricular hypertrophy (LVH) were found to be significantly increased in hypertensive patients with IAB. Increased LAD (OR=1.082; 95% CI: 1.006–1.164; p=0.034) and LVH (OR=3.051; 95% CI: 1.164–7.994; p=0.023) were found to be independent predictors of IAB. In the receiver operating characteristic curve analyses, LAD values above 38 mm predicted IAB with a sensitivity of 68%, and a specificity of 58% (AUC= 0.678; 95% CI: 0.601–0.754; p<0.001).

Conclusion

A significant association exists between the presence of IAB and echocardiographic parameters related to left ventricular hypertrophy and left atrial dilatation in patients with essential hypertension. The presence of IAB may be used as an electrocardiographic marker of cardiac remodelling and myocardial fibrosis in hypertensive patients.

A Rare Complication of Boerhaave's Syndrome: Tension Pneumothorax

Boerhaave's syndrome is a very rare disease characterised by spontaneous rupture of the oesophagus. Clinical presentation is varied and may depend on the cause, location, size, degree of contamination, and site of injury. Patients may present with abdominal pain, pneumothorax, hydropneumothorax, and pneumomediastinum. Tension pneumothorax after esophageal perforation has been rarely reported in the medical literature. In our report, a case of tension pneumothorax secondary to Boerhaave's syndrome in a 44-year-old male is presented here.

Diagnostic value of copeptin in acute myocardial infarction

OBJECTIVE

The aim of this study was to investigate the effectiveness of copeptin in the early diagnosis of acute myocardial infarction (AMI), and to compare the diagnostic efficacy of copeptin with other cardiac markers.

PATIENTS AND METHODS

A total of 160 cases were enrolled in the study. All were over 18 years of age, and consisted of 54 non-ST elevation MI (NSTEMI), 54 ST segment elevation MI (STEMI), and 52 healthy subjects (controls). Serum troponin-I, CK-MB mass, copeptin and CRP levels were measured in each of the cases, and were compared between the three groups for statistical differences.

RESULTS

The copeptin levels in the STEMI (p < 0.001) and NSTEMI (p = 0.042) groups were found to be significantly higher than the control group. Spearman's correlation analysis showed a significant positive correlation between the level of copeptin and the presence of AMI (r = 0.285, p < 0.001), CK-MB mass (r = 0.246, p = 0.002), and troponin-I (r = 0.199, p = 0.012). Sensitivity, specificity, and AUC values of the tests, according to ROC analysis performed for the diagnosis of AMI were; troponin-I > 0.1 ng/mL (71.0%, 100.0%, and 0.855); CK-MB mass > 3.59 ng/mL (77.8%, 92.3%, and 0.911); CRP > 6.37 mg/L (53.7%, 88.5%, and 0.769); and copeptin > 2.47 ng/mL (66.7%, 75.0%, and 0.676), respectively (p < 0.001).

CONCLUSIONS

Cardiac troponin remains the gold standard biomarker for the diagnostic evaluation of AMI. Copeptin can be used as a diagnostic marker in patients with suspected AMI in combination with other biomarkers, but, copeptin alone should not be considered as a single diagnostic marker in patients with suspected AMI.

High hemodialysis vascular access flow and impaired right ventricular function in chronic hemodialysis patients

There are limited data showing right ventricular preload increase due to high-flow arteriovenous fistulas (AVFs). This cross-sectional study investigated whether high AVF flow had an impact on right ventricular function in patients undergoing hemodialysis. Sixty-four patients aged between 18 and 85 years who were on routine hemodialysis with >2 hemodialysis sessions per week for at least 3 months via an AVF were studied. Patients with inadequate flow fistulas, severe chronic obstructive pulmonary disease, history of pulmonary embolism, primary pulmonary hypertension, severe mitral, aortic or pulmonary regurgitation, and/or stenosis were excluded. After an initial evaluation, 44 patients (mean age: 58.50 ± 16.84, male:female = 23:21) were considered eligible. Right ventricular function was assessed by tricuspid annular plane systolic excursion (TAPSE). AVF blood flow was measured with duplex ultrasound. There were 15 patients (34.1%) with a TAPSE of <16 mm. AVF blood flow was significantly higher in patients with impaired versus normal right ventricular function (1631.53 ± 738.17 vs. 1060.55 ± 539.92 min/ml, respectively, P = 0.003). Low left ventricular ejection fraction (odds ratio [OR]: 1.15, 95% confidence intervals [CI]: 1.007-1.334, P = 0.04), high interventricular septum thickness (OR: 1.64, 95% CI: 1.104-2.464, P = 0.01), and high AVF blood flow (OR: 1.00, 95% CI: 1.000-1.003, P = 0.03) were independent predictors of impaired right ventricular function. In addition to known risk factors that predominantly increase right ventricular afterload, excessive AVF blood flow was found to be independently associated with impaired right ventricular function, possibly by increasing right ventricular preload.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

BACKGROUND

A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging.

RESULTS

We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2.

CONCLUSIONS

The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.

Tools and data services registry: a community effort to document bioinformatics resources

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.

Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.

As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

A Very Rare Case - Hairy Cell Leukemia in Patient with Sarcoidosis

Although the coexistence of hairy cell leukemia with sarcoidosis has been reported in a few cases in the literature, in our case the patient had been diagnosed and followed about 10 years with sarcoidosis and massive splenomegaly. It has been demonstrated that T helper 1 cells exist in organs influenced by sarcoidosis. These cells produce IL-2 and IFN-γ and induce a nonspecific inflammatory response and granuloma formation. Also these cytokines may play a role in the development of hairy cell leukemia.Key words: hairy cell leukemia -  sarcoidosis - massive splenomegaly.

Omental torsion without a whirl sign

Omental torsion is a very rare cause of acute abdomen. Its primary diagnostic modality is CT. The whirl sign visible in CT images is pathognomonic. The whirl sign is not present in all cases. When no whirl sign is seen, omental torsion is rather difficult to be differantieted radiologically from omental infarct and epiploic appendicitis. The diagnosis of these three entites is clinically important due to their different treatments. We present in this paper an omental torsion case where whirl sign was not present and diagnosis was made by other suggestive CT image findings.

Degradation of xenobiotic substances using sulfate-reducing bacteria in a UASB reactor

An upflow anaerobic sludge blanket (UASB) reactor was successfully applied to continuous degradation of ferric ethylene diamine tetraacetate (Fe-EDTA) as a typical xenobiotic substance contained in photo-processing wastewater. The sludge in the UASB reactor had an abundance of sulfate-reducing bacteria (SRB), which had been anaerobically cultivated in a sulfate-rich culture medium including Fe-EDTA and yeast-extract as the carbon sources. Since the prominent reductions of Fe-EDTA and sulfate ion were observed, the contribution of SRB to Fe-EDTA degradation in the UASB reactor was confirmed. The aggregated sludge in the UASB reactor became gradually large reaching steady state with an equivalent diameter of 60-90 microm after 124 days operation. An increase of the amount of yeast extract addition to feed solution improved the Fe-EDTA removal efficiency up to 90%. Moreover, the combination of ozone treatment with SRB treatment further improved removal efficiency of total organic carbon (TOC) in an actual photo-processing wastewater composed of fixing and developing wastes.

The effects of VEGF on survival of a random flap in the rat: examination of various routes of administration

The purpose of the present study was to determine the effects of vascular endothelial growth factor (VEGF) on survival of a full thickness random pattern, McFarlane musculocutaneous flap in the rat. In addition, this study examined a number of different methods of VEGF delivery in an attempt to determine the most effective route of administration. A 2 x 8 cm full thickness dorsal flap with the pedicle remaining attached at the anterior end was elevated in 72 male Sprague-Dawley rats. The rats were randomised into six groups and immediately received the following treatment: Group I (n = 12): systemic VEGF injection into the femoral vein (50 microg/ml); Group II (n = 10): multiple systemic VEGF injections at 0, 24 and 48 h post flap elevation (50 microg/ml); Group III (n = 12): subdermal VEGF injection into the flap (1 microg/ml); Group IV (n = 12): subfascial VEGF injections into the recipient bed (1 microg/ml); Group V (n = 10): topical VEGF onto the recipient bed (1 microg/ml); Group VI (n = 16): control group with no treatment. Following 5 days recovery, the area of flap survival was measured. Mean flap survival ranged from 91% in Group II to 78% in Group V, and was significantly greater in all experimental groups (P< 0.001 for Groups I-IV and P< 0.05 for Group V) as compared to the control group (mean survival of 66%). The only significant difference between the experimental groups was between the mean survival in Group II and Group V (P< 0. 05). Histological analysis demonstrated a qualitatively greater amount of granulation tissue and neovascularisation in the experimental groups. These results support the notion that VEGF rescues tissue at risk of hypoxic damage by inducing angiogenesis, and the use of growth factors such as VEGF holds promise as a method of increasing skin viability.

Saphenous neurocutaneous island flap model in the rat: evaluation of vascular supply

Neurocutaneous flaps are utilized routinely in reconstructive surgery and even more so during the past decade. In this study, the vascular supply of the neurocutaneous flap in the rat model is presented and evaluated. Thirty-six flaps (3.5x3 cm2) were dissected on the medial aspect of the leg based on a pedicle of the saphenous nerve, saphenous artery, great saphenous vein, and the surrounding fascial tissues. Animals in the experiment were divided into five groups with different circulatory patterns of pedicle dissections. In group I (N = 12), the pedicle artery, vein, nerve, and fascia were preserved. In group II (neurocutaneous flap model, N = 24), the saphenous artery was transected and the vein, nerve, and fascia were preserved. In group III (intraneural vascular plexus circulation pattern, N = 12), the saphenous artery and the fascia were transected. In group IV (extraneural vascular plexus circulation pattern, N = 12), the saphenous artery and nerve were transected. In group V (N = 12), the entire pedicle was transected completely. Flap survival was evaluated grossly on postoperative day 7. All flaps survived in group I, but in group II 19 of 24 flaps survived completely, 3 of 24 had partial necrosis, and 2 of 24 were completely necrotic. Complete necrosis was observed in all group III flaps. In group IV, 6 of 12 flaps survived completely, 3 of 12 flaps survived partially, and 3 of 12 flaps were necrotic (p<0.05 vs. group I). Only one flap with partial necrosis survived in group V. In group II, the average survival area was not significantly different from group I (p>0.05). In conclusion, the saphenous neurocutaneous flap in the rat is a reliable microsurgical model. The saphenous neurocutaneous flap is commonly supplied by both the intraneural and extraneural vascular plexus, and although the latter is more important, neither provides sufficient vascular supply on its own.

Prolonged perivascular use of verapamil or lidocaine decreases skin flap necrosis

During this experiment the authors investigated whether prolonged local use of verapamil or lidocaine prevents vasoconstriction and establishes better blood supply to the rat epigastric skin flap, hence reducing the necrosis that occurs otherwise. Abdominal wall skin flaps of 45 Sprague-Dawley rats, based on a single pedicle of the femoral vessels, were elevated. A subcutaneous pocket for the microport valve was created, and the adjacent catheter tip was sewn next to the femoral vessels. In the control and the two treatment groups, 0.5 ml saline or vasodilator solution respectively was injected through the microport every 12 hours for 5 days. On postoperative day 5 there was no statistical difference between the flap surfaces in all groups. The area of flap necrosis was significantly lower in the verapamil- (p = 0.001) and the lidocaine-treated (p = 0.012) groups vs. the control group as determined by analysis of variance with Bonferroni's post hoc test. In conclusion, topical application of verapamil and lidocaine solutions for 5 postoperative days decreased flap marginal necrosis significantly. Prolonged injection of vasodilators in the vicinity of the vascular pedicle prevents vasospasm and improves blood supply to the flap.

Effects of VEGF administration following ischemia on survival of the gracilis muscle flap in the rat

The incidence of free flap transplantation failure is only 3% to 5%, yet still occurs in cases in which the flap suffers prolonged ischemia. The purpose of the current study was to determine the effects of vascular endothelial growth factor (VEGF)--a potent angiogenic agent with a suspected role in the protection of endothelium--on flap survival in a model of ischemia-reperfusion injury. The model chosen was the rat gracilis muscle flap. A total of 36 adult male Sprague-Dawley rats were divided into three groups (N = 12). One experimental group received VEGF treatment and the other received heparin. A third group was treated with saline and served as the control. The gracilis muscle flap was dissected and isolated based on a vascular pedicle originating at the femoral vessels. Following 3.75 hours of ischemia, induced by clamping the femoral vessels, either VEGF, heparin, or saline was infused directly into the pedicle of the flap via a cannula. The flaps were evaluated both grossly and histologically after 72 hours of reperfusion. Eleven of the 12 flaps from the VEGF group survived, whereas the survival rate was 6 of 12 and 5 of 12 flaps for the heparin- and saline-treated groups respectively. Flap survival was significantly greater in the VEGF-treated group compared with the heparin- and saline-treated groups (p < 0.025, p < 0.01 respectively). Furthermore, there was no significant difference between the heparin and saline groups. These results indicate that VEGF plays a role in reducing the damage that occurs in ischemia-reperfusion injury, and that the use of VEGF holds promise as a potential therapy for increasing flap survival.

Quadriceps femoris muscle flap: largest muscle flap model in the rat

The purpose of this paper is to present a new muscle flap in the rat: the quadriceps femoris muscle flap based on a pedicle consisting of the femoral vessels. In order to establish the anatomic details of this model, seven rats were explored bilaterally, and the regional anatomy of the thigh was examined. The technical aspect of the model was established by the unilateral harvesting of 18 quadriceps femoris muscles. Findings were that this muscle is primarily supplied by a muscular branch originating at the superficial circumflex iliac artery. The average muscle weight was 6 g and the average pedicle length with femoral vessels was 6 mm. Eight of the harvested flaps were transplanted to the contralateral thigh, and the pedicle was anastomosed to the femoral vessels. The other ten flaps were resutured back to their beds. At 72 hr postoperatively, all flaps were viable with the exception of one of the transplanted flaps which was found to be necrotic. The quadriceps femoris muscle flap is technically both a reliable and simple model. With an average weight of 6 g, this flap is by far the largest described in the rat, and offers a convenient model for testing flap-related techniques and outcomes.

Shortening of rat teeth prevents autocannibalization of surgical flaps

Self-biting in laboratory rats is an irritating problem that can impede progress and affect the credibility of experimental interventions. Autocannibalization frequently complicates the epigastric skin flap model that is often used to evaluate flaps. In one of the authors' studies, the autocannibalization rate of 55.6 percent in nine rats with unprotected skin flaps of the entire abdominal wall necessitated the application of previously reported plastic collars and protective vests to hinder self-biting. Because the use of these devices resulted in distress symptoms in nine of 11 rats with collars and flap congestion in five of five rats with vests, rat incisor teeth shortening was introduced as a stress-free method to prevent chewing. Careful teeth cutting obviated autocannibalization in 19 of 20 rats (p<0.01) during a 5-day follow-up. Rat incisor teeth shortening performed every 3 or 4 days is a simple, inexpensive, and reliable method to prevent autocannibalization in the rat, while maintaining the well-being of the animal.

An unusual variation of extensor digitorum brevis manus: a case report and literature review

An unusual variation of the extensor digitorum brevis manus in a male cadaver is presented. The band-shaped muscle was located at the ulnar side of the hand between the fourth and fifth extensors. It originated from the deep carpal fascia and inserted to the extensor tendons of the fourth and fifth fingers with a tendon and a slip, respectively. The origin, insertion, and location of the muscle differ from those previously reported; with these anatomic features, the muscle variation cannot be placed into the current classifications. The phylogenetic and ontogenetic implications of the muscle are reviewed.