jimnoneill/paper-to-field-training huggingface dataset:
Predicting transcription factor binding using ensemble random forest models

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Background: Understanding the location and cell-type specific binding of Transcription Factors (TFs) is important in the study of gene regulation. Computational prediction of TF binding sites is challenging, because TFs often bind only to short DNA motifs and cell-type specific co-factors may work together with the same TF to determine binding. Here, we consider the problem of learning a general model for the prediction of TF binding using DNase1-seq data and TF motif description in form of position specific energy matrices (PSEMs). Methods: We use TF ChIP-seq data as a gold-standard for model training and evaluation. Our contribution is a novel ensemble learning approach using random forest classifiers. In the context of the ENCODE-DREAM in vivo TF binding site prediction challenge we consider different learning setups. Results: Our results indicate that the ensemble learning approach is able to better generalize across tissues and cell-types compared to individual tissue-specific classifiers or a classifier applied to the data aggregated across tissues. Furthermore, we show that incorporating DNase1-seq peaks is essential to reduce the false positive rate of TF binding predictions compared to considering the raw DNase1 signal. Conclusions: Analysis of important features reveals that the models preferentially select motifs of other TFs that are close interaction partners in existing protein protein-interaction networks. Code generated in the scope of this project is available on GitHub: https://github.com/SchulzLab/TFAnalysis (DOI: 10.5281/zenodo.1409697).
Solution to Morgan Problem

Field: Computer Science (Physical Sciences)

In this paper, some preliminaries about Morgan problem, signal flow graph and controllable linear time-invariant standard system are first introduced in detail. In order to synthesize the necessary and sufficient condition for decoupling system, the first and second necessary conditions, and a sufficient condition for decoupling a controllable linear time-invariant system are secondly analyzed respectively. Therefore, the nonregular static state feedback expression for decoupling system that ensures the internal stability of the uncontrollable subsystem of the decoupled system at the same time is deduced. Then the pole assignment for the controllable subsystem of a decoupled system while ensuring its decoupled state is introduced. Finally, two examples combined with their corresponding signal flow graphs show the simplicity and feasibility of the necessary and sufficient condition for decoupling system described in the paper.
Law and Economics of Discrimination

Field: Economics, Econometrics and Finance (Social Sciences)

This important volume introduces the reader to the key theoretical and empirical issues concerning the topical field of law and economics of discrimination. The book begins with readings from Gary Beckerâ€™s seminal work on the economics of discrimination followed by a series of papers that try to evaluate the degree of discrimination in labour markets and the extent to which government intervention has reduced this discrimination. In addition to examining discrimination on the basis of race, gender, and sexual orientation in the labour market, Professor Donohue explores the problem of discrimination in various consumer markets, in the criminal justice sphere, in education and in health care. Along with an original introduction, this valuable collection will be of immense use to both scholars and practitioners with an interest in the law and economics of discrimination.
Tabu search with ejection chains for the vehicle routing problem with private fleet and common carrier

Field: Decision Sciences (Social Sciences)

Abstract The problem reported in this paper is a variant of the classical vehicle routing problem, where customer requests for a transportation company can be served either by its private fleet of vehicles or assigned to an external common carrier. The latter case occurs if the demand exceeds the total capacity of the private fleet or if it is more economical to do so. Accordingly, the objective is to minimize the variable and fixed costs of the private fleet plus the costs charged by the common carrier. A tabu search heuristic with a neighbourhood structure based on ejection chains is proposed to solve this problem. It is empirically demonstrated that this algorithm outperforms the best approaches reported in the literature on a set of benchmark instances with both homogeneous and heterogeneous fleets.
An inbred line of Syrian hamsters with frequent spontaneous adrenal tumors.

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Summary Two new inbred lines of Syrian hamsters are described in their 13th to 20th and 24th to 34th generations of brother-sister mating. One of the two lines, identified as BIO 4.24, shows a high incidence of adrenal tumors (in about 50% of the animals). The other, BIO 45.5, shows a significantly lower incidence (in about 17% of the animals). Histologically, these were the types of adrenal tumors previously described in this species. In 12 other inbred strains the adrenal tumor incidence averaged 23%. The BIO 4.24 line (high incidence of adrenal tumors) also showed a higher incidence of histological anomalies of sex glands and pituitary which, however, was not related to the adrenal neoplasms. There was also present a high incidence of obesity in females which was not correlated with the observed anomalies of the endocrine system. Genetic factors seem to explain the previously reported highly variable incidence of spontaneous adrenal tumors of hamsters.
A Hybrid Evolutionary Algorithm Based on Solution Merging for the Longest Arc-Preserving Common Subsequence Problem

Field: Computer Science (Physical Sciences)

The longest arc-preserving common subsequence problem is an NP-hard combinatorial optimization problem from the field of computational biology. This problem finds applications, in particular, in the comparison of arc-annotated Ribonucleic acid (RNA) sequences. In this work we propose a simple, hybrid evolutionary algorithm to tackle this problem. The most important feature of this algorithm concerns a crossover operator based on solution merging. In solution merging, two or more solutions to the problem are merged, and an exact technique is used to find the best solution within this union. It is experimentally shown that the proposed algorithm outperforms a heuristic from the literature.
Inflammatory Bowel Disease in Adult HIV-Infected Patients-Is Sexually Transmitted Infections Misdiagnosis Possible?

Field: Medicine (Health Sciences)

Background. The aim of our study was to describe 50 cases of inflammatory bowel disease (IBD) and HIV co-existence that are under medical supervision in Warsaw. Methods. This was a retrospective descriptive study. Fifty HIV-infected patients, diagnosed with IBD during the years 2001–2019, were identified. IBD was diagnosed endoscopically and then confirmed by biopsy. All data was obtained from medical records. Results. All studied patients were male with a median age of 33 years old (range 20–58 years). All, except one, were men who have sex with men (MSM). The median CD4 cell count was 482 cells/µL (range 165–1073 cells/µL). Crohn’s disease (CD) was diagnosed in 7 patients (14%), ulcerative colitis (UC) in 41 patients (82%), and 2 patients (4%) had indeterminate colitis. Forty-nine patients (98%) reported a history of unprotected receptive anal intercourse and different sexual transmitted infections (STIs). Only in 10 patients (20%) were one or more IBD relapses observed. Conclusions. We recommend HIV testing for every MSM with IBD suspicion. Moreover, STIs testing should be performed in every IBD patient with colorectal inflammation, using molecular and serological methods. Persons who reported unprotected receptive anal intercourse seem to have the biggest risk of STI-associated proctitis or proctocolitis mimicking IBD.
Characterization of the c9orf72 GC-rich low complexity sequence in two cohorts of Italian and Turkish ALS cases

Field: Medicine (Health Sciences)

Large expansions of a noncoding GGGGCC repeat in the C9orf72 gene are the main cause of amyotrophic lateral sclerosis (ALS). The GGGGCC repeat is contiguous with another GC-rich region. Recent studies reported a significantly higher frequency of insertions/deletions within the GC-rich region in patients carrying the GGGGCC expansion. A GTGGT motif comprised within the GC-rich region, which joins two 100% GC sequences, was frequently deleted, supporting the hypothesis that these deletions could make the region more prone to slippage and pathological expansion. To confirm this hypothesis, we sequenced the GC-rich region adjacent the GGGGCC repeat in ALS patients, 116 C9orf72 expansion carriers, 219 non-carriers, and 223 healthy controls, from Italian and Turkish cohorts. Deletions were significantly more frequent in C9orf72 expansion carriers (6%) compared to non-carrier ALS patients (0.46%, OR =14.00, 95% CI =1.71-306.59, p = 0.003), to controls (0%, OR =16.29, 95% CI =2.12-725.99, p = 4.86 × 10-4) and to the whole cohort of non-carriers (0.2%, OR =28.51, 95% CI =3.47-618.91, p = 9.58 × 10-5). Among expansion carriers, deletions with or without the GTGGT motif were equally distributed (4 vs. 3). The frequency of insertions was not statistically different between C9orf72 expansion carriers and any other group including the whole cohort of non-carriers (p = 0.439, Fisher's exact test). Our data confirmed the association between deletions within GC-rich region and the GGGGCC expansion in Italian and Turkish cases, although we did not confirm a role of the GTGGT element deletion. Further studies will be therefore necessary to assess the causal relationships between contiguous deletions of the GC-rich region and the GGGGCC expansion.
Metabolism of Amino Acids in the Brain (VI)

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

With a view to make biochemical comparison the author studied the transamination of various amino acids, and α-ketoglutaric acid in the brain of frog (Rana Nigromaculata), and compared these results with those obtained with the brains of mice, catfish and common turtle.1. α-amino acids in the brains of frog show on the whole a lower transaminase activity as compared with those in the brains of catfish and mice, but glycine and methionine that show no transamination other than a slight transaminase activity in the brain of catfish reveal a fairly active transamination in the frog brain.2. In the frog brain threonine and tyrodine are not at all transaminated.3. Phenylalanine is not at all transaminated in the brains of cold-blooded animals.4. Of ω-amino acids with an exception of γ-aminobutyric acid in the brain of catfish, all other show a low transaminase activity in the brains of cold-blooded animals.5. The degree of the enzyme activity of di-amino acids does not differ to any marked extent in different animals.
Maternal and Neonatal Listeriosis: Report of Case and Brief Review of Literature of Listeriosis in Man

Field: Medicine (Health Sciences)

Ethacrynic acid is an effective diuretic in doses ranging from 25 to 450 mg.daily.It is more potent than either organomercurial or benzothiadiazine diuretics.An excessive diuresis may occur after ethacrynic acid, and a test dose is recommended for patients new to the drug.Benzothiadiazines given with ethacrynic acid formed the most potent combination of diuretics tried.Urinary potassium losses are greater after ethacrynic acid than after benzothiadiazines.In resistant cases spironolactone (Aldactone-A) given with ethacrynic acid did not prevent high rates of potassium excretion.Potassium chloride supplements are desirable whenever ethacrynic acid is prescribed, alone or in combination with potassium-sparing agents.The incidence of hypochloraemic hypokalaemic alkalosis is discussed.Agranulocytosis was observed in two patients, but the causal relationship was not established with any certainty.Ethacrynic acid is best used in the treatment of patients with resistant oederna: in such cases we have found it invaluable.
Carotid endarterectomy operation in patients with resistant arterial hypertension

Field: Medicine (Health Sciences)

Цель исследования – изучить течение резистентной артериальной гипертензии (АГ) в отдалённом периоде после выполнения операции каротидной эндартерэктомии (КЭАЭ). <br/><br/>Материал и методы. В исследование включены 105 больных, у которых было выявлено сочетание значимого (70% и более) стеноза каротидной бифуркации и резистентной АГ. Всем больным в период с 2007 по 2011 г. была выполнена операция КЭАЭ по эверсионной методике с удалением каротидного гломуса. До и после операции проводили суточное мониторирование артериального давления (АД). Оценивали изменение АД (по данным суточного мониторирования) в раннем (до 30 сут) и позднем (до 7 лет) послеоперационном периодах. Критерии оценки – возможность достижения целевого АД и динамика снижения давления в послеоперационном периоде. <br/><br/>Результаты. Целевого уровня АД в раннем послеоперационном периоде удалось достигнуть у 70 (66,7%) больных. В отдалённом периоде гипотензивный эффект сохранился у 92 (87,6%) больных. При расчёте критерия Уилкоксона разница оказалась статистически значимой (Z –8,826 при р<0,0001). Неудовлетворительный результат – невозможность достижения в отдалённом периоде после операции целевого уровня АД и толерантность к медикаментозной терапии – отмечен у 13 (12,4%) пациентов. При этом было установлено, что все больные с неудовлетворительным результатом имели стаж артериальной гипертензии до операции более 7 лет. Средний уровень суточного систолического АД до операции составлял 173,9 ± 14,9 мм рт. ст., в раннем послеоперационном периоде 138±23,7 мм рт. ст., в отдаленном периоде 140,3±20,6 мм рт. ст. (р<0,001). Индекс времени систолического АД снизился с 78,2±14,6% до операции до 49,8±15,1% в отдалённом послеоперационном периоде, индекс времени диастолического АД – с 76,3±15,7 до 51,5±13,1%. Кроме того, было зарегистрировано стойкое уменьшение вариабельности колебания как систолического, так и диастолического АД, преимущественно в ночное время. <br/><br/>Заключение. Больным с резистентной АГ следует выполнять ультразвуковое исследование брахиоцефальных сосудов. Прогрессирующий стеноз каротидной бифуркации является причиной формирования вторичной цереброваскулярной гипертензии. Этот факт служит дополнительным обоснованием необходимости оперативного лечения больных со значимым стенозом каротидной бифуркации и резистентной артериальной гипертензией. HTML
Survival of Miamiensis avidus (Ciliophora: Scuticociliatia) from antibody-dependent complement killing

Field: Immunology and Microbiology (Life Sciences)

Previously, we had reported that some Miamiensis avidus, a major pathogen of scuticociliatosis in cultured olive flounder, strongly agglutinated by flounder immune sera could escape from the agglutinated mass within a few hours. In the present study, we observed that M. avidus not only escaped from the agglutinated mass but also conducted division(s) before shedding its old covering. Furthermore, ciliates that survived the antibody-dependent complement killing (ADCK) assay were not killed even when re-exposed to a freshly prepared ADCK assay. This result suggests that the liberated ciliates from the ADCK assay might change not only their i-antigen types but also the epitopes of major surface antigens, which debilitate antibody-mediated complement killing ability.
Influence of phallotoxins and metal ions on the rate of proteolysis of actin

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

The rate of proteolytic degradation of rabbit skeletal muscle actin by trypsin, alpha-chymotrypsin, and, mainly, subtilisin was followed by dual wavelength spectroscopy at 285 nm by reference at 320 nm. Phalloidin and phallacidin, two toxic bicyclic heptapeptides from the mushroom Amanita phalloides, protect F-actin against degradation by the proteolytic enzymes. G-actin, which does not combine with phalloidin when maintained in the monomeric state by working at low ionic strength, and bovine serum albumin, which also has no affinity to the toxin, are hydrolyzed at the same rates in the presence or absence of phalloidin. The proteolysis of F-actin is distinctly retarded by KCl alone, i.e., without phalloidin, whereas Mg2+ or Ca2+ as sole cations permit a rather high rate of hydrolysis. An even faster degradation of F-actin by subtilisin is observed in the presence of Mg2+ plus cytochalasin B. Adenosine diphosphate and triphosphate have no influence on the rate of the enzymatic degradation. The S sulfoxide of phalloidin, the nontoxic diastereomer of the toxic R form, exerts only a limited inhibitory effect on the enzymatic hydrolysis; secophalloidin, another nontoxic derivative, which does not bind to F-actin has practically no effect.
Transcriptomic analyses reveal molecular mechanisms underlying regulation of floral attributes in Lonicera japonica Thunb.

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract Background Lonicera Japonica Thunb. is a perennial, semi-evergreen and twining vine in the family of Caprifoliaceae, which is widely cultivated in Asia. Thus far, L. japonica is often used to treat some human diseases including COVID-19, H1N1 influenza and hand-foot-and-mouth diseases, however, the regulatory mechanism of intrinsic physiological processes during different floral developmental stages of L. japonica remain largely unknown. Results The complete transcriptome of L. japonica was de novo-assembled and annotated, generating a total of 195850 unigenes, of which 84657 could be functionally annotated. 70 candidate genes involved in flowering transition were identified and the flowering regulatory network of five pathways was constructed in L. japonica . The mRNA transcripts of AGL24 and SOC1 exhibited a downward trend during flowering transition and followed by a gradual increase during the flower development. The transcripts of AP1 was only detected during the floral development, whereas the transcript level of FLC was high during the vegetative stages. The expression profiles of AGL24 , SOC1 , AP1 and FLC genes indicate that these key integrators might play the essential and evolutionarily conserved roles in control of flowering switch across the plant kingdom. We also identified 54 L. japonica genes encoding enzymes involved in terpenoid biosynthesis pathway. Most highly expressed genes centered on the MEP pathway, suggesting that this plastid pathway might represent the major pathway for terpenoid biosynthesis in L. japonica . In addition, 33 and 31 key genes encoding enzymes involved in the carotenogenesis and anthocyanin biosynthesis pathway were identified, respectively. PSY transcripts gradually increased during the flower development, supporting its role as the first rate-limiting enzyme in carotenoid skeleton production. The expression level of most anthocyanin biosynthetic genes was dramatically decreased during the flower developmental stages, consistent with the decline in the contents of anthocyanin. Conclusion These results identified a large number of potential key regulators controlling flowering time, flower color and floral scent formation in L. japonica , which improves our understanding of the molecular mechanisms underlying the flower traits and flower metabolism, as well as sets the groundwork for quality improvement and molecular breeding of L. japonica .
Analysis of the Conditions of Mechanical Equilibrium on the Curved Surface of a Vapor–Liquid System in a Gravitational Field

Field: Physics and Astronomy (Physical Sciences)

A thermodynamic analysis of mechanical equilibrium conditions is performed for the curved interface of a vapor–liquid system in the gravitational field potential with regard to ratios of experimental times of relaxation of thermodynamic parameters (momentum, energy, and mass). In a kinetic analysis of the relaxation stage of reaching the equilibrium state, it is revealed that it is important to consider the physical nature of the boundary of separating phases. The mechanical model of the boundary is one with an intermediate foreign film preventing the attainment of chemical equilibrium between the neighboring phases. The real boundary of coexisting phases has a variable density profile corresponding to the condition of the constant chemical potential throughout the region of transition and in the neighboring coexisting phases. The absence of an intermediate film excludes the priority of the mechanical equilibrium over the chemical equilibrium and results in pressure being the function of local temperature and chemical potential values (excluding the application of the Laplace equation). Considering times of relaxation is found to change the familiar Gibbs expression for the pressure jump between coexisting vapor and fluid as functions of the boundary in the gravitational field potential. A consequence of considering the correct ratio of momentum and mass times of relaxation is discussed: the phase equilibrium conditions of a separating vapor–liquid system in combined gravitational and surface force fields must be analyzed in order to solve problems of the capillary theory.
Smith and the Merits of the Poor

Field: Economics, Econometrics and Finance (Social Sciences)

Economists concerned with social welfare problems are not in the habit of looking to Adam Smith for guidance. Such problems all too often require the of the state in order to alter the results achieved the market, and Adam Smith is best known for his defense of free markets and his arguments against state in eco? nomic affairs. Thus, most of our colleagues would agree with the views expressed in an article one of the editors in the recent in? augural issue of the International Journal of Social Economics. It makes the point that Smith avoided the problems arising from con? flicting economic and social priorities by the convenient intervention of the invisible hand. [Showier, p. 7; for another illustration of this view see Rohrlich, p. 18.] It would be silly at this late date to argue that Smith was not in favor of laissez-faire after all, yet, it is of some interest to examine his thinking insofar as it relates to the welfare of the lower classes. The reasons why a man like Adam Smith takes a negative policy position are usually much more instructive than the position itself. The main point which this paper intends to com? municate is that modern social economists who see an activist role for