jimnoneill/paper-to-field-training huggingface dataset:
Peptide Transporter CstA Imports Pyruvate in Escherichia coli K-12

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

ABSTRACT Pyruvate is an important intermediate of central carbon metabolism and connects a variety of metabolic pathways in Escherichia coli . Although the intracellular pyruvate concentration is dynamically altered and tightly balanced during cell growth, the pyruvate transport system remains unclear. Here, we identified a pyruvate transporter in E. coli using high-throughput transposon sequencing. The transposon mutant library (a total of 5 × 10 5 mutants) was serially grown with a toxic pyruvate analog (3-fluoropyruvate [3FP]) to enrich for transposon mutants lacking pyruvate transport function. A total of 52 candidates were selected on the basis of a stringent enrichment level of transposon insertion frequency in response to 3FP treatment. Subsequently, their pyruvate transporter function was examined by conventional functional assays, such as those measuring growth inhibition by the toxic pyruvate analog and pyruvate uptake activity. The pyruvate transporter system comprises CstA and YbdD, which are known as a peptide transporter and a conserved protein, respectively, whose functions are associated with carbon starvation conditions. In addition to the presence of more than one endogenous pyruvate importer, it has been suggested that the E. coli genome encodes constitutive and inducible pyruvate transporters. Our results demonstrated that CstA and YbdD comprise the constitutive pyruvate transporter system in E. coli , which is consistent with the tentative genomic locus previously suggested and the functional relationship with the extracellular pyruvate sensing system. The identification of this pyruvate transporter system provides valuable genetic information for understanding the complex process of pyruvate metabolism in E. coli . IMPORTANCE Pyruvate is an important metabolite as a central node in bacterial metabolism, and its intracellular levels are tightly regulated to maintain its functional roles in highly interconnected metabolic pathways. However, an understanding of the mechanism of how bacterial cells excrete and transport pyruvate remains elusive. Using high-throughput transposon sequencing followed by pyruvate uptake activity testing of the selected candidate genes, we found that a pyruvate transporter system comprising CstA and YbdD, currently annotated as a peptide transporter and a conserved protein, respectively, constitutively transports pyruvate. The identification of the physiological role of the pyruvate transporter system provides valuable genetic information for understanding the complex pyruvate metabolism in Escherichia coli .
Comparative epidermal leaf anatomy of some Brassicaceae with emphasis on its systematic implication

Field: Agricultural and Biological Sciences (Life Sciences)

Some epidermal leaf anatomy characteristics such as the absence/of presence trichomes and stomata and trichome types in adaxial and abaxial leaf surfaces within different species, subspecies, varieties, and populations are afforded valuable taxonomic characteristics in their determination. This study aimed to investigate the leaf epidermal characteristics in 72 populations belonging to 46 wild and native Brassicaceae taxa collected from central Iran. The adaxial and abaxial leaf epidermis was examined using light microscopy. Results showed that all studied samples lack crystals in their epidermis. They can be divided into three groups: 1) without trichomes in both adaxial and abaxial leaf surfaces, 2) having trichomes just on the abaxial side (Lepidium sativum and Sisymbrium irio), and 3) trichomes in both adaxial and abaxial surfaces. Two Choriospora species can be separated by their trichomes. C. iberica has glandular trichome, while C. tenella has no trichomes. This study revealed that just epidermal leaf anatomy characters are not sufficient to identify members of the Brassicaceae members, but can be helpful along with other features and may support the systematic value of taxa in this family.
Understanding the Role and Constraints of Rice-based Agriculture for Improving Rural Livelihoods in North-Eastern Region of India

Field: Agricultural and Biological Sciences (Life Sciences)

The rice-based agriculture is a key source of livelihood for about 40 million people in North-East Region (NER).But crop yields are very low much below the national average..This paper examines the the importance of rice-based food system and its growth performance, bring out constraints and suggest a roadmap to improve livelihoods of about 40 million people of NER.Series of secondary data on rice and other food products for the past fifteen years for each state of NER were collected from published and unpublished reports, and same were analysed using regression for estimation of compound growth rates.There has been considerable increase in food grain production from about 6 to 8.1 million tonnes over the past fifteen years due to special efforts by However Union Government after 2004 to improve livelihoods of rural households in NER.But the NER continues to be in food deficit by about half million tonnes per year.Low crop yields, despite high rainfall and fertile soils, is the primary reason for food insecurity in the region.Further, lack of adequate value addition and market access, high levels of illiteracy, poor infrastructure, etc. are some more reasons why low-income levels persist in the region, and thereby food and nutritional insecurity.Without improving productivity and income from rice-based agri-food systems, improved household food and nutritional security cannot be achieved in NER.Major constraints to increasing farm productivity and, thereby, incomes of rice-farming households include: lack of a wide range of varietal choice suitable for diverse production environments for rice and pulses/vegetables, very low seed replacement rate (ca.12%), poor water management and poor drainage systems, low fertilizer use (less than 20 kg /ha), unwillingness to take up rice in the second season due to perceived losses from animal grazing, absence of electricity in many rural areas of NER for pumping groundwater in the dry season, lack of marketing systems to purchase any marketable surplus at affordable price, absence of post-harvest loss management, lack of farmer-acceptable farm machinery, and increase wage rates of farm laborers.Based on critical analysis of growth performance, and potential opportnities and challenges, a 3pronged strategy is suggested in the paper for improving productivity and nutritional quality of rice-based agri-food systems in the NER. K e y w o r d sRice, North-east region, Food and nutritional security
The Understanding of Death in Terminally Ill Cancer Patients in China: An Initial Study

Field: Nursing (Health Sciences)

Abstract: Patient’s needs and rights are the key to delivering state-of-the-art modern nursing care. It is especially challenging to provide proper nursing care for patients who are reaching the end of life (EOL). In Chinese culture nursing practice, the perception and expectations of these EOL patients are not well known. This article explores the feelings and wishes of 16 terminally ill Chinese cancer patients who are going through the dying process. An open-ended questionnaire with eight items was used to interview 16 terminally ill Chinese cancer patients, and was then analyzed by a combined approach employing grounded theory and interpretive phenomenological analysis. Four dimensions were explored: first, patient’s attitudes towards death, such as accepting the fact calmly, striving to survive, and the desire for control; second, the care desired during the dying process, including avoiding excessive treatment and dying with dignity; third, the degree of the patient’s acceptance of death; and fourth, the consequences of death. This cognitive study offers a fundamental understanding of perceptions of death of terminally ill cancer patients from the Chinese culture. Their attitude toward death was complex. They did not prefer aggressive treatment and most of them had given a great deal of thought to their death.
This is Your Father’s Paradigm: Government Intrusion and the Case of Qualitative Research in Education

Field: Arts and Humanities (Social Sciences)

This talk was the Egon Guba Invited Lecture at the American Educational Research Association annual conference, April, 2003, Chicago. This article mobilizes three counterdiscourses to critique the federal government’s incursion into legislating scientific method in the realm of educational research via the “evidence-based” movement of the No Child Left Behind Act of 2001. Foucauldian policy analysis, feminism via Luce Irigaray, and postcolonialism via Stuart Hall are used to situate such scientism as a racialized masculinist backlash against the proliferation of research approaches that characterize the past 20 years of social inquiry. Congressional disdain for educational research is addressed within a context of the Science Wars and the needs of neoliberal states, including conservative restoration.
258 ULTRASTRUCTURAL STUDY OF STALLION SPERM FOLLOWING THAWING, CAPACITATING AND IVF PROCEDURES: EFFECT OF THE PRESENCE OF CUMULUS-ENCLOSED OOCYTES

Field: Veterinary (Health Sciences)

The use of IVF in horses has a limited efficiency, reflecting low oocyte developmental competence and inadequate sperm capacitation procedures. In a preliminary study, using carboxyfluorescein diacetate/propidium iodide staining, we determined that the freezing-thawing procedure left only 56.6 ± 3.4 % of the sperm cells with an intact membrane. The following incubation in TALP-IVF induced membrane damage at high rates with only 9.58 ± 1.8 % of them intact after 18 h. However, the presence of at least four cumulus-enclosed oocytes (CEO) in the medium significantly increased the number of membrane-intact spermatozoa at the end of incubation (53.87 ± 1.99%). This indicated that the sperm thawing and capacitating procedures can damage the cell membrane but the presence of four or more CEO in TALP-IVF could prevent further damages. The aim of the study was to investigate in detail the membrane damages and to analyze the differences induced by the presence of CEO. Spermatozoa were thawed in water at 37°C, and centrifuged for 30 minutes at 600g in a 45–90% Percoll gradient made with modified Tyrode’s medium. The sperm pellet was washed once in the same medium and diluted to a final concentration of 1 × 106 spermatozoa/ml TALP supplemented with 0.6% (w/v) BSA fatty acid free and 12 µg mL-1 heparin (TALP-IVF). Sperm cells were incubated with 0 or 4 in vitro-matured CEO. Sperm cells were examined after thawing, 0, 2 and 18 h from the beginning of incubation in TALP-IVF. Each experiment was replicated at least 3 times. Both scanning and transmission electron microscopy were performed on sperm samples fixed in 2.5% glutaraldehyde in 0.1 M phosphate buffer, pH 7.2, using standard procedures. Specimens for scanning electron microscopy were examined under a field emission gun JEOL JSM 6301 microscope. For transmission electron microscopy the samples were examined with a JEOL JEM 100 SX. A minimum of 25 cells were analyzed for each group. Immediately after thawing, damaged spermatozoa showed, on the surface of their heads, small vesicles correlated to a progressive process of vacuolisation and degeneration of membrane integrity. The same lesions were visible at all the successive time points taken into account. Moreover, a loss of the acrosome integrity with acrosomal swelling and a decrease of content homogeneity were observed particularly in the spermatozoa cultured for 18 h without CEO. When CEO were present in the IVF medium lesions were visible in a lower percentage of spermatozoa but the type of lesions did not differ from those observed in their absence. These observations confirmed our previous data and gave more details on the lesions that occur during the IVF procedures in the horse. Supported by MURST COFIN grant n. 2001078849.
Ultradense sphere packings derived from disordered stealthy hyperuniform ground states.

Field: Physics and Astronomy (Physical Sciences)

Disordered stealthy hyperuniform (SHU) packings are an emerging class of exotic amorphous two-phase materials endowed with novel optical, transport, chemical, and mechanical properties. Such packings of identical spheres have been created from SHU ground-state point patterns via a modified collective-coordinate optimization scheme that includes a soft-core repulsion, in addition to the standard "stealthy" pair potential. To explore the maximal ranges of the packing fraction ϕ, we investigate the distributions of minimum pair distances as well as nearest-neighbor distances of ensembles of SHU point patterns without and with soft-core repulsions in the first three space dimensions as a function of the stealthiness parameter χ and number of particles N within a hypercubic simulation box under periodic boundary conditions. Within the disordered regime (χ < 0.5), we find that the maximal values of ϕ, denoted by ϕmax(χ, d), decrease to zero on average as N increases if there are no soft-core repulsions. By contrast, the inclusion of soft-core repulsions results in very large ϕmax(χ, d) independent of N, reaching up to ϕmax(χ, d) = 1.0, 0.86, 0.63 in the zero-χ limit and decreasing to ϕmax(χ, d) = 1.0, 0.67, 0.47 at χ = 0.45 for d = 1, 2, 3, respectively. We obtain explicit formulas for ϕmax(χ, d) as functions of χ and N for a given value of d in both cases with and without soft-core repulsions. In two and three dimensions, our soft-core SHU ground-state packings for small χ become configurationally very close to the corresponding jammed hard-particle packings created by fast compression algorithms, as measured by their pair statistics. As χ increases beyond 0.20, the particles in this family of disordered packings form fewer contacts and linear polymer-like chains as χ tends to 1/2. The resulting structure factors Sk and pair correlation functions g2r reveal that soft-core repulsions significantly alter the short- and intermediate-range correlations in the SHU ground states. We show that the degree of large-scale order of the soft-core SHU ground states increases as χ increases from 0 to 0.45 for d = 2, 3. We also compute the spectral density χ̃Vk, which can be used to estimate various physical properties, including electromagnetic properties, fluid permeability, and mean survival time of SHU two-phase dispersions. Our results offer a new route for the discovery of novel disordered hyperuniform two-phase materials with unprecedentedly high density.
Tissue Culture with Phalaenopsis Root-tip

Field: Agricultural and Biological Sciences (Life Sciences)

Protocorm-Like Bodies(PLBs) were induced from the root-tip of phalaenopsis of RSW1 test-tube plants.The effects of different concentration of 6-benzyladenine(BA) and α-Naphthalacetic acid(NAA) combinations,different cutting mode,different organic compounds(coconut milk,peptone,potato juice,banana juice),different pH value,different culture mode(solid,liquid) on the propagation of Phalaenopsis PLB(Protocorm-like body) were studied.The rusults showed that the basic medium without hormone promoted propagation of PLB.Proliferation ratio of PLB was higher when added with organic compounds,and 150mL/L banana juice was best.A higher proliferation ratio could be got with PLB poked by tweezer for multiplication and the PLB could not become brown;The effect of propagation in liquid culture was better than in solid culture,The best pH value is 5.0.The proliferation ratio reached 6.53 in optimized media after 30 days' culture.
A process capability study to establish process hygiene microbiological criteria for wild venison at an Irish game handling establishment

Field: Agricultural and Biological Sciences (Life Sciences)

This study formulates process hygiene microbial criteria (PHMC) for wild venison. Baseline data were acquired from 80 carcasses – a 100 cm2 area was swabbed with an abrasive swab on each of the haunch, saddle, neck and shoulder post-dressing and pre-chilling. Samples were pooled prior to analysis for total viable count (TVC) and total Enterobacteriaceae count (TEC) using standard methods. The action limit m and unacceptable limit M were determined as 70% and 90% respectively of the baseline distribution. PHMC for wild venison were thus determined as the action limit m=3.3 and 1.5 log10cfu/cm2 for TVC and TEC, respectively, and the unacceptable limit M=4.1 and 2.0 log10cfu/cm2 for TVC and TEC, respectively. Should future performance trend towards or exceed these acceptability limits, operators can implement timely corrective and preventative actions to its systems to restore control. In the absence of legally mandated PHMC, it is recommended that each processor follow the protocols outlined in this study so as to establish their own PHMC.
Faculty Opinions recommendation of The COPD assessment test (CAT): response to pulmonary rehabilitation. A multicentre, prospective study.

Field: Health Professions (Health Sciences)

BACKGROUND: The COPD (chronic obstructive pulmonary disease) assessment test (CAT) is a recently introduced, simple to use patient-completed quality of life instrument that contains eight questions covering the impact of symptoms in COPD. It is not known how the CAT score performs in the context of clinical pulmonary rehabilitation (PR) programmes or what the minimum clinically important difference is.METHODS: The introduction of the CAT score as an outcome measure was prospectively studied by PR programmes across London. It was used alongside other measures including the St George's Respiratory Questionnaire, the Chronic Respiratory Disease Questionnaire, the Clinical COPD Questionnaire, the Hospital Anxiety and Depression score, the Medical Research Council (MRC) dyspnoea score and a range of different walking tests. Patients completed a 5-point anchor question used to assess overall response to PR from 'I feel much better' to 'I feel much worse'.RESULTS: Data were available for 261 patients with COPD participating in seven programmes: mean (SD) age 69.0 (9.0) years, forced expiratory volume in 1 s (FEV(1)) 51.1 (18.7) % predicted, MRC score 3.2 (1.0). Mean change in CAT score after PR was 2.9 (5.6) points, improving by 3.8 (6.1) points in those scoring 'much better' (n=162), and by 1.3(4.5) in those who felt 'a little better' (n=88) (p=0.002). Only eight individuals reported no difference after PR and three reported feeling 'a little worse', so comparison with these smaller groups was not possible.CONCLUSION: The CAT score is simple to implement as an outcome measure, it improves in response to PR and can distinguish categories of response. PMID: 21398686 Funding information This work was supported by: Medical Research Council, United Kingdom Grant ID: G1002113 Department of Health, United Kingdom Grant ID: DHCS/07/07/009
Seasonal Adjustments in Metabolism and Insulation in the Dark-Eyed Junco

Field: Agricultural and Biological Sciences (Life Sciences)

Trends during summer and winter in body mass and composition, insulation, body temperature, and metabolism were investigated in seasonally acclimatized Dark-eyed Juncos (Junco hyemalis) from western Oregon to determine if patterns of acclimatization were similar to those of passerines inhabiting harsher winter habitats. Body mass was significantly increased in winter (19.4 ± 0.2 g) compared to summer (17.8 ± 0.1 g), primarily because of elevated stored fat. Lean dry mass was seasonally constant. Dry mass of contour plumage was measured as an index of insulation and increased by 31.7% in winter birds. Little seasonal variation in body temperature was apparent and there was no evidence of torpor and only a very mild regulated nocturnal hypothermia at either season. Standard metabolic rate was significantly elevated in winter-acclimatized juncos (1.02 ml O2/min, 3.45 ml O2· g-1· hr-1) relative to summer-acclimatized birds (0.87 ml O2/min, 3.16 ml O2· g-1· hr-1). In addition, winter juncos demonstrated an ability to decrease thermal conductance below thermoneutrality. Insofar as winter increments in insulation do not offset increased thermogenic requirements at temperatures characteristic of this season, winter-acclimatization in Dark-eyed Juncos from western Oregon is similar to that for passerines from more severe winter climates in that it is primarily a metabolic process.
Propagation of Radio Signals in V2V/V2I Communications

Field: Engineering (Physical Sciences)

These Approach the data transmission/reception problems in radio environment by Communication Automotive version 1.0. (CommA_v.1.0.) system with using RFM12B radio module, by simulating various meteorological phenomena, brings a new vision on the way of radio communication in this field on these frequency bands. Significant reduction in radio signal propagation due to weather phenomena, which helps to monitor vehicle behavior and infrastructure in these cases.
Investigation on the Drying Induced Phase Transformation of Mesoporous Silica; A Comprehensive Understanding toward Mesophase Determination

Field: Chemistry (Physical Sciences)

Phase transformation of mesoporous silica during the drying process is investigated. As-synthesized hexagonal p6mm obtained under the conditions used in this study is transformed to cubic Ia3d as drying proceeds, even at room temperature. Prolonged synthesis results in the formation of a well-ordered hexagonal mesophase, with almost no phase transformation. Drying at a higher temperature promotes the phase transformation of not only hexagonal to cubic, but also cubic to lamellar mesophases. Release of water is detected during drying, which is followed by the phase transformation of the mesophases. The phase transformations observed here proceed against the direction estimated on the basis of the state-of-the-art understanding. Here, considering the degree of silicate condensation and the amount of residual water in the as-synthesized mesoporous silica, a comprehensive explanation of mesophase determination is proposed including thermodynamic and kinetic aspects to account for the results observed here and those in the literature.
Study of Atmospheric Plasma-Based Mass Separation System for High-Level Radioactive Waste Treatment

Field: Engineering (Physical Sciences)

Solid spent nuclear fuel from nuclear power plants has 3.4% fission products (80-160amu), contributing to over 99.8% radioactivity. On the other hand, liquid high-level radioactive waste (HLRW) from spent fuel reprocessing has 98.9% bulk elements (0-60amu) with 0.1% radioactivity. A separation mechanism on the mass categories as groups presents unique opportunities in managing HLRW for the long term with a considerable cost reduction. This paper proposes a thermal plasma-based separation system incorporating atmospheric pressure plasma torches for HLRW mass separation into low-resolution mass groups. Several engineering issues, such as waste preparation, waste injection into the plasma and waste collecting after mass separation, need to be addressed. Using COMSOL Multiphysics simulation, the generic system can be studied using noble gas mass separation and further analyze the mass filter capabilities. This paper provides the history of plasma-based mass separation. Functional modelling of a thermal plasma mass separation system is proposed under atmospheric pressure. Finally, aspects of mass separation simulation using noble gas Argon and Helium inside the plasma mass separation system were studied in COMSOL Multiphysics.