Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention

Understanding the impact of genomic variants on transcription factor binding and gene regulation remains a key area of research, with implications for unraveling the complex mechanisms underlying various functional effects. Our study delves into the role of DNA's biophysical properties, including thermodynamic stability, shape, and flexibility in transcription factor (TF) binding. We developed a multi-modal deep learning model integrating these properties with DNA sequence data. Trained on ChIP-Seq (chromatin immunoprecipitation sequencing) data in vivo involving 690 TF-DNA binding events in human genome, our model significantly improves prediction performance in over 660 binding events, with up to 9.6% increase in AUROC metric compared to the baseline model when using no DNA biophysical properties explicitly. Further, we expanded our analysis to in vitro high-throughput Systematic Evolution of Ligands by Exponential enrichment (SELEX) and Protein Binding Microarray (PBM) datasets, comparing our model with established frameworks. The inclusion of DNA breathing features consistently improved TF binding predictions across different cell lines in these datasets. Notably, for complex ChIP-Seq datasets, integrating DNABERT2 with a cross-attention mechanism provided greater predictive capabilities and insights into the mechanisms of disease-related non-coding variants found in genome-wide association studies. This work highlights the importance of DNA biophysical characteristics in TF binding and the effectiveness of multi-modal deep learning models in gene regulation studies.

Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial

BACKGROUND

Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001).

INTERPRETATION

Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor.

FUNDING

Boehringer Ingelheim and Eli Lilly.

Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial

BACKGROUND

The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1).

INTERPRETATION

In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease.

FUNDING

Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.

Examining DNA breathing with pyDNA-EPBD

MOTIVATION

The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion. This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others.

RESULTS

We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo algorithm.

AVAILABILITY AND IMPLEMENTATION

pyDNA-EPBD is supported across most operating systems and is freely available at https://github.com/lanl/pyDNA_EPBD. Extensive documentation can be found at https://lanl.github.io/pyDNA_EPBD/.

Examining DNA Breathing with pyDNA-EPBD

Motivation

The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion.This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others.

Results

We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop- Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo (MCMC) algorithm.

Deep residual learning for neuroimaging: An application to predict progression to Alzheimer's disease

BACKGROUND

The unparalleled performance of deep learning approaches in generic image processing has motivated its extension to neuroimaging data. These approaches learn abstract neuroanatomical and functional brain alterations that could enable exceptional performance in classification of brain disorders, predicting disease progression, and localizing brain abnormalities.

NEW METHOD

This work investigates the suitability of a modified form of deep residual neural networks (ResNet) for studying neuroimaging data in the specific application of predicting progression from mild cognitive impairment (MCI) to Alzheimer's disease (AD). Prediction was conducted first by training the deep models using MCI individuals only, followed by a domain transfer learning version that additionally trained on AD and controls. We also demonstrate a network occlusion based method to localize abnormalities.

RESULTS

The implemented framework captured non-linear features that successfully predicted AD progression and also conformed to the spectrum of various clinical scores. In a repeated cross-validated setup, the learnt predictive models showed highly similar peak activations that corresponded to previous AD reports.

COMPARISON WITH EXISTING METHODS

The implemented architecture achieved a significant performance improvement over the classical support vector machine and the stacked autoencoder frameworks (p <  0.005), numerically better than state-of-the-art performance using sMRI data alone (> 7% than the second-best performing method) and within 1% of the state-of-the-art performance considering learning using multiple neuroimaging modalities as well.

CONCLUSIONS

The explored frameworks reflected the high potential of deep learning architectures in learning subtle predictive features and utility in critical applications such as predicting and understanding disease progression.

Prevalence of White Coat Hypertension among the Patients Visiting in a Tertiary Care Center, Kathmandu, Nepal

Background Hypertension is a major cardiovascular risk factor. White coat hypertension refers to elevated office blood pressure but normal out of office blood pressure. White-coat hypertension has a risk of cardiovascular events more than normotensives. Objective To identify the prevalence of white coat hypertension among patients presented in the cardiology department. Method The descriptive cross-sectional study was conducted among 165 patients who visited the cardiology outpatient department of Kathmandu Medical College and Teaching Hospital from December 2017 to November 2018. Blood pressure was measured at the hospital, and ambulatory blood pressure device was used to monitor 24hrs pattern. Hypertension is classified as per recent guideline. Data were entered and analysed using Statistical Package for social sciences version 20. Result Out of 165 ambulatory blood pressure monitoring conducted patients, 140 participants were enrolled in the study based on inclusion criteria. Among them 55% (77) were male, and 45% (63) were female. Age ranged from 18-78 years with a mean of 43.82 ± 12.31 years. Overall among 140 participants 14.28% had white coat hypertension, however, after excluding twenty-two high normal group, among 118 participants who were hypertensive according to office BP, 16.9% (20) had white coat hypertension, and 33.57% of patients did not have nocturnal dipping of blood pressure. Conclusion The white coat hypertension is prevalent among around one-sixth of hypertensive patients visiting tertiary care centre, and one third have non-dipping which needs to be considered in the management of hypertension.

CMOS approach to compressed-domain image acquisition

A hardware implementation of a real-time compressed-domain image acquisition system is demonstrated. The system performs front-end computational imaging, whereby the inner product between an image and an arbitrarily-specified mask is implemented in silicon. The acquisition system is based on an intelligent readout integrated circuit (iROIC) that is capable of providing independent bias voltages to individual detectors, which enables implementation of spatial multiplication with any prescribed mask through a bias-controlled response-modulation mechanism. The modulated pixels are summed up in the image grabber to generate the compressed samples, namely aperture-coded coefficients, of an image. A rigorous bias-selection algorithm is presented to the readout circuit, which exploits the bias-dependent nature of the imager's responsivity. Proven functionality of the hardware in transform coding compressed image acquisition, silicon-level compressive sampling, in pixel nonuniformity correction and hardware-level implementation of region-based enhancement is demonstrated.

More Crop and Profit per Drop of Water: Drip Irrigation for Empowering Distressed Small Farmers

In the light of the rapid decline in the irrigation water potential and increasing demand for water from different sectors in India, there is a need of the emergence of small-scale irrigation technology to conserve scarce water resources. Drip irrigation is one such technology that has been introduced to reduce water consumption in the agriculture sector, leading to sustainability of this sector. It allows farmers to cultivate crops without moisture stress even under water-scarce conditions, thereby increasing farm productivity. Earlier studies have analyzed the economics of drip irrigation in the case of high-value crops, which are mostly cultivated by rich farmers. Drip irrigation is also suitable for cultivating vegetable crops that are mostly cultivated by small farmers. However, in the Indian context, research on the effectiveness of drip irrigation is rare for these crops. We show that farmers cultivating green chilli could reduce the use of water by about two-thirds and increase productivity by more than half by adopting the drip irrigation method, compared to the same crop cultivated under conventional flood irrigation. The farm profitability too is impressive. The discounted cash flow analysis shows that the investment in drip irrigation for green chilli cultivation is economically viable even without the state subsidy. Despite such favourable outcomes, poor awareness prevailing among small farmers prevents adoption of drip irrigation. We suggest that there is a need to spread the benefits of cultivating vegetable crops under drip irrigation through a quality extension network on a continuous basis through various means. It would curtail the distress of the small farmers as well.

Exploring the Diagnosis and Management of Bouveret's Syndrome

Bouveret's syndrome is an unusual cause of gastric outlet obstruction secondary to gallstone impaction. It is so rare that it is commonly missed in clinical practice if it is not considered in differential diagnoses of intestinal obstruction more specifically in man who does not report the history of gall stone. Furthermore, there are no definitive guidelines on approach and management of this condition. We present a seventy eight year old man who developed acute abdominal symptoms due to impaction of a gallstone in the duodenum. He did not have history of gall stone. The diagnosis was supported via CT abdomen and Endoscopy. The patient was successfully managed by exploratory laparotomy followed by anterior pylorotomy to remove the stone without cholecystectomy and fistula repair.

Pancreatic Abscess: An Unusual Presentation of Pancreatic Tail Cancer

Pancreatic abscess usually occurs in the setting of pancreatitis especially if complicated by pseudocysts or pancreatic necrosis. On the other hand, pancreatic body and tail cancer is relatively uncommon cancer and rarely does it present as a pancreatic abscess. We describe a 50-year-old man with sepsis due to underlying pancreatic abscess, who was later diagnosed to have pancreatic tail adenocarcinoma with the help of endoscopic ultrasound guided fine needle aspiration cytology.

Adherence to Antihypertensive Medications: Population Based Follow up in Eastern Nepal

BACKGROUND

Poor adherence toward antihypertensive drugs is a worldwide problem that results in poor health outcomes and increased health care costs. Community based study related to adherence to antihypertensive medication is limited in context of Nepal.

METHODS

This study was conducted to explore the extent of adherence towards prescribed antihypertensive treatment and to identify the factors of non adherence. Community based cross sectional study was conducted in Dharan Municipality of Eastern Region of Nepal from September 2009 to February 2010. Out of 975 hypertensive patients, 154 calculated samples were selected following simple random sampling method. Data was collected by interview method and adherence was measured by using four items Morisky Medicine adherence scale. Data was analyzed using SPSS by descriptive and inferential (Chi square and logistic regression analysis) Statistical method.

RESULTS

Among the 154 hypertensive patients, only 56.5% patients were adherent to antihypertensive medication. The important predictors of non adherence by logistic regression analysis at 95% Confidence Interval were illiteracy (OR 5.34, CI= 1.23 -23 , P=0.025), expensive price of medicine (OR 5.14, CI=1.1-23.9, P=0.037), missed medicine due to cost (OR 0.143,CI=0.02-0.78, P= 0.025), no family history of hypertension (OR 4.46,CI= 1.21-16.4, P=0.024), irregular follow up (OR 6.39,CI=1.22-33.3, P=0.028), more than one pills per day ( OR 5.33,CI=1.19-23.7, P= 0.028).

CONCLUSIONS

Around half of the population was non adherent towards antihypertensive medications so identified gap need to be addressed to increase adherence level.

[Attitude of intensive care specialists toward deceased organ donation in Germany. Results of a questionnaire at the 12th Congress of the German Interdisciplinary Association for Intensive and Emergency Medicine]

BACKGROUND

Organ transplantation is the only treatment option for many patients with end-organ failure. Due to lack of transplantable organs, patients already on the waiting list die every day. The number of organ donors in Germany fell in 2012 by 12.8 %, reaching its lowest level since 2002. The medical and nursing personnel in intensive care units have a key role in the recruitment of potential organ donors; therefore, a survey was conducted on this subject.

MATERIALS AND METHODS

At the 12th Congress of the German Interdisciplinary Association for Intensive and Emergency Medicine (DIVI) in December 2012, a point prevalence study using a paper-pencil survey was performed.

RESULTS

A total of 1045 questionnaires were analyzed. Of respondents, 81 % favor organ donation in the event of their own brain death. The approval rate in the medical profession was 84 % and 75 % of the nursing profession. Only 45.3 % of the participants (47 % physicians, nursing 44 %) had an organ donor card and nearly half (45 %) had already confided their opinion towards organ donation to their family or friends. The main reasons for a lack of acceptance of organ donation was the concept of brain death (40 %), fear of abuse by organ trade (29 %), and the lack of integrity of the body after death (11 %). The particularly intense discussion about organ donation and transplantation in 2012 resulted in a predominantly negative change of attitude in 45 % of respondents.

CONCLUSION

The vast majority of the intensive care personnel supports organ donation, but less than half of the respondents have an organ donor card. The reports of irregularities in the organ allocation were scrutinized, but had apparently no significant impact on the individual and collective fundamental donor decision.

Primary salivary gland tumors in eastern Nepal tertiary care hospital

BACKGROUND

The knowledge of the distribution and pattern of salivary gland tumors in the tertiary care center can provide overview of the disease pattern in the region. It also helps in planning the strategies to treat the disease and launch the awareness program in the community to this largely curable disease.

METHODS

A retrospective observational study of all the salivary gland tumors treated in the department of Otolaryngology, B. P. Koirala Institute of Health Sciences during April 2004 to March 2009 was done. Age, sex, presenting features, radiological findings, histopathological type of the tumor and type of surgery were recorded and descriptive analysis was done to calculate frequencies, percentage and their relations.

RESULTS

Out of total 51 cases, 81% (n=41) were benign and 19% (n=10) malignant tumors. Male to female ratio was 1:2.1. Mean age for benign and malignant tumors were 32.3 and 46.5 years respectively. Parotid tumor outnumbered all other sites comprising 69%, followed by submandiibular 18% and minor glands 13%. Pleomorphic adenoma was the commonest tumor (76%) of all primary salivary gland tumors. Benign to malignant tumor ratio of parotid, submandibular and minor glands were 6:1, 3.5:1 and 1.3:1 respectively. Adenoid cystic carcinoma (40%) and mucoepidermoid carcinoma (30%) were commonest malignant tumors.

CONCLUSIONS

The principal site for salivary gland tumors in eastern Nepal population was the parotid and the pleomorphic adenoma outnumbered all other tumors. Most of the cases in both benign and malignant group presented with painless lump often misleading the gravity of disease.

"Safety pin"--a question to its safety!

Foreign body ingestion is not an uncommon problem in children. They can ingest various foreign objects and one of such objects is a safety pin. The ingestion of such foreign body is not widely reported in the literature. This case highlights the risk of accidental ingestion of safety pin used on child's clothing to protect him from cold that can result in lethal complications. In a poor developing country like Nepal, this case serves to address all mothers alerting them of their ignorance while using safety pin in infants. In addition, physicians are reminded to obtain a detailed inquiry of suspected foreign body ingestion in every child with the history of dysphagia.

An fMRI study of working memory in first-degree unaffected relatives of schizophrenia patients

Identifying intermediate phenotypes of genetically complex psychiatric illnesses such as schizophrenia is important. First-degree relatives of persons with schizophrenia have increased genetic risk for the disorder and tend to show deficits on working memory (WM) tasks. An open question is the relationship between such behavioral endophenotypes and the corresponding brain activation patterns revealed during functional imaging. We measured task performance during a Sternberg WM task and used functional magnetic resonance imaging (fMRI) to assess whether 23 non-affected first-degree relatives showed altered performance and functional activation compared to 43 matched healthy controls. We predicted that a significant proportion of unaffected first-degree relatives would show either aberrant task performance and/or abnormal related fMRI blood oxygen level dependent (BOLD) patterns. While task performance in the relatives was not different than that of controls they were significantly slower in responding to probes., Schizophrenia relatives displayed reduced activation, most markedly in bilateral dorsolateral/ventrolateral (DLPFC/VLPFC) prefrontal and posterior parietal cortex when encoding stimuli and in bilateral DLPFC and parietal areas during response selection. Additionally, fMRI differences in both conditions were modulated by load, with a parametric increase in between-group differences with load in several key regions during encoding and an opposite effect during response selection.

ABCDEFG IS - the principle of constructive feedback

Feedback is an integral part of any learning experience. Constructive feedback is a powerful instrument and facilitates the learner's professional and personal development. "ABCDEFG IS", a mnemonic for the principles of constructive feedback, stands for Amount of the information, Benefit of the trainees, Change behaviour, Descriptive language, Environment, Focused, Group check, Interpretation check, and Sharing information. The eight important steps of feedback are: Ensure prior information, Collect data, Make appropriate meeting arrangement, Begin by encouraging self assessment by the trainee, Highlight areas where the trainee is doing well, Give feedback, Handle reaction maintaining the dignity and Plan actions. Communication and reflection also share many of the principles and steps of constructive feedback and giving regular feedback, thus, helps to improve communication and reflection. The feedback provider would be able to provide genuine feedback by following the appropriate steps and principles of constructive feedback and realize how important and rewarding its role is in teaching learning activities.

Descending necrotizing mediastinitis: a fatal complication of neglected esophageal foreign body

Descending necrotising mediastinitis due to a neglected esophageal foreign body is uncommon. It is a lethal disease if it develops with full blown clinical picture. A case is reported of descending necrotising mediastinitis caused by a foreign body in oesophagus which is rarely reported in world literature. It is emphasized that prompt diagnosis and aggressive surgical mediastinal drainage is very important for the survival of these patients. Delayed diagnosis and treatment in our case may have been the cause of death of the patient. Delayed diagnosis in our case is due to the unavailability proper health facility in remote area in developing countries like Nepal.

HIV AIDS Related Knowledge, Attitude and Practice among High School Students in Eastern Nepal

Abstract