jimnoneill/paper-to-field-training huggingface dataset:
Surveying the welfare of farmed fish species on a global scale through the fair‐fish database

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract Fish welfare is a critical issue that needs to be addressed by the rapidly growing aquaculture industry. Scientific knowledge regarding the natural behaviors of species and the conditions in which they are kept in farms is essential for improving their welfare in aquaculture. To provide a consistent overview of the welfare of farmed fish, the organization fair‐fish has created the online platform fair‐fish database , which gathers ethological knowledge categorized into profiles of farmed aquatic species. The WelfareChecks on this platform are profiles based on criteria that are rated based on the likelihood and potential of the species to experience a high level of welfare in aquaculture systems, together with the certainty about the findings. A score (WelfareScore) is calculated from these ratings, serving as a reference to identify knowledge gaps, assess welfare, and suggest ways to improve it. Here, we performed an in‐depth analysis of the species with WelfareChecks already published in the fair‐fish database based on their respective WelfareScores. In general, although just a small percentage of farmed aquatic species (~5%) have at least a 20% chance of experiencing a good level of welfare under minimal aquaculture conditions, 60% of them have at least some potential to achieve good welfare under high‐standard conditions, with more than a third of the species (~37%) having at least a 20% potential. Despite that, several species exhibit a very high frequency of low chances and potential for experiencing good welfare levels under aquaculture conditions, besides a low degree of certainty based on literature reviews. Furthermore, many others show a very frequent occurrence of unclear or nonexistent knowledge in their profiles. The current welfare state is therefore poor for the majority of farmed aquatic species; yet, there is considerable potential for improvement. However, many species are very unlikely to achieve good welfare, even under high‐standard conditions. Importantly, large knowledge gaps remain for an accurate assessment of the welfare of several farmed species.
sj-pdf-1-jso-10.1177_23971983241231082 – Supplemental material for Assessing hand and global disability in a cohort of Algerian patients with systemic sclerosis: Construct validities of the Arab Hand Function Index and the Arabic Health Assessment Questionnaire

Field: Medicine (Health Sciences)

Supplemental material, sj-pdf-1-jso-10.1177_23971983241231082 for Assessing hand and global disability in a cohort of Algerian patients with systemic sclerosis: Construct validities of the Arab Hand Function Index and the Arabic Health Assessment Questionnaire by Nouria Benmostefa, Rachid Malek, Marie Robert, Benjamin Chaigne, Samy Slimani, Samir Rouabhia, Daoud Roula, Mallem Djamel and Luc Mouthon in Journal of Scleroderma and Related Disorders
Author response: H3-OPT: Accurate prediction of CDR-H3 loop structures of antibodies with deep learning

Field: Computer Science (Physical Sciences)

Accurate prediction of the structurally diverse complementarity determining region heavy chain 3 (CDR-H3) loop structure remains a primary and long-standing challenge for antibody modeling. Here, we present the H3-OPT toolkit for predicting the 3D structures of monoclonal antibodies and nanobodies. H3-OPT combines the strengths of AlphaFold2 with a pre-trained protein language model, and provides a 2.24 Å average RMSDCα between predicted and experimentally determined CDR-H3 loops, thus outperforming other current computational methods in our non-redundant high-quality dataset. The model was validated by experimentally solving three structures of anti-VEGF nanobodies predicted by H3-OPT. We examined the potential applications of H3-OPT through analyzing antibody surface properties and antibody-antigen interactions. This structural prediction tool can be used to optimize antibody-antigen binding, and to engineer therapeutic antibodies with biophysical properties for specialized drug administration route.
pn Junction Delineation in Si Devices Using Scanning Capacitance Spectroscopy

Field: Engineering (Physical Sciences)

Abstract The scanning capacitance microscope is a carrier-sensitive imaging tool based upon the well-known scanning-probe microscope (SCM). Scanning capacitance spectroscopy (SCS) is useful to utilize an SCM to delineate pn junctions in Si devices. This article reports the applications of SCS to Si devices such as CMOS and BiCMOS. SCS is shown to resolve device features on the 10 nm scale for several technologies. Ongoing work includes verifying the reproducibility of SCS measurements and using physical modeling to support the empirical assignment of depletion region width and electrical pn junction position from SCS data. Another technology area where two-dimensional pn junction data is useful is in CMOS device isolation.
<title>Radio frequency needle hyperthermia of normal and cancerous animal tissue</title>

Field: Medicine (Health Sciences)

Capacitative radio frequency (RF) was met with little success when used to treat human cancer. Conductive rf needle hyperthermia (RFNH) is used successfully for human tissue ablation in neurosurgery, cardiology, and recently in urology. RFNH ablates tissue by causing thermal damage limited to the vicinity of the rf needle. We conducted a series of studies to evaluate the effect of RFNH on cancerous and normal tissue. RFNH was applied to normal porcine livers during open surgery. Liver function tests were elevated two days post treatment, then returned to normal. Pigs were sequentially sacrificed. RFNH induced lesions were found to be maximal in size on days 2 - 4 post treatment and later became smaller as liver regenerated. Phase 2 included mice bearing two subcutaneous murine bladder tumors (MBT2). The rf needle was inserted into both tumors of each mouse, but rf current was applied to one tumor only. Energies of 3 to 7.5 watts were applied for 30 seconds to 5 minutes using a 0.02 inch needle. Mice were sacrificed 0, 1, and 3 days after treatment. Necrotic lesions 0.5 - 1.2 cm in diameter were found within the treated tumors. In phase 3, mice bearing a single 8 - 18 mm subcutaneous tumor were treated by RFNH aiming for complete tumor destruction. All control mice died of huge tumors within 31 days. Treated mice were alive with no signs of tumor when sacrificed 60 days after treatment. In phase 3 RFNH is capable of complete tumor eradication with little damage to surrounding normal tissue. It may have clinical applications for percutaneous endoscopic and laparoscopic treatment of tumors.
Conditioning regimens for allotransplants for diffuse large B-cell lymphoma: myeloablative or reduced intensity?

Field: Medicine (Health Sciences)

Abstract The best conditioning regimen before allogeneic transplantation for high-risk diffuse large B-cell lymphoma (DLBCL) remains to be clarified. We analyzed data from 396 recipients of allotransplants for DLBCL receiving myeloablative (MAC; n = 165), reduced intensity (RIC; n = 143), or nonmyeloablative conditioning (NMAC; n = 88) regimens. Acute and chronic GVHD rates were similar across the groups. Five-year nonrelapse mortality (NRM) was higher in MAC than RIC and NMAC (56% vs 47% vs 36%; P = .007). Five-year relapse/progression was lower in MAC than in RIC/NMAC (26% vs 38% vs 40%; P = .031). Five-year progression-free survival (15%-25%) and overall survival (18%-26%) did not differ significantly between the cohorts. In multivariate analysis, NMAC and more recent transplant year were associated with lower NRM, whereas a lower Karnofsky performance score (< 90), prior relapse resistant to therapy, and use of unrelated donors were associated with higher NRM. NMAC transplants, no prior use of rituximab, and prior relapse resistant to therapy were associated with a greater risk of relapse/progression. In conclusion, allotransplantation with RIC or NMAC induces long-term progression-free survival in selected DLBCL patients with a lower risk of NRM but with higher risk of lymphoma progression or relapse.
Complete Blood Count Reference Interval Diagrams Derived from NHANES III: Stratification by Age, Sex, and Race

Field: Medicine (Health Sciences)

There are age-dependent trends for many of the tests, notably in RDW, MCMV, platelet count, and granulocyte and lymphocyte percentages. Sex-dependent changes involved hemoglobin values, and race-related trends centered around mononuclear and lymphocyte percentages, hematocrit, MCHC, MCH, and hemoglobin. This study reveals the potential for using data mining of large samples to yield potentially useful reference ranges.
Image Denoising with Graph-Convolutional Neural Networks

Field: Computer Science (Physical Sciences)

Recovering an image from a noisy observation is a key problem in signal processing. Recently, it has been shown that data-driven approaches employing convolutional neural networks can outperform classical model-based techniques, because they can capture more powerful and discriminative features. However, since these methods are based on convolutional operations, they are only capable of exploiting local similarities without taking into account non-local self-similarities. In this paper we propose a convolutional neural network that employs graph-convolutional layers in order to exploit both local and non-local similarities. The graph-convolutional layers dynamically construct neighborhoods in the feature space to detect latent correlations in the feature maps produced by the hidden layers. The experimental results show that the proposed architecture outperforms classical convolutional neural networks for the denoising task.
The ridgeback anomaly

Field: Medicine (Health Sciences)

In Reply.—

We wish to thank Dr Williams for her insightful comments. The study of trichoglyphics was established in animals with subsequent comparisons made with those patterns seen in human beings. This is best exemplified in the classic treatise by Kidd1comparing follicular patterns in apes and man. These comparative observations are the cornerstone of our current understanding of scalp pattern development in man. Descriptive names for diseases seen in human beings (ie, Michelin tire baby, blueberry muffin baby, and pine cone man) are well established in the medical literature. These descriptive names are a tremendous aid in remembering the various disorders as opposed to diseases named after principal investigators. Dr Williams is correct, genetic contributions cannot be absolutely excluded. In addressing genetic contributions for scalp pattern development, a number of points need to be kept in mind. Mendelian inheritance patterns have been implicated in frontal hair patterns, but have
Discovery of a Potent Dual Inhibitor of Wild-Type and Mutant Respiratory Syncytial Virus Fusion Proteins

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

A novel series of macrocyclic pyrazolo[1,5-a]pyrimidine derivatives as respiratory syncytial virus (RSV) fusion glycoprotein (F protein) inhibitors were designed and synthesized based on docking studies of acyclic inhibitors. This effort resulted in the discovery of several macrocyclic compounds, such as 12b, 12f, and 12h, with low nanomolar to subnanomolar activities against the wild-type RSV F protein A2. In addition, 12h showed a single-digit nanomolar potency against the previously reported drug-resistant mutant D486N. Molecular modeling and computational analyses suggested that 12h binds to the D486N mutant while maintaining a rigid bioactive conformation via macrocyclization and that it interacts with a hydrophobic cavity of the mutant using a new interaction surface of 12h. This report describes the rational design of macrocyclic compounds with dual inhibitory activities against wild-type and mutant RSV F proteins.
Whole-Genome Sequence Analysis of Pseudomonas syringae pv. phaseolicola 1448A Reveals Divergence among Pathovars in Genes Involved in Virulence and Transposition

Field: Agricultural and Biological Sciences (Life Sciences)

ABSTRACT Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis . Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific.
GAN for object detection under rainy conditions

Field: Computer Science (Physical Sciences)

Artificial Intelligence (AI) is gaining prominence in our daily life. The world is amidst of trying to replace day to day regular activities. One such activity is driving. In order to achieve autonomous driving, object detection is one of the crucial aspect to improve upon. Object detection is also an important aspect of AI. The performance of object detector deteriorates during rainy conditions as they are not designed for adverse weather conditions. The objective of this project is to develop an object detection system that is able to detect objects during rainy conditions with higher accuracy. A deep learning model will be trained and tested with data that will be collected for clear weather conditions and together with pre-collected rain data. This trained model will be used to generate de-rained (rainless) image from a rainy image. A classifier will be trained with dataset to be able to classify various objects. After training, a dataset of rain image and its corresponding de-rained image will be fed to the classifier. Accuracy of the reading will be tabulated and conclusion on the result will be discussed. Lastly, how the system can be improved to achieve better results and function in a more robust manner will be discussed.
Increasing non-exercise physical activity : extended theory of planned behaviour model testing and the role of stress within sedentary parents

Field: Psychology (Social Sciences)

Loosveldt, Justine Sofie Paulette, 2015. Increasing non-exercise physical activity: extended Theory of Planned Behaviour model testing and the role of stress within sedentary parents. Master’s thesis in Sport and Exercise Psychology. Department of Sport Sciences. University of Jyvaskyla. 56 pages. Although much research has been done in studying physical activity and its health benefits, inactive behaviour has obtained little attention. The main purpose of the present study is to test the Theory of Planned Behaviour (TPB) in predicting sedentary behaviour to a group of parents with young children and a sedentary job. The secondary purpose of this study is to explore if stress explains additional variation when is entered as an additional variable between intention and sedentary behaviour. The sample consisted of 68 sedentary adults with young children, both men (N = 29) and women (N = 39), (M = 37.8 years and SD = 5.8). Participants were divided into two groups: an experimental group who received the intervention and a control group who was not exposed to the intervention but underwent the same measurements. Sedentary behaviour has been assessed with EMG data and calculated to sedentary ratio. Variables of the TPB model (intention, attitude strength, perceived behaviour control , self-identity and perceived knowledge) were assessed by questionnaires. Occupational stress was measured by Heart Rate Variability (HRV) where RMSSD functioned as an indicator for stress. Linear regression analyses indicated that the extended TPB model explained the variance only in the experimental group. Stress has been found to explain larger amount of variation in the control group than in the experimental group. This study shows that the intervention to increase non-exercise physical activity makes people aware of their sedentary behaviour. Also, stress seems to be a factor that interferes between intention and behaviour for sedentary people. Overall, paying attention to diminishing sitting time should be beneficial for public health and increase health outcomes. People need to be aware of the harming effects of their sedentary behaviour and how to increase their non-exercise physical activity in order to be able to make small changes in their everyday routine, ultimately leading to the reception of health benefits elicited from these changes. Moreover, stress management strategies should be included in future interventions, as stress might be seen as a barrier in increasing non-exercise physical activity.
Peach Trees Grow in the Spaces Between People: Counselling Practices in the Territory of Violence

Field: Psychology (Social Sciences)

In this paper the authors reflect on how therapeutic practices wove a community of care and concern with a young man in South Africa who was at risk of anger ruling his life. A counselor and outsider witnesses participated in responding to the problems the young man and his family faced. The authors discuss the steps they took in the therapeutic journey and describe how their personal and professional lives were shaped by this collaboration. This work inspires and sustains their enthusiasm in seeking to understand how to best respond when positioned to counsel.
Hubungan Status Gizi Ibu Bersalin dengan Kejadian Berat Badan Lahir Rendah (Bblr)

Field: Medicine (Health Sciences)

Low Birth Weight (LBW) is the first cause of infant mortality in West Java. Babies born with LBW need to get serious treatment, because in these conditions babies are easily distracted. Factors that influence the occurrence of LBW are age, nutritional status, pregnancy distance and maternal parity (Manuba, 2010). The purpose of this study was to determine the relationship between maternal nutritional status and the incidence of low birth weight (LBW). This study used a descriptive analytic using a cross sectional approach. The research was conducted in August 2020 - December 2020 at RSIA dr. Djoko Pramono. The sample of this study were all deliveries at RSIA dr. Djoko Pramono from August-16 October 2020, totaling 182. Data collection techniques with secondary data were arranged using a master table. The results of the study were analyzed bivariately using the chi Square test. Based on the results of statistical analysis with chi square, it was found that there was a significant relationship between nutritional status and the incidence of LBW, with a p value of 0.000 (<0.05), OR = 16.684. Women because they will conceive and give birth and so that there is no further deficiency of pregnancy status, so as to reduce the level of morbidity and mortality of infants. Abstrak Bayi dengan Berat Badan Lahir Rendah (BBLR) merupakan penyebab pertama kematian bayi di Jawa Barat. Bayi yang lahir dengan BBLR perlu mendapatkan penanganan yang serius, karena pada kondisi tersebut bayi mudah sekali mengalami gangguan. Faktor yang mempengaruhi terjadinya BBLR yaitu umur, status gizi, jarak kehamilan dan paritas ibu (Manuba, 2010). Tujuan penelitian ini untuk mengetahuiubungan status gizi ibu dengan kejadian Berat Badan Lahir Rendah (BBLR). Penelitian ini menggunakan desain diskriptif analitik dengan menggunakan pendekatan cross sectional. Populasi Penelitian ini adalah ibu bersalin pada Agustus 2020 – Desember 2020 di RSIA dr. Djoko Pramono. Sampel penelitian ini adalah seluruh ibu bersalin di RSIA dr. Djoko Pramono dari bulan Agustus-16 Oktober 2020 yang berjumlah 182. Teknik pengumpulan data dengan data sekunder yang disusun menggunakan master table dan dianalisis menggunakan chi square. Hasil Penelitian terdapat hubungan yang signifikan antara status gizi dengan kejadian BBLR, dengan hasil p value 0.000 (< 0,05) OR = 16,684. Saran bagi pasien yaitu diharapkan untuk pasien agar lebih maksimal memperhatikan asupan makanan (status gizi) terutama .
An Ensemble Fuzzy-MCDM Approach for Evaluation of Approved Monkeypox Vaccines

Field: Decision Sciences (Social Sciences)

Abstract Objective : Monkeypox, a disease caused by a deoxyribonucleic acid (DNA) based virus (MPXV) has posed global health challenges to the entire populace. MPXV is a zoonotic disease with public health concerns, rapid prevalence, and geographical spread resulting in swift preventive techniques, especially for vulnerable nations (population). Its incidence and global widespread have necessitated immediate intervention thus the use of vaccination. This study analyzed three globally recommended monkeypox vaccines, LC16m8, ACAM2000, and JYNNEOS, by assessing their safety and effectiveness in controlling monkeypox. Methods : Multi-criteria decision-making (MCDM) methods; the fuzzy Preference Ranking Organization Method for Enrichment Evaluations (fuzzy PROMETHEE) and the fuzzy Technique for Order Preference by Similarities to Ideal Solution (fuzzy TOPSIS), were applied for the evaluation of these vaccines considering 20 different criteria, mainly focusing on the route of administration, dosage, safety, adverse effects, affordability, and overall effectiveness of the vaccine. Results : LC16m8 ranked the most preferable vaccine from both MCDM methods with a net outranking flow of 0.4365 and Closeness coefficient value of 0.7916 (95% CI, 0.242-0.894). In terms of safety, both LC16m8 and JYNNEOS vaccines showed equal performance in their profiles mostly in vulnerable populations like human immunodeficiency virus-positive populations, pregnant women, and children, as well as cardiovascular disease patients. Conclusion : The MCDM models could be flexibly applied to other areas of public health as it has shown their reliability in assessing the monkeypox vaccines and can provide a decision guide for different health policy agencies.
Shakespeare appropriation and queer Latinx empowerment in Josh Inocéncio’s Ofélio

Field: Arts and Humanities (Social Sciences)

Latinx William Shakespeare's origins can be traced to West Side Story, which debuted in 1957, and this trend has grown rapidly in the last decade alongside the cultural influence of Latinxs in the United States. By invoking Ophelia to express the experience of a rape survivor, Josh Inocencio joins a feminist tradition of reproducing Shakespeare's heroine to give voice to those who are marginalized or victimized. Latinx Shakespeare productions such as Ofelio reckon with Shakespeare's cultural primacy, often regarded as an impediment to the flourishing of Latinx theater. As Elizabeth Klein and Michael Shapiro suggest, attending to local productions can challenge dominant understandings of "what 'Shakespeare' is or what 'Shakespeare' should sound like", problematizing received notions of Shakespeare's universality. Inocencio's Ofelio rejects this history of whitewashing Ophelia and instead interrogates Shakespeare's cultural supremacy and, more broadly, white Anglo hegemony.