jimnoneill/paper-to-field-training huggingface dataset:
Detection of STAT4 in Multiple Sclerosis patients by polymerase chain reaction and flowcytometry.

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

Multiple sclerosis (MS) is a disease of the central nervous system, characterized by progressive demyelination and inflammation. MS is characterized by immune system attacks on the myelin sheath surrounding nerve fibers. Genome-wide association studies revealed a polymorphism in the signal transducer and activator of transcription 4 (STAT4) gene that increases risk for MS. This polymorphism affects the T helper1 (Th1) cells to secrete the cytokine interferon-gamma when stimulated by interleukin (IL)-12. This study aimed to determine the association of MS active disease with STAT4 genotypes, detected by the polymerase chain reaction (PCR) and STAT4 protein level detected by flowcytometry. The study included 80 MS patients, and 70 controls matched for age and gender. We used the restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR) and flowcytometry to detect STAT4 gene polymorphism. Our results showed that, in MS patients, STAT4 genotypes of GC and CC as detected by PCR, were more common when compared to controls. The C allele of the STAT4 gene was also more common in MS patients than controls. The STAT4 GC genotype was associated with MS disease activity. Active MS patients also had a much greater frequency of the STAT4 C allele than the G allele or the control group. The STAT4 proteins level by flowcytometry among the active MS studied patients was higher than its level in the inactive patients and controls. In conclusion, this study demonstrated that both techniques are complementary to each other to detect STAT4 level in MS patients and its association with the disease activity. STAT4 proteins expression detected by flowcytometry in the peripheral blood leukocytes could be used as a biomarker for monitoring disease activity in MS patients.
Checkpoints couple transcription network oscillator dynamics to cell-cycle progression

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

The coupling of cyclin dependent kinases (CDKs) to an intrinsically oscillating network of transcription factors has been proposed to control progression through the cell cycle in budding yeast, Saccharomyces cerevisiae. The transcription network regulates the temporal expression of many genes, including cyclins, and drives cell-cycle progression, in part, by generating successive waves of distinct CDK activities that trigger the ordered program of cell-cycle events. Network oscillations continue autonomously in mutant cells arrested by depletion of CDK activities, suggesting the oscillator can be uncoupled from cell-cycle progression. It is not clear what mechanisms, if any, ensure that the network oscillator is restrained when progression in normal cells is delayed or arrested. A recent proposal suggests CDK acts as a master regulator of cell-cycle processes that have the potential for autonomous oscillatory behavior. Here we find that mitotic CDK is not sufficient for fully inhibiting transcript oscillations in arrested cells. We do find that activation of the DNA replication and spindle assembly checkpoints can fully arrest the network oscillator via overlapping but distinct mechanisms. Further, we demonstrate that the DNA replication checkpoint effector protein, Rad53, acts to arrest a portion of transcript oscillations in addition to its role in halting cell-cycle progression. Our findings indicate that checkpoint mechanisms, likely via phosphorylation of network transcription factors, maintain coupling of the network oscillator to progression during cell-cycle arrest.
Public Valuations of Managing Compromised Molars: A Discrete Choice Experiment

Field: Health Professions (Health Sciences)

There is limited evidence to support optimal patient-centered management for compromised first permanent molars (cFPM) in children. Based on an online discrete choice experiment (DCE), this study elicits UK adult general population preferences and calculates willingness to pay (WTP) for pathways to manage cFPM. The DCE was designed with information from semistructured interviews and literature reviews, as well as focus groups with an expert panel of dentists, citizens, and policy makers. A statistically optimal D-efficient design generated 18 choice tasks, split across 2 blocks. Each respondent answered one block of 9 tasks to reduce survey fatigue. Choice tasks varied across 5 attributes: type of treatment, provider of care, who makes the management decision, number of future visits avoided, and cost. An opt-out was included (no treatment). Conditional logit models (fixed effects) were used for data analysis, and marginal WTP for each attribute level was calculated. An overall 430 respondents completed the DCE. Respondents valued children receiving care as compared with not. Restoring a cFPM was valued equally to spontaneous or orthodontic gap closure. In contrast, having a partial gap, prosthetic replacement with a bridge, or a full unit gap was valued less than restoration or full gap closure. General dentists were preferred to dentists with enhanced skills, but there was no evidence of a preference for general dentists over specialists in pediatric dentistry. Respondents preferred to be wholly or partly involved in the decision-making process as opposed to the dentist making the decision alone. Respondents preferred less costly treatments and the avoidance of future dental work. Dental care service providers must consider service user preferences for health and nonhealth outcomes in any service redesign. Furthermore, the results provide marginal WTP estimates that can be used to value dental care services.
Bulletin No. 277 - A Study of Utah's Winter Range: Composition of Forage Plants and Use of Supplements

Field: Agricultural and Biological Sciences (Life Sciences)

Range forage provides the foundation for the maintenance ration available for most sheep wintered in Utah. The nature and amount of supplemental concentrate or roughage needed with this forage to provide an adequate and efficient ration for sheep naturally depends on the nature and amount of range forage available. Present uncertainty as to the relative merits of the various available supplements originates largely through a lack of definite knowledge as to the composition and feeding value of the various range plants that go to make up the range-forage supply on the particular range in question.\nE. J. Maynard
A Church That is Empowered by the Spirit -- Acts 2:1-18

Field: Arts and Humanities (Social Sciences)

Series: The Church Though Which God Moves Village Baptist Church Pastor John Johnson September 19-20, 2009 Acts 2:1-18 Sermon "A Church That is Empowered by the Spirit" on Acts 2:1-18 by Pastor John Johnson from the series "The Church Though Which God Moves" of Village Baptist Church, Beaverton, Oregon.
Effects of Auxiliary Chemicals on the Ozonation of Industrial Dyes

Field: Environmental Science (Physical Sciences)

The effect of commonly used auxiliary chemicals (primasol, sodium hydroxide and sodium hydrosulphite) and the initial dye concentration on the oxidation of three industrial dyes (Vat Blue, Disperse Blue 79 and Disperse Red 72) has been studied. In the batch studies, the oxidation of dye molecules by ozone was examined with single-solute dye solution. Our results showed that the efficiencies of dye removal were in the range 68-74% and 80-85% at an oxidation time of 10 minutes and 2 hours respectively. The effect of each of the three auxiliaries on the single- and multi-solute dye solutions were assessed in terms of colour, COD and TOC variation. The addition of primasol showed exertion on ozone demand as reflected by the COD and TOC results while sodium hydroxide enhanced the oxidation of Disperse Blue 79. The presence of sodium hydroxide also reduced the colour removal and the reduction of COD in the oxidation of Vat Blue dye as well as the mixture of three dyes studied. Sodium hydrosulphite being a strong reducing agent exerted a significant demand on ozone, reducing amount of ozone available to oxidize the dye molecules.
Application of a robust dynamic flux balance analysis framework to a wine fermentation for understanding and steering aroma formation

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

Various commercial S. cerevisiae yeast strains are available for use in industrial wine fermentations, each with its owncombination of growth characteristics and organoleptic (sensory) profiles. However, the metabolism underlying thesedifferences is complex and not well understood, making manipulation of these strains difficult. One tool for elucidatingstrain-to-strain differences and identifying key metabolic pathways related to flavor production is the use of genome-scale metabolic models (GSMM). Despite progress in the field, most current models either focus on aerobic systems,contain models that focus on a carbon-limited medium, and/or lack the detailed coverage of Ehrlich and amino aciddegradation metabolic pathways that have been shown experimentally to be highly correlated with aroma formation.One way to capture the power of these models is to use dynamic flux balance analysis (dFBA) to predict the fluxdistribution of all the metabolites within the cell over the course of an entire fermentation. Using this approach, it ispossible to test the predictive capability of these models by comparing predictions with experimental fermentation data.Once the models fit dynamic data, they can be used to understand differences between commercial strains andsuggest genetic modification strategies towards steering certain aroma formation in strains of interest. Here, in thiswork, we applied a robust dFBA framework to an expanded GSMM of S. cerevisiae over the course of a winefermentation. Recently, we showed that ester production during alcohol fermentation is regulated by a newlydiscovered family of alcohol acyl transferases (AATs) in S. cerevisiae. However, mysteries still persist regarding thewhether other metabolic mechanisms are responsible for ester formation. By applying our expanded GSMM of yeast,which has the most comprehensive representation aroma forming pathways, we can more accurately predict metabolicfluxes for various yeast strains. Furthermore, this model can be calibrated with experimental data to reasonablypropose genetic and process engineering strategies to improve the enological performance S. cerevisiae strains ofinterest.
Cognitive impairment in Parkinson's disease

Field: Neuroscience (Life Sciences)

パーキンソン病 (Parkinson's Disease : PD) は運動症状を主体とする疾患であるが, 近年ではさまざまな非運動症状をきたすことが報告され, 注目を集めている。本稿では, 多岐に渡る PD の非運動症状の中でも認知機能障害に焦点を当て, とくに社会的認知機能について詳しく述べる。社会的認知とは, 他者の情動表出や内的な心理状態などのコミュニケーションに重要な情報処理を担う, よりよい人間関係を築くために必要な機能である。これまでの研究により, PD 患者では他者の表情を見て情動を読み取る表情認知や, 損得の情報を学習し適切な行動を選択する意思決定過程において, 健常者とは異なるパターンが観察されている。また最近では, 社会的認知の重要な基盤のひとつである「心の理論」機能の障害の有無が検討されている。これらの認知機能障害は PD 患者の日常生活や社会活動に影響を及ぼす可能性があり, 慎重に評価する必要があると思われる。
Pentatricopeptide repeat protein EspX1 facilitates the virulence of avian pathogenic Escherichia coli

Field: Immunology and Microbiology (Life Sciences)

Abstract

Avian pathogenic Escherichia coli (APEC) can infect poultry and cause colibacillosis, leading to significant economic losses in the poultry industry. APEC is similar to human Extraintestinal pathogenic Escherichia coli (ExPEC) in serotype, phylogenetic clustering and virulence genes, and is a repository of ExPEC virulence and drug resistance genes. We identified a pentatricopeptide repeat (PPR) protein EspX1 in APEC, but its function is unknown. The espX1 gene mutant and complemented strains of APEC were constructed and characterized. The results showed that EspX1 does not affect the growth or motility of APEC. The espX1 deletion mutant exhibited enhanced biofilm formation and cell adhesion but reduced serum resistance and intracellular survival. Furthermore, the mutant strain showed decreased colonization in the liver and spleen during systemic infection and attenuated virulence in vivo. Additionally, EspX1 was found to inhibit the expression of inflammatory cytokines TNF-α, IL-1β, and IL-8 in host cells. These findings suggest that EspX1 plays a crucial role in the pathogenicity of APEC by modulating multiple virulence-related phenotypes and host immune responses. In addition, EspX1 enhances APEC resistance to ciprofloxacin. This study provides novel insights into the functions of PPR proteins in prokaryotes and lays a theoretical foundation for developing new strategies to control APEC infections.
Germany and reparations: the reconciliation agreement with Namibia

Field: Social Sciences (Social Sciences)

In 2015 Germany admitted that the warfare in its colony South West Africa was tantamount to genocide. Bilateral negotiations with the Namibian government resulted in May 2021 in a so-called reconciliation agreement. This is not yet ratified. This article critically examines its limitations. It explains why this – despite being a step in the right direction – has so far been insufficient and a form of tokenism. In the absence of true efforts to reconcile with the descendants of the local communities most affected by the genocide, the government-to-government negotiations have failed so far to achieve any meaningful reconciliation.
Serological and molecular screening for viruses in blood donors from Ntcheu, Malawi: High prevalence of HIV‐1 subtype C and of markers of hepatitis B and C viruses

Field: Medicine (Health Sciences)

Abstract The prevalence of antibodies to human immunodeficiency virus type 1 (HIV‐1), hepatitis C virus (HCV), human T lymphotropic virus I (HTLV‐I), and hepatitis B (HBV) surface antigen (HBsAg) was determined in blood donors from Ntcheu, Malawi. Each donation was also screened for HIV‐1 RNA and HCV RNA. Among 159 blood donations, the prevalence of HIV‐1 infection was 10.7%, 8.1% for HBV carriage, 6.8% for anti‐HCV, and 2.5% for anti‐HTLV‐I. HIV‐1/HTLV‐I and HIV‐1/HCV dual infections were observed in 1.2% of the donations. Consequently, 13% of blood donors from Ntcheu should be deferred for retroviral infections and 15% for hepatitis viral infections. Sequence analyses of the HIV‐1 strains revealed a relatively homogeneous circulation of subtype C viruses in Malawi. These findings confirm the high endemicity of blood‐borne viruses in Malawi and the need for a sensitive viral screening of blood donations to improve blood safety. J. Med. Virol. 65:1–5, 2001. © 2001 Wiley‐Liss, Inc.
AVL-EQUIPPED VEHICLES AS SPEED PROBES : (PHASE 2)

Field: Engineering (Physical Sciences)

In this report, the authors document the second phase of a three-phase project what will create a robust set of virtual sensors for freeways and arterials. The first phase was a proof of principle that investigated the statistics of successfully using transit vehicles as traffic probes. In this phase, an optimal filter method is described for estimating acceleration, speed, and position as a function of space and time. In the third phase, a server will be used to place speed estimates from the transit probe virtual sensors into the Washington State Department of Transportation (WSDOT) Region's operational traffic management system.
Applicability of prompt gamma-ray analysis to the initial analysis of the extraterrestrial materials for chemical composition

Field: Earth and Planetary Sciences (Physical Sciences)

When extraterrestrial materials are returned to the earth by future space missions, these materials are to be subjected to the initial examination. For such purposes, measurements are desired to be done non-destructively. In this study, we investigated the applicability of non-destructive prompt gamma-ray analysis (PGA) for determining chemical composition of the returned materials, focusing on levels of induced radioactivities and the effect on isotopic composition by PGA. Under current conditions applied for the PGA facility at the Japan Atomic Energy Research Institute, essentially no residual radioactivities remain after appropriate cooling, making the same specimen analyzed by PGA usable for further research without any restriction. The effect on isotopic composition by PGA was examined both for neutron-induced reactions and for neutron-induced nuclear fission of 235U. No significant effect can be brought by neutron-induced reactions even for some noble gas nuclides such as 80Kr and 128I, which can be augmented by (n, γ) reactions on neighboring halogens. Neutron-induced nuclear fission reactions of 235U yield essentially no effect on isotopic composition. In addition, PGA has several advantages over other nondestructive analytical methods such as instrumental neutron activation analysis (INAA) and synchrotron radiation x-ray fluorescence (SR-XRF); INAA leaves a significant level of induced-radioactivities and SR-XRF yields less reliable and less accurate values for elemental composition. Judging from these features and characteristics, it is concluded that PGA can be one of the most suitable analytical methods potentially applicable for initial analysis of returned samples from space.
Compositionality and the Prospect of a Pluralistic Semantic Theory

Field: Arts and Humanities (Social Sciences)

A semantic theory is committed to semantic monism just in case every particular semantic property posited by the theory is a member of the same kind. The commitment to semantic monism appears to draw some support from the need to provide a compositional semantics, since taking a single kind of semantic property as key to a semantic theory affords a uniform pattern on the basis of which the meaning of any given sentence can be compositionally determined. This line of support highlights a tension between the principle of compositionality and taking a more pluralistic approach to semantic theorizing. In this essay, that tension is relieved, leaving open the prospect of a pluralistic semantic theory that observes the principle of compositionality.
Effect of Spiking Contact Times on the Analytical Recovery of Aflatoxins

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Summary Aflatoxins are toxic secondary metabolites of fungi, mainly Aspergillus flavus and Aspergillus parasiticus the most common of which are aflatoxins B1, B2, G1 and G2, and M1 in milk. Aflatoxin B1 is normally predominant. The determination of aflatoxins, by extraction, immunoaffinity clean up and liquid chromatography with fluorescence detection is common practice. Recovery correction of the results obtained is mandatory in official analysis for which the only practical approach is separate determination of the analyte added either to aliquots of the sample or matrix blanks, a process commonly referred to as “spiking”. Variations in the spiking contact times before extraction could have an effect on the recovery of aflatoxins from the matrix. Herein we describe two studies, a short term (0.5 – 65 hours) and a long term (1 hr - 8 weeks) investigation of the effect of contact time on spike recovery in peanuts, figs and chilli powder. Generally it was found that recovery is dependent upon contact time and this effect is statistically significant for short contact times (less than 24 hours) while thereafter the recovery stabilises. The results from both studies indicated a small effect on contact times in some matrix/aflatoxin/storage condition combinations, however any effect is statistically insignificant compared to the method uncertainty.
Laser welding in the manufacture of superalloy components

Field: Engineering (Physical Sciences)

Summary This paper describes the welding of superalloys using high-power CO2 and Nd:YAG lasers, to be applied to the manufacture of aeroengine and power plant components. The rapidly solidified microstructures in the fusion zone and the microfissures in the heat-affected zone (HAZ) have been investigated using scanning and transmission electron microscopes (SEM, TEM). With Inconel 718 superalloy, microfissure-free welds were achieved in the annealed state with grain sizes of ASTM 10 or finer. Laser-welded aeroengine components made of rolled and cast Inconel 718 are presented. The characteristics of joints obtained were also assessed via fatigue tests at high temperature. Laser cutting combined with laser welding techniques are applied to demonstrate that the manufacture of welded structures can be simplified with minimum deformation, thereby reducing costs.
Survivable Traffic Grooming with Path Protection at the Connection Level in WDM Mesh Networks

Field: Computer Science (Physical Sciences)

Survivable traffic grooming (STG) is a promising approach to provide reliable and resource-efficient multigranularity connection services in wavelength division multiplexing (WDM) optical networks. In this paper, we study the STG problem in WDM mesh optical networks employing path protection at the connection level. Both dedicated protection and shared protection schemes are considered. Given the network resources, the objective of the STG problem is to maximize network throughput. To enable survivability under various kinds of single failures such as fiber cut and duct cut, we consider the general shared risk link group (SRLG) diverse routing constraints. We first resort to the integer linear programming (ILP) approach to obtain optimal solutions. To address its high computational complexity, we then propose three efficient heuristics, namely separated survivable grooming algorithm (SSGA), integrated survivable grooming algorithm (ISGA) and tabu search survivable grooming algorithm (TSGA). While SSGA and ISGA correspond to an overlay network model and a peer network model respectively, TSGA further improves the grooming results from SSGA and ISGA by incorporating the effective tabu search method. Numerical results show that the heuristics achieve comparable solutions to the ILP approach, which uses significantly longer running times than the heuristics.
Enhancement of energy storage in epitaxial PbZrO3 antiferroelectric films using strain engineering

Field: Materials Science (Physical Sciences)

We demonstrate an approach to enhance the energy storage density W of antiferroelectric film through simple altering a crystallographic orientation of the substrate. We reveal that the antiferroelectric phase stability of PbZrO3 can be enhanced for the (110) or (111) SrTiO3 substrate orientation, thus suppresses the antiferroelectric-ferroelectric phase transition to higher electric field with ∼120 kV/cm increment. In addition, the polarization values of these films are also favorably increased hence increases W by 5.3 J/cm3 at 700 kV/cm. The observed enhancement is found to originate from a high sensitivity of phase transition to mechanical confinements due to the volume expansion at the transition.