jimnoneill/paper-to-field-training huggingface dataset:
Higher-order correction of persistent batch effects in correlation networks

Abstract Motivation Systems biology analyses often use correlations in gene expression profiles to infer co-expression networks that are then used as input for gene regulatory network inference or to identify functional modules of co-expressed or putatively co-regulated genes. While systematic biases, including batch effects, are known to induce spurious associations and confound differential gene expression analyses (DE), the impact of batch effects on gene co-expression has not been fully explored. Methods have been developed to adjust expression values, ensuring conditional independence of mean and variance from batch or other covariates for each gene, resulting in improved fidelity of DE analysis. However, such adjustments do not address the potential for spurious differential co-expression (DC) between groups. Consequently, uncorrected, artifactual DC can skew the correlation structure, leading to the identification of false, non-biological associations, even when the input data are corrected using standard batch correction. Results In this work, we demonstrate the persistence of confounders in covariance after standard batch correction using synthetic and real-world gene expression data examples. We then introduce Co-expression Batch Reduction Adjustment (COBRA), a method for computing a batch-corrected gene co-expression matrix based on estimating a conditional covariance matrix. COBRA estimates a reduced set of parameters expressing the co-expression matrix as a function of the sample covariates, allowing control for continuous and categorical covariates. COBRA is computationally efficient, leveraging the inherently modular structure of genomic data to estimate accurate gene regulatory associations and facilitate functional analysis for high-dimensional genomic data. Availability and implementation COBRA is available under the GLP3 open source license in R and Python in netZoo (https://netzoo.github.io).

Topic: Bioinformatics and Genomic Networks
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Pan-Proteomics to Analyze the Functional Complexity of Organisms

Proteomics is rapidly expanding with the advent of high throughput technologies and offers a greater understanding of the complexity of life and the process of evolution. Protein profile comparison between genetically heterogeneous individuals may provide important insights into physiological diversity and function. A new term, pan-proteomics, has also been introduced that permits the qualitative and quantitative comparison of proteomes of genetically heterogeneous organisms. Here in this chapter, various aspects of pan-proteomics along with its basic methodology and applications have been discussed.

Topic: Advanced Proteomics Techniques and Applications
Subfield: Spectroscopy
Field: Chemistry
Domain: Physical Sciences
Pretreatment with a Low Concentration of Methyl Viologen Decreases the Effects of Salt Stress on Chloroplast Ultrastructure in Rice Leaves (<i>Oryza sativa</i>L.)

We investigated the effects of pretreatment with a low concentration of methyl viologen (MV) on the salinity-induced chloroplast degeneration in rice seedlings. The seedlings grown in hydroponic culture containing nutrient solution for 3 wks were treated with 100 nM MV mixed in the hydroponic culture for 3 days, and then with 200 mM NaCl without MV for 3 days. In the plants without MV pretreatment, the chlorophyll content drastically decreased during the NaCl treatment accompanied by swelling of thylakoids and destruction of thylakoid membranes. These damages were alleviated by the pretreatment with MV. The activities of CuZn-SOD and Fe-SOD, which localize in chloroplasts, increased under salt stress in both plants with and without MV pretreatment. In the plants under salt stress without MV pretreatment, ascorbate peroxidase (APX) activity did not differ from that of control. However, in MV-pretreated plants, APX activity under salt stress was about 1.2- to 1.3-fold higher than that of the control. Catalase (CAT) activity in NaCl treated plants was decreased to 52% of the control and the reduction in CAT activity was suppressed by MV pretreatment. These results suggest that MV reduced the damages by salt stress in chloroplasts by increasing APX activity and preventing the decrease in CAT activity.

Topic: Plant Stress Responses and Tolerance
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
A CLINICAL STUDY OF NEWLY-DIAGNOSED HIV PATIENTS AT ICTC, BASAVESHWARA HOSPITAL WITH CORRELATION TO CD4+ COUNT

BACKGROUND&#13;\nTimely assessment of the burden of HIV/AIDS is essential for policy setting and programme evaluation. Human&#13;\nImmunodeficiency Virus (HIV) infection is a global pandemic with cases reported from virtually every country. According to&#13;\nWorld Health Organization (WHO), globally 35 million (32.8-38.8 million) people were living with HIV at end of 2013. To study&#13;\nthe various pulmonary opportunistic infections in HIV/AIDS and association with CD+4 T-cell count.&#13;\nThe aim of the study is to study clinical profile of pulmonary opportunistic infections. A cross-sectional study was done&#13;\namong 100 newly-diagnosed HIV patients of all the age groups and either gender admitted from March 2013 to April 2014 in&#13;\nBasaveshwara Teaching and Teaching Hospital attached to MR Medical College, Kalaburagi.&#13;\nMATERIALS AND METHODS&#13;\nA detailed history was recorded with emphasis on personal history, high-risk behaviour, history of migration, mode of&#13;\ntransmission of infection and complete thorough clinical examination was done. Data analysis was done by calculating P value&#13;\nusing Chi-square test. ICTC was done in Basaveshwara Hospital for confirming HIV status of the patients.&#13;\nRESULTS&#13;\nOut of 100 patients, 3 patients were asymptomatic, while 97 patients were symptomatic. Main symptoms were cough (75%),&#13;\nfever (65%), weight loss (55%), dyspnoea (32%) and diarrhoea (10%). The most common opportunistic infection was&#13;\npulmonary tuberculosis (77%) followed by candidiasis (58%).&#13;\nCONCLUSION&#13;\nThe Antiretroviral Therapy (ART) has reduced the incidence of OI among HIV infected individuals. Majority of the patients with&#13;\nopportunistic infections have CD4 count less than 200 cells/µL. Enormous progress has been made in reducing HIV deaths,&#13;\nespecially in low-income countries through the expansion of prevention of mother-to-child transmission and by early detection&#13;\nof HIV infection by easily available and free of cost ICTC testing through the ART programmes funded largely through&#13;\ndevelopment assistance for HIV.&#13;\n

Topic: Pneumocystis jirovecii pneumonia detection and treatment
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences
CCDC 836682: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Topic: Crystallization and Solubility Studies
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Dynamic Measurement of Spindle Errors of CNC Machine Tools by Capacitive Sensors During Aircraft Parts Machining

The work presents characteristics and practical application of Spindle Error Analyzer, an innovative bespoke diagnostic system, designed for precision measurement of spindles used in high-precision Computerized Numerical Control - CNC machining centres, dedicated to aircraft parts machining. Ultra-precise and high-speed spindles constitute one of the most expensive elements of the CNC machine tool. Their control, diagnostics and proper use should be the matter of utmost importance at any production plant. Dynamic diagnostics of spindles is possible partly due to spindle error analyzers. Static measurements, conducted at low or zero speed, have become inadequate for the determination of the tilt of the spindle, which behaves considerably different in dynamic conditions, when the rotational speed amount to considerable values. The synchronous and asynchronous error motions and radial runout measured at high RPM enables, indirectly, evaluation of bearings condition, backlash, insufficient stiffness or unbalance. Literature analysis indicates that, however important, geometric accuracy of the machining tool alone does not ensure high precision of aircraft parts machining, as spindle error motion is of great significance.

Topic: Advanced Measurement and Metrology Techniques
Subfield: Mechanical Engineering
Field: Engineering
Domain: Physical Sciences
Determination of IC<sub>50</sub> values of anticancer drugs on cells by D<sub>2</sub>O – single cell Raman spectroscopy

A simple, sensitive and repeatable D 2 O-single cell Raman spectroscopy method was established to quantify the IC 50 values of anticancer drugs by detecting C–D/(C–D + C–H) Raman peak area ratios after H and D exchange occurs in cell metabolism.

Topic: Spectroscopy Techniques in Biomedical and Chemical Research
Subfield: Biophysics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Predicting the Protein Folding Rate Based on Sequence Feature Screening and Support Vector Regression

Folding rate prediction plays an important role in clarifying the protein folding mechanism. In this work, we collected 115 protein samples with known folding rates including two-, multi-, and mixed-state proteins.To characterize the primary structure information of the protein molecules more comprehensively, we considered sequence length, residue components with different scales, k-space features for pair residues, and geostatistics association features among different locations of the residues substituted with corresponding physical-chemical properties. Each protein sequence was represented by a numeric vector containing 9357 numbers. We selected23 features with a clear meaning from the above-mentioned high-dimensional features for each sample, after conducting an improved binary matrix shuffling filter and a worst descriptor elimination multi-round method. We constructed a nonlinear support vector regression(SVR) model based on the folding rate and the 23 retained features. The correlation coefficient of the Jackknife cross validation was 0.95. Our prediction accuracy was superior to other results from the literature and other reference feature selection methods. Finally, we established an interpretability system for SVR, and our data showed that the nonlinear regression relationship between the folding rates and the reserved features was highly significant. By further analyzing the effects of each retained descriptor on protein folding rates, the results showed that the protein folding rate might be closely related to the sequence length, the features associated with the medium- and short-range, the triplet residues component features, etc.

Topic: Protein Structure and Dynamics
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Impact of immunosuppressive drugs in the therapeutic efficacy of autoimmune skin diseases

Background: Autoimmune skin diseases such as pemphigus vulgaris and psoriasis and systemic sclerosis require long-term treatment. Immunosuppressive drug therapy is a gold standard treatment choice in the management of autoimmune skin disease. 

Aim and Objective: The aim of the study was to assess the efficacy of immunosuppressive drugs in the management of chronic skin diseases. 

Materials and Methods: A total of 120 cases of both genders (75 males and 45 females), above 18 years and newly started with immunosuppressant drugs for psoriasis (methotrexate therapy-weekly once), Pemphigus Vulgaris and Systemic Sclerosis (pulse therapy  monthly once) were recruited. The clinical response of drugs was assessed by psoriasis area severity index score (PASI), modified Rodnan Skin Score (MRSS), and Pemphigus Area and Activity Score (PAAS). 

Results: The PAAS score, PASI score, and MRSS scores were significantly decreased from the beginning to the end of the 6th month and the difference was statistically significant (P < 0.005). Nausea/ vomiting were the common adverse effects in all groups followed by gastritis and weight gain. 

Conclusion: The usage of immunosuppressant drugs such as methotrexate in the management of psoriasis and dexamethasone-cyclophosphamide therapy in the management of pemphigus vulgaris and systemic sclerosis is effective and did not show any major adverse effects.

Topic: Autoimmune Bullous Skin Diseases
Subfield: Pathology and Forensic Medicine
Field: Medicine
Domain: Health Sciences
[Glucagonoma - a rare neuroendocrine tumor (NET) that typically originates in the pancreas].

One of the primary indicators of this condition is a painful and migratory dermatitis. Additionally, early signs often include weight loss and diabetes. Patients with glucagonoma commonly first encounter general practitioners or dermatologists. Unfortunately, due to the nonspecific nature of symptoms such as eczema-like dermatitis, weight loss and diabetes, diagnosis is frequently delayed, often by 2-3 years. Consequently, by the time patients are diagnosed, the tumor has usually grown and metastasized, often spreading to the liver. As a result, surgical intervention is often not possible, and treatment options are usually limited to palliative care. However, with early diagnosis of glucagonoma, treatment can be curative. Therefore, it is crucial for medical professionals who initially meet these patients, including dermatologists, general practitioners, endocrinologists, and others, to be aware of this condition to ensure an early diagnosis. By recognizing the signs and symptoms early, doctors can potentially improve patient outcomes and save lives.

Topic: Neuroendocrine Tumor Research Advances
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences
Agrobiological evaluation of narrow-leaved lupin varieties in the conditions of the Middle Urals

Abstract Research and production introduction of the multipurpose use of narrow-leaved lupin varieties in fodder production in the region will increase the agricultural efficiency with developed dairy cattle breeding. The aim of the research was to study the adaptive properties of narrow-leaved lupin varieties in the Udmurt Republic, to analyze the efficiency of its cultivation. The studies were carried out in the southern agroclimatic region of the Udmurt Republic on gray forest soil. The arable soil layer was characterized by a humus content of 2.1-2.6%, mobile phosphorus - 100-101 mg/kg of soil, mobile potassium - 101-170 mg/kg of soil, and pH KCl from moderately acidic to almost neutral (5.0 -5.6). By the content of crude protein (32%) in grain, narrow-leaved lupin is the leader in the region among leguminous crops. During the research period, a relatively high yield of 1.36-4.95 t/ha was formed by Snezhet’ variety. Varieties Snezhet’ and Vector (S 2 d = 0.05…0.14) were distinguished by their high resistance to changes in agro-ecological conditions. The combination of ecological plasticity indicators (bi = 0.60) and phenotypic stability (S 2 d = 0.60) of Crystal variety indicates its high adaptive properties.

Topic: Botanical Research and Chemistry
Subfield: Ecology, Evolution, Behavior and Systematics
Field: Agricultural and Biological Sciences
Domain: Life Sciences
RECOGNITION OF UZBEK HANDWRITTEN TEXTS BY SELECTION OF ACTIVATION FUNCTIONS FOR CONVOLUTIONAL NEURAL NETWORK

<em>Activation functions are important in each neural network. This article highlights the advantages and disadvantages of activation functions in convolutional neural network recognition of handwritten text images. A comparative analysis is presented based on the remaining neural network models through selected activation functions. 95 percent recognition efficiency was achieved through the organized convolutional neural network.</em>

Topic: Engineering and Agricultural Innovations
Subfield: Aquatic Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Preliminary comparison of skin transcriptome from sheep with different wool fibre diameters

Context Wool is one of the most important animal fibres for the textile industry, and its diameter directly affects its economic value. However, the molecular mechanisms underlying wool fibre diameter (FD) in sheep have not been fully elucidated. Aims The aims of the work were to make an initial comparison of skin transcriptomes from sheep with wool of high and low FD, and to identify key genes affecting FD. Methods High-throughput RNA-Seq technology was employed to explore the skin transcriptome, using three sheep with fine wool (FD &amp;lt;21.0 μm) and three sheep with coarse wool (FD &amp;gt;27.0 μm). Key results We obtained 28 607 228 bp of clean sequence data, 78.9% (±3.8%) of which uniquely aligned to the reference genome across the six samples. In total, 19 914 mRNA transcripts were expressed (FPKM &amp;gt;0) in the six skin samples, among which were certain well-known genes involved in the skin–hair cycle, such as KRTAP7-1, KRT14, Wnt10b, Wnt2b, β-catenin and FGF5. Furthermore, 467 genes were significantly differentially expressed between the fine-wool and coarse-wool groups, including 21 genes with upregulated and 446 genes with downregulated expression in the sheep with lower FD. These differentially expressed genes were particularly enriched in the gene ontology processes related to lipid metabolism, skin development, differentiation and immune function (P &amp;lt; 0.05). The biological processes were involved in collagen catabolism, negative regulation of macromolecule metabolism, steroid hormone stimulation and lipid metabolism. A significant Kyoto Encyclopedia of Genes and Genomes pathway involving the metabolism of lipids and lipoproteins was also enriched, revealing that lipid metabolism might be one of the key factors affecting FD. The expression of these differentially expressed genes that were involved in the metabolism of lipids and lipoproteins pathway was verified by quantitative real-time PCR (qPCR). The correlation between the mRNA expression level from qPCR and RNA-Seq data was 0.999 (P &amp;lt; 0.001). Conclusions The 467 differentially expressed genes, especially those involved in lipid metabolism and immune function, may play key roles in wool follicle metabolism and the expression of wool FD. Implications This study provided valuable data for future studies aimed at elucidating the mechanisms that underlie wool follicle metabolism and wool FD. The work may also have implications for studies of the human hair follicle.

Topic: Skin Protection and Aging
Subfield: Dermatology
Field: Medicine
Domain: Health Sciences
The potential of emerging new therapeutics for the treatment of perivascular epithelioid cell tumors (PEComa)

Introduction: Perivascular epithelioid cell tumor (PEComa) constitutes a family of rare mesenchymal soft-tissue tumors. These tumors pose a significant diagnostic challenge, given their cytomorphology and characteristic co-expression of both melanocytic and myogenic markers. While most PEComas show benign behavior, a subset of PEComas can act malignantly. Historically, cytotoxic chemotherapy used in other soft-tissue sarcomas has shown little benefit. However, a growing understanding of the role of aberrant mTOR pathway activation in these tumors has yielded multiple reports of durable tumor responses and clinical benefit with mTOR inhibitors such as sirolimus, temsirolimus, and everolimus.Areas covered: We describe the histopathology, molecular features and differential diagnosis of the PEComa family and review available data on treatment strategies for localized and advanced PEComa. A literature search was performed using PubMed, American Society of Clinical Oncology, and ClinicalTrials.gov websites.Expert opinion: mTOR inhibitors are emerging as the standard approach to the management of advanced PEComa. Results of the clinical trial for advanced PEComa with ABI-009, a nanoparticle albumin-bound mTOR inhibitor, will provide the first prospective data of mTOR inhibition in PEComa, and may establish a relationship between genotype and outcome.

Topic: Tuberous Sclerosis Complex Research
Subfield: Physiology
Field: Medicine
Domain: Health Sciences
Moisture content evaluation of biomass using CFD approach

In grass conservation systems, drying in the field is an essential process upon which the quality and quantity of the material to be conserved is dependent on. In this study a Computational Fluid Dynamics (CFD) model, previously validated, was used to assess qualitatively and quantitatively the field drying process of cut grass under different weather conditions and structural specifications of the grass. The use of the CFD model depicts the climate heterogeneity in the grass area with a special focus on moisture distribution, influence of the weather conditions, in order to create the possibility of applying the model as a decision support tool for an enhanced treatment of the grass after cutting.

Topic: Greenhouse Technology and Climate Control
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Working memory load recognition with deep learning time series classification

Working memory load (WML) is one of the widely applied signals in the areas of human–machine interaction. The precise evaluation of the WML is crucial for this kind of application. This study aims to propose a deep learning (DL) time series classification (TSC) model for inter-subject WML decoding. We used fNIRS to record the hemodynamic signals of 27 participants during visual working memory tasks. Traditional machine learning and deep time series classification algorithms were respectively used for intra-subject and inter-subject WML decoding from the collected blood oxygen signals. The intra-subject classification accuracy of LDA and SVM were 94.6% and 79.1%. Our proposed TAResnet-BiLSTM model had the highest inter-subject WML decoding accuracy, reaching 92.4%. This study provides a new idea and method for the brain-computer interface application of fNIRS in real-time WML detection.

Topic: EEG and Brain-Computer Interfaces
Subfield: Cognitive Neuroscience
Field: Neuroscience
Domain: Life Sciences
Ultrasonic evaluation of normal pancreatic echogenicity and its relationship to fat deposition.

Normal pancreatic ultrasound studies of 28 patients were evaluated as to pancreatic echogenicity and correlated with the morphologic appearance of the pancreas on CT to test the hypothesis that increasing pancreatic echogenicity is related to greater fat infiltration. Statistical analysis indicates that fat is a major but not the only determining factor of increasing echogenicity.

Topic: Pancreatitis Pathology and Treatment
Subfield: Surgery
Field: Medicine
Domain: Health Sciences