jimnoneill/paper-to-field-training huggingface dataset:
Molecular determinants and heterogeneity underlying host response to EV-A71 infection at single-cell resolution

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

The pathogenic human enterovirus EV-A71 has raised serious public health concerns. A hallmark of EV-A71 infection is the distortion of host transcriptomes in favour of viral replication. While high-throughput approaches have been exploited to dissect these gene dysregulations, they do not fully capture molecular perturbations at the single-cell level and in a physiologically relevant context. In this study, we applied a single-cell RNA sequencing approach on infected differentiated enterocyte cells (C2BBe1), which model the gastrointestinal epithelium targeted initially by EV-A71. Our single-cell analysis of EV-A71-infected culture provided several lines of illuminating observations: 1) This systems approach demonstrated extensive cell-to-cell variation in a single culture upon viral infection and delineated transcriptomic differences between the EV-A71-infected and bystander cells. 2) By analysing expression profiles of known EV-A71 receptors and entry facilitation factors, we found that ANXA2 was closely correlated in expression with the viral RNA in the infected population, supporting its role in EV-A71 entry in the enteric cells. 3) We further catalogued dysregulated lncRNAs elicited by EV-A71 infection and demonstrated the functional implication of lncRNA CYTOR in promoting EV-A71 replication. Viewed together, our single-cell transcriptomic analysis illustrated at the single-cell resolution the heterogeneity of host susceptibility to EV-A71 and revealed the involvement of lncRNAs in host antiviral response.
Maternal high-fat diet impairs cardiac function in offspring of diabetic pregnancy through metabolic stress and mitochondrial dysfunction

Field: Medicine (Health Sciences)

Offspring of diabetic pregnancies are at risk of cardiovascular disease at birth and throughout life, purportedly through fuel-mediated influences on the developing heart. Preventative measures focus on glycemic control, but the contribution of additional offenders, including lipids, is not understood. Cellular bioenergetics can be influenced by both diabetes and hyperlipidemia and play a pivotal role in the pathophysiology of adult cardiovascular disease. This study investigated whether a maternal high-fat diet, independently or additively with diabetes, could impair fuel metabolism, mitochondrial function, and cardiac physiology in the developing offspring's heart. Sprague-Dawley rats fed a control or high-fat diet were administered placebo or streptozotocin to induce diabetes during pregnancy and then delivered offspring from four groups: control, diabetes exposed, diet exposed, and combination exposed. Cardiac function, cellular bioenergetics (mitochondrial stress test, glycolytic stress test, and palmitate oxidation assay), lipid peroxidation, mitochondrial histology, and copy number were determined. Diabetes-exposed offspring had impaired glycolytic and respiratory capacity and a reduced proton leak. High-fat diet-exposed offspring had increased mitochondrial copy number, increased lipid peroxidation, and evidence of mitochondrial dysfunction. Combination-exposed pups were most severely affected and demonstrated cardiac lipid droplet accumulation and diastolic/systolic cardiac dysfunction that mimics that of adult diabetic cardiomyopathy. This study is the first to demonstrate that a maternal high-fat diet impairs cardiac function in offspring of diabetic pregnancies through metabolic stress and serves as a critical step in understanding the role of cellular bioenergetics in developmentally programmed cardiac disease.
SpecSims: A Scalable Speculative Tree-based Simulation Cloning Framework for Finite Memory Machines

Field: Computer Science (Physical Sciences)

Simulation cloning is a technique in which cloned simulations whose state spaces differ partially from their parent simulation due to intervening events are spawned at runtime and concurrently advanced. It is a powerful method to carry out what-if analysis by speculatively exploring and evaluating the impact of various permutations of intervening cascade of events. Due to the exponential growth in the number of possible clones even for a small number of distinct intervening events, the practical efficacy of the approach is often severely limited by the maximum available memory of the computing host. In this paper, we introduce a novel speculative simulation cloning framework that executes a simulation cloning campaign capable of efficiently exploring an exponentially large space of clone simulations created by permutation of intervening events under a finite memory constraint. We provide a theoretical analysis of the runtime characteristics of our proposed approach and highlight its novel advantages such as memory-aware and as-long-as-needed execution. In support of our analytical findings and to demonstrate its practical feasibility, we implement a prototype of the cloning framework on a shared memory system and report its performance characteristics in the context of a heat diffusion simulation, and a power grid simulation subject to cascading disruptions from geomagnetic disturbances.
Neurosteroids: 3 alpha-hydroxy-5 alpha-pregnan-20-one and its precursors in the brain, plasma, and steroidogenic glands of male and female rats.

Field: Neuroscience (Life Sciences)

A RIA procedure for measuring progesterone (PROG), 5 alpha-pregnane-3,20-dione (5 alpha-DH PROG), and 3 alpha-hydroxy-5 alpha-pregnan-20-one (3 alpha,5 alpha-TH PROG) has been developed and validated by GLC/mass spectrometry. Measurements were made in intact and adrenalectomized (ADX) male rats, in cyclic, pregnant, spayed, and spayed-ADX females, and in both males and spayed females injected with PROG. The predominant contribution of the ovary to the concentrations of 3 alpha,5 alpha-TH PROG in plasma and brain, was indicated by its larger levels in females, in particular during pregnancy, and by its presence in ovarian tissue and disappearance after ovariectomy. An additional adrenal origin in both males and females was shown. Neither PROG nor 5 alpha-DH PROG disappeared from brain, contrary to plasma, after combined adrenalectomy and gonadectomy, thus suggesting that PROG might be synthetized de novo in brain. However, the concentrations of 3 alpha,5 alpha-TH PROG in plasma and brain of female rats were positively correlated with the concentrations of PROG in plasma, indicating that plasma PROG was the major precursor of 3 alpha,5 alpha-TH PROG. The direct formation of 3 alpha,5 alpha-TH PROG from PROG in brain was strongly suggested by the increased 3 alpha,5 alpha-TH PROG/PROG ratios in brain vs. plasma, when measured in control females, and after injection of PROG to both males and OVX females. It was previously reported that 3 alpha,5 alpha-TH PROG is a sedative/anxiolytic steroid, as a result of its binding to gamma-aminobutyric acid (GABA)A receptors and allosteric potentiation of GABAcergic neurotransmission. Its concentrations in brain reach indeed the neuroactive range in cyclic and pregnant females, and are compatible with a physiological role of this neurosteroid.
CAPrompt: Cyclic Prompt Aggregation for Pre-Trained Model Based Class Incremental Learning

Field: Computer Science (Physical Sciences)

Recently, prompt tuning methods for pre-trained models have demonstrated promising performance in Class Incremental Learning (CIL). These methods typically involve learning task-specific prompts and predicting the task ID to select the appropriate prompts for inference. However, inaccurate task ID predictions can cause severe inconsistencies between the prompts used during training and inference, leading to knowledge forgetting and performance degradation. Additionally, existing prompt tuning methods rely solely on the pre-trained model to predict task IDs, without fully leveraging the knowledge embedded in the learned prompt parameters, resulting in inferior prediction performance. To address these issues, we propose a novel Cyclic Prompt Aggregation (CAPrompt) method that eliminates the dependency on task ID prediction by cyclically aggregating the knowledge from different prompts. Specifically, rather than predicting task IDs, we introduce an innovative prompt aggregation strategy during both training and inference to overcome prompt inconsistency by utilizing a weighted sum of different prompts. Thorough theoretical analysis demonstrates that under concave conditions, the aggregated prompt achieves lower error compared to selecting a single task-specific prompt. Consequently, we incorporate a concave constraint and a linear constraint to guide prompt learning, ensuring compliance with the concave condition requirement. Furthermore, to fully exploit the prompts and achieve more accurate prompt weights, we develop a cyclic weight prediction strategy. This strategy begins with equal weights for each task and automatically adjusts them to more appropriate values in a cyclical manner. Experiments on various datasets demonstrate that our proposed CAPrompt outperforms state-of-the-art methods by 2%-3%.
Negative priming in free recall reconsidered.

Field: Psychology (Social Sciences)

Negative priming in free recall is the finding of impaired memory performance when previously ignored auditory distracters become targets of encoding and retrieval. This negative priming has been attributed to an aftereffect of deploying inhibitory mechanisms that serve to suppress auditory distraction and minimize interference with learning and retrieval of task-relevant information. In 6 experiments, we tested the inhibitory account of the effect of negative priming in free recall against alternative accounts. We found that ignoring auditory distracters is neither sufficient nor necessary to produce the effect of negative priming in free recall. Instead, the effect is more readily accounted for by a buildup of proactive interference occurring whenever 2 successively presented lists of words are drawn from the same semantic category.
Cell design, management and continuous improvement

Field: Decision Sciences (Social Sciences)

A cellular manufacturing system is a shop floor that has been organised into groups of dissimilar machines producing groups of similar parts. Each group of machines is called a cell and each group of parts is called a part family. The main advantage of a cellular manufacturing system is low material handling, since ideally, a part need only travel to the cell it belongs to in order to be manufactured. If a cell can manufacture its part family without any member of that part family having to travel to another cell, then that cell is said to be independent. In reality, cells are rarely independent and this causes many complications when trying to design a cellular manufacturing system. To address these complications, a strategy for cell design, management and continuous improvement was developed. This comprises three stages: (i) Determine cell configurations. (ii) Position cells and the workstations within them. (iii) Carry out Capability Analysis to identify targets for continuous improvement. Black Box Clustering is used to determine cell configurations by clustering a workstation-part matrix representation of routings. The Cellect layout tools identify the best position for each cell and the relative positions of the workstations within them based on material handling costs. This data combined with user interaction can be used to identify the precise locations of individual workstations. Capability Analysis is a methodology developed to assess groups of performance measures that should be
Integrated Approach for Calculating the Mineral Assemblages and Oxide Percentage of Crystalline Rock based on Object-Based Image Analysis and Electron Probe Microscopic Analyzer

Field: Earth and Planetary Sciences (Physical Sciences)

Identification of minerals in thin sections using intelligent methods is a very complex and challenging task, which mineralogists and computer scientists are faced with. In order to effectively calculate the the mineral assemblages and oxide percentage of crystalline rock, we proposed an integrated approach based on object-based image analysis (OBIA) and electron probe microscopic analyzer (EPMA). This approach contains the following steps: 1) acquisition of mineral chemistry data and back-scattered electron (BSE) images; 2) image segmentation and classification; 3) calculating the oxide percentage based on the proportional relationship. It is worth noting that the optimal scale parameter for image segmentation is essential for subsequent image classification, which also defines the proportional relationship for calculating the oxide percentage. The experimental results show that the novel method has characteristics of simple extraction approach, little extraction parameter, easy implementation and accurate recognition ratio.
Correlation Energy from the Adiabatic Connection Formalism for Complete Active Space Wave Functions

Field: Chemistry (Physical Sciences)

Recently, the adiabatic connection (AC) formula for the electron correlation energy has been proposed for a broad class of multireference wave functions (Pernal, K. Electron Correlation from the Adiabatic Connection for Multireference Wave Functions. Phys. Rev. Lett. 2018, 120, 013001). We show that the AC formula used together with the extended random phase approximation (ERPA) can be efficiently applied to complete active space (CAS) wave functions to recover the remaining electron correlation. Unlike most of the perturbation theory approaches, the proposed AC-CAS method does not require construction of higher than two-electron reduced density matrices, which offers an immediate computational saving. In addition, we show that typically the AC-CAS systematically reduces the errors of both the absolute value of energy and of the energy differences (energy barrier) upon enlarging active spaces for electrons and orbitals. AC-CAS consistently gains in accuracy from including more active electrons. We also propose and study that the performance of the AC0 approach resulting from the first-order expansion of the AC integrand at the coupling constant equal to 0. AC0 avoids solving the full ERPA eigenequation, replacing it with small-dimension eigenproblems, while retaining good accuracy of the AC-CAS method. Low computational cost, compared to AC-CAS or perturbational approaches, makes AC0 the most efficient ab initio approach to capturing electron correlation for the CAS wave functions.
Simulating Damage Mechanics of Electromigration and Thermomigration

Field: Materials Science (Physical Sciences)

Electromigration (EM) and thermomigration (TM) are processes of mass transport which are critical reliability issues for next generation nanoelectronics and power electronics. The purpose of this project is to develop a computational tool for simulating damage mechanics of EM and TM and their interaction. In this paper, a model for EM and TM processes is proposed and has been implemented in a general purpose finite-element code. The governing equations utilized for the model include mass conservation, force equilibrium, heat transfer and electricity conduction. A damage evolution model based on thermodynamics is introduced to evaluate the degradation in solder joints subjected to high current densities and high temperature gradients. The simulation results are compared with experimental data to validate the model.
ANALISIS KEMAMPUAN DAN KEMAUAN DALAM MEMBAYAR TARIF PADA PENGGUNA JASA MODA TRANSPORTASI KAPAL LAUT (Rute Ternate-Sanana)

Field: Economics, Econometrics and Finance (Social Sciences)

Sea transportation mode in this case ship is an alternative transportation mode that is most often chosen by the community when traveling on the Ternate - Sanana route. For this type of transportation mode, it is relatively smooth because almost every day it is available, there are 3 ships operating in one week. One important factor in the management of sea transportation services is fare. This is the reason people use this mode of transportation, because the fare is considered quite affordable. Therefore, this study was conducted to determine the Ability To Pay (ATP) and Willingness To Pay (WTP) users of the Ternate Sanana sea ship services, which can later be taken into consideration in evaluating the appropriate fare. From the data that has been processed, the Ability To Pay (ATP) value of Rp.471,722 and the Willingness to Pay (WTP) value of Rp.229,100. Keywords : Ability to Pay (ATP), Willingness To Pay (WTP), Fare, Sea Transportatio Mode, Ternate, Sanana.
Effects of Quality Nursing on Pulmonary Function and Quality of Life in Elderly Patients with Chronic Obstructive Pulmonary Disease

Field: Nursing (Health Sciences)

Aim: To investigate the clinical effect and value of quality nursing on lung function and quality of life in elderly COPD patients.Methods: A total of 80 elderly COPD patients admitted to our hospital from March 2015 to March 2017 were randomly selected and divided into two groups (n = 40).The control group received routine nursing interventions, the treatment group using high-quality care, compared with two groups after the clinical effect of nursing.Results: The FEV1, FEV1 / FVC and FEV1 scores in the control group were (1.37 ± 0.41), (48.06 ± 5.77) and (51.84 ± 7.84) respectively lower than those in the treatment group (2.57± 0.39 and 68.15 ± 5.61), (67.87 ± 7.71).In the evaluation table of the quality of life of the treatment group, the patients' psychological function, emotional function and social function score were also significantly better than those of the control group.The difference between the two groups was significant and statistically significant (P <0.05) Conclusion: The implementation of quality care for elderly patients with COPD can effectively improve lung function, improve quality of life, reduce mortality and ensure the recovery of patients' health.
The Antwerp tsetse fly laboratory: A new start

Field: Agricultural and Biological Sciences (Life Sciences)

After the decease of professor Evens, the continuation of a tsetse fly laboratory at the Antwerp State University Center has been uncertain until two years ago, when the author decided to start a new research team for the study of the biology of tsetse flies. This paper reports on the first results, obtained on the following subjects: An automatic feeding device for rearing tsetse flies. A tan eyed mutant colony of Glossina palpalis palpalis. The possible effect of hormones in the diet on the fecundity of tsetse flies. The effect of ivermectin on the reproduction biology of Glossina palpalis palpalis.
Cachexia in head and neck squamous cell carcinoma (HNSCC) patients (pts) after cisplatin-based chemoradiation (CRT): A cross-sectional study.

Field: Medicine (Health Sciences)

e23138 Background: Cachexia is a wasting syndrome that may affect HNSCC pts, contributing to their dismal prognosis. We aimed to study the frequency of cachexia in HNSCC survivors treated with CRT with curative intent. Methods: Cross-sectional study that included 120 consecutive pts from Jan/2014 to Feb/2017, over 18 y.o. and who were previously treated with definitive or adjuvant CRT for HNSCC (nasopharynx, oropharynx [OP], oral cavity [OC], hypopharynx and larynx [L]). Eligible pts were in regular follow-up for at least 2 years in the multidisciplinary team, with no evidence of disease. Medical history, body weight, height, mid-arm muscle circumference (MAMC) and muscle strength (MS, handgrip dynamometer) were measured, and laboratory tests (hemoglobin [Hb], albumin and C-reactive protein [CRP]) were obtained. Cachexia was diagnosed when there was any weight loss in the previous year, and at least 3 of the following: reduced grip muscle strength, fatigue, anorexia, low lean body mass, or laboratorial alterations (Hb < 12 g/dL, serum albumin < 3.2 g/dL or CRP > 5.0 mg/L). A subjective assessment of nutritional status was made based on the Patient-Generated Subjective Global Assessment (PG-SGA) in its short form. Results: Median age 59 y.o. (21-78), 88 male (73%). Most common primary sites were OP (42%), L (24%) and OC (19%). Median follow-up was 42 mo. (24-125). There was a predominance of locally advanced disease at diagnosis: 73% T3/T4 and 72% N+. The mean weight was 64.5 kg (±14.6) pre-CRT, 57.8 kg (±12.2) post-CRT (p 0.02) and 63 kg (±11.8) in the present evaluation (p NS). Dysphagia was a complaint in 88 pts (73%). Cachexia was diagnosed in 42 pts (35%). As expected, cachectic pts (CP) presented lower MAMC (25.1 vs. 27.2 cm, p 0.0002) and MS (24.3 vs. 29.5 kgf, p 0.004). Higher mean CRP (12.7 vs. 4.2 mg/L, p 0.0001) and lower Hb (13.1 vs.13.9 g/dL, p 0.01) were also seen in CP. The PG-SGA score was higher in CP (7.9 vs. 5.7, p 0.006). Conclusions: Cachexia was frequently diagnosed in HNSCC pts with NED after CRT in a long-term follow-up, without evident weight loss. More effective preventive and therapeutic strategies are warranted. Supported in part by FAPESP grant 2014/00172-9.
Allelic variation in Helicobacter pylori : progress but no panacea

Field: Medicine (Health Sciences)

See article on page 499 Helicobacter pylori colonisation in the stomach is associated with increased risk for the development of peptic ulcer disease and non-cardia gastric adenocarcinoma.1 However, the incidences of these diseases vary in different parts of the world, and these rates have been changing over the past century. It now is clear that the mere presence of H pylori is insufficient to account for this variation. Alternative hypotheses to explain differing outcomes include variation in bacterial strains, in host related factors, or in the particular interactions governing the long term equilibrium between H pylori strain populations and the colonised host.2 In this issue, Kidd et al (see page 499) explore whether H pylori strain differences are related to illness occurrence in South African patients undergoing endoscopy. Why was such a study undertaken?

Despite overall conservation of most genes, H pylori are a highly diverse bacterial species.3Their population structure indicates that they are freely recombining,4 which tends to eliminate clonal or allelic variation. Yet, in accordance with previous work, Kidd et al …
The Past in the Present

Field: Arts and Humanities (Social Sciences)

The theory-deadness of antiquity under the ideology of modernism, the theory-deadness of Asia under Eurocentrism, and the theory-deadness of the precolonial under post-colonial theory converge to hide the aliveness of ancient Indian phonological analysis in the present. This case study of the hiddenness of the past in the present leads to a consideration of how historians of the ancient world may act to illuminate the present.
The Political Premium of Television Celebrity

Field: Economics, Econometrics and Finance (Social Sciences)

This paper studies the electoral consequences of television stardom through the career of Ronald Reagan. I utilize quasi-experimental variation in television reception to estimate the causal effect of celebrity exposure on political support. I find that Reagan’s tenure as the host of a 1950s entertainment television program translated into support for his candidacy, in terms of votes and political donations, nearly two decades after the show’s first airing. Placebo checks suggest that this impact is not driven by unobserved heterogeneity or omitted variable bias. The effect was especially pronounced in the 1976 Republican primary elections relative to the general presidential elections and partially dissipated in locations where Reagan was a known political entity. Using the American National Election Studies (ANES) surveys, I provide evidence on possible mechanisms. Consistent with rational updating, nonpolitical media increased voters’ assessment of Reagan’s character and leadership, personalizing political considerations in elections featuring him. (JEL D72, L82, Z13)