jimnoneill/paper-to-field-training huggingface dataset:
Crystal Direct: a new system for automated crystal harvesting

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

The photosynthetic process is initiated by the absorption of light energy by pigment-protein complexes called light harvesting antennas that transfer the absorbed energy to the photochemical reaction centers with a quantum efficiency of near unity.In cyanobacteria and red algae the major antenna is called the Phycobilisome (PBS) which is one of the most efficient antenna systems that exists in nature.The PBS is an extremely large complex, with a molecular weight of 3-7MDa which is made up of pigmented proteins known as phycobiliproteins and unpigmented proteins known as linker proteins.Our research goal is to obtain high resolution crystal structures of the entire PBS complex and the two major PBS sub-complexes, (rods and cores), isolated from the cyanobacterium Thermosynechococcus vulcanus (T.vulcanus) and the novel Acaryochloris marina (A.marina) with its simplest of all PBS.Intact PBS from T.vulcanus and A .marina were isolated in high phosphate buffer.The PBS from both organisms was crystallized in the presence of high phosphate concentration and special additives that mimicked the crowding of the PBS in vivo and provided suitable conditions for crystallization.T. vulcanus PBS Crystals and protein obtained from the dissolution of extensively washed crystals were analyzed by fluorescence spectroscopy, SDS-PAGE, mass spectrometry and confocal microscopy.The results of these experiments indicate that the crystals contain intact, functional PBS complex.Diffraction experiments have showed that the present crystals diffract to a resolution of ~ 3.5Å.In addition, preliminary TEM images indicate that the isolated T. vulcanus PBS forms dimers.This leads to a novel suggested model for the PBS arrangement in the crystal.A. marina PBS crystals were also analyzed by confocal microscopy.By utilizing the confocal microscope, the emission spectra of a single crystal at all different positions and depths were identical and presented an intact and functional PBS.Currently, additional experiments are being held in order to obtain well diffracting crystals.In addition, during the process of T. vulcanus PBS isolation, fractions of the two subcomplexes (rods and core) were also obtained, and successfully crystallized.Large blue rod crystals, containing phycocyanin (one of the PBPs proteins located in the rod) and the three rod linker proteins were obtained.The structure was determined by molecular replacement to a resolution of 1.5 Å, with a monomer in the asymmetric unit [1].Core crystals have also been obtained, however they require further improvement in order to perform structure determination.
Comparing different muscle activation dynamics using sensitivity analysis

Field: Neuroscience (Life Sciences)

In this paper, we mathematically compared two models of mammalian striated muscle activation dynamics proposed by Hatze and Zajac. Both models are representative of a broad variety of biomechanical models formulated as ordinary differential equations (ODEs). The models incorporate some parameters that directly represent known physiological properties. Other parameters have been introduced to reproduce empirical observations. We used sensitivity analysis as a mathematical tool for investigating the influence of model parameters on the solution of the ODEs. That is, we adopted a former approach for calculating such (first order) sensitivities. Additionally, we expanded it to treating initial conditions as parameters and to calculating second order sensitivities. The latter quantify the non-linearly coupled effect of any combination of two parameters. As a completion we used a global sensitivity analysis approach to take the variability of parameters into account. The method we suggest has numerous uses. A theoretician striving for model reduction may use it for identifying particularly low sensitivities to detect superfluous parameters. An experimenter may use it for identifying particularly high sensitivities to facilitate determining the parameter value with maximised precision.
Racial Disparity in Neonatal Outcomes in Pregnancies Conceived Via In Vitro Fertilization [A277]

Field: Medicine (Health Sciences)

INTRODUCTION: Increased adverse maternal and neonatal outcomes are seen in Black compared to White U.S. women. Pregnancies conceived via in vitro fertilization (IVF) represent a unique population, often with appropriate pre-pregnancy medical care, access to prenatal care, and overall higher socioeconomic status. Thus, we set out to assess whether similar racial disparities exist in pregnancies following IVF. METHODS: We performed a retrospective analysis of the CDC's natality database (2016–2018) of births conceived via IVF in women who self-identified as non-Hispanic Black and non-Hispanic White. Pearson's Chi-square test was used to compare several pregnancy and neonatal outcomes among women of both races. Multivariate logistic regression adjusted the outcomes for potential confounders. Results are presented as adjusted odds ratios (aORs) with a 95% confidence interval (CI). Statistical significance was set as P -value less than .05. RESULTS: Non-Hispanic Black women had a lower risk for gestational diabetes (aOR 0.8, CI 0.7–0.9), hypertensive disorders of pregnancy (aOR 0.8, CI 0.7–0.9), eclampsia (aOR 0.9, CI 0.9–1), and neonatal immediate and prolonged ventilation (aOR 0.7, CI 0.7–0.8; aOR 0.75, CI 0.6–0.8; respectively) than non-Hispanic White women. No difference was found in the rate of preterm deliveries, maternal intensive care unit admissions, gravid hysterectomies, neonatal intensive care unit admissions, and newborn antibiotics ( P >.05). CONCLUSION: Based on this extensive U.S. database, maternal and neonatal complications that are generally seen more frequently in Black women are, in fact, lower in Black compared to White women in the IVF population. These findings may indicate that different socioeconomic factors, rather than race per se, are at play. Further research is needed to explore the causes of this disparity.
A survey on energy‐efficient resource allocation schemes in device‐to‐device communication

Field: Computer Science (Physical Sciences)

Summary Device‐to‐device (D2D) communication is an emanating and robust technology for next‐generation wireless networks. It aims to minimize load from the centralized base station (BS) and lets the device communicate directly in the presence or absence of it. Further, to increase the spectral efficiency, it operates in an underlay mode, where D2D devices/users reuse the spectrum of cellular users (CUs), resulting in unusual intercell/intracell interferences. Managing resources efficiently can drastically reduce the effect of interference but on the cost of high energy consumption. The research community is diligently studying the optimal methods for energy‐efficient resource allocation in D2D systems. As per the literature, there exists no comprehensive survey that studied the existing energy‐efficient resource allocation schemes in the D2D environment. Motivated from this, we present a survey on recently adopted solutions for energy‐efficient power, channel, and spectrum allocation in D2D communication, which includes artificial intelligence (AI), optimization, dynamic programming, heuristic approach, game theory, and graph models. In addition, we also highlighted the open research issues and technical challenges while allocating resources to D2D users (DUs).
Eunotia deficiens Metzeltin, Lange-Bertalot & Garcia- Rodriguez

Field: Agricultural and Biological Sciences (Life Sciences)

Eunotia deficiens Metzeltin, Lange-Bertalot & García-Rodríguez, Iconogr. Diatomol, 15: 48, pl. 22, fig. 5. 2005. (Figs. 47-49) Valves with dorsal margin convex, and slightly concave ventral margin. Ends rounded, slightly subcapitate, not detached from the valve body. Striae are parallel to slightly radiate, equidistant, and more concentrated at the ends. Length: 30-63 μm; width: 7.5-9.5 μm; striae 8-11 in 10 μm. The studied population is consistent with the type of material described in Metzeltin et al. (2005). E. deficiens resembles E. luna var. aequalis Hustedt but they differing in valve dimensions and striae density. E. luna var. aequalis present larger width values (12.6-15.3), dorsal margin more convex, and higher striae density (12-14) (Bicca et al. 2009, Metzeltin et al. 2005, Simonsen 1987). Material examined: BRAZIL, MATO GROSSO DO SUL: Taquaruçú, Patos Lake, 23.III.2018, sediment, D.T. Ruwer (Nupélia UEM - 18098-99, 18101-122). Occurrence: first citation for Upper Paraná River floodplain.
Kisspeptins: a multifunctional peptide system with a role in reproduction, cancer and the cardiovascular system.

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

The pairing of the kisspeptins (KP) with the KISS1 (GPR54) receptor has received growing attention since the description of the receptor as a molecular switch for puberty. The role of KP and its receptor, GPR54, in puberty is the most exciting finding made in the field of reproductive biology since the discovery of Gonadotropin Releasing Hormone (GnRH) in 1970s. A significant body of evidence across several species now suggests that KISS1 (GPR54) activation is a critical point in the commencement of puberty, although further investigation is required to characterize the interaction between KP and GnRH cascade. Given such pivotal roles of kisspeptins and GPR54 as gatekeepers of reproductive function, and the proven ability of sex steroids to physiologically regulate this system, it is plausible that environmental compounds with ability to interfere oestrogen and/or androgen signaling (agonists or antagonists) may target the hypothalamic kiss-1/GPR54 system, thereby inducing functional alterations of the hypothalamic-pituitary-gonadal axis. Synthetic agonists targeting KISS1 (GPR54) may represent novel therapeutic agents for the treatment of hypogonadotrophic hypogonadism in some affected individuals. The diverse multifunctional nature of the KP is beginning to unravel. The unexpected role of these peptides in puberty has raised a number of important questions that remain to be answered.
THE TROUBLE WITH MANSFIELD PARK

Field: Arts and Humanities (Social Sciences)

Jane Austen's worst mistake in this novel of brilliant patches and stultifying flaws is her writing into it near the end several chapters set in Portsmouth. For these chapters tell us how vivid and dynamic life outside of Mansfield is, and by contrast make the idealized Mansfield of the later chapters seem even more vacuous. Such, clearly, was not Jane Austen's intention; but in detesting Portsmouth and regretting Mansfield as she does, Fanny Price testifies eloquently to the poverty of conception and the misjudgment of life so clearly betrayed by this most eccentric of Jane Austen's novels. Readers of Mansfield Park have often felt uneasy with it, and there is a substantial critical literature cataloguing the novel's failures1 (and its successes as well). It is my feeling that the novel's disturbing quality is chiefly the result of something beyond and more crucial than the usual reasons cited?e. g., the dullness of the heroine, the pomposity of the hero, the ponderous handling of the ordination theme, the ambivalent and humorless treatment of the theatrical, the novel's clumsy and rather viperish satire, its essential conservatism, its unusual and heavy-handed didacticism, the coldness of its comic irony, and so forth. What is wrong with Mansfield Park is its tone, the angle of its moral perspective?its failure to recognize life where it exists, its narrow identification of moral existence with decorum and placidity, and its identification of impro? priety with action and noise. One gets the impression at times that Mans? field Park was written by a neurasthenic nun. It seems less the work of the author of Pride and Prejudice than that of Mrs. Clennam. It is my contention that Mansfield in this novel represents vapidity and Portsmouth life, and that Jane Austen not only ultimately fails to see this but fails as well to see that she has got them reversed in her mind. What is wrong with Mansfield? Almost everything. Its leading peo? ple are locked into patterns of heartlessness (Sir Thomas Bertram), in
Quantitative analysis of the relationship of bacteria based on the dinucleotide frequency profile

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

Objective To analyze the relationship of biology sequences quantitatively by using bioinformatics methods.Methods The dinucleotide frequency features of a sequence were calculated in order to construct its dinucleotide frequency profile vector.PCC distance was used to measure the relationship between two profile vectors.Results 119 different bacteria organisms were used as the research data.The result was that the nearer the relationship between the species was,the smaller the PCC distance was.Conclusion This method is a helpful attempt for quantitatively analyzing and modeling the relationship of biology species.
Table_3_Polymorphonuclear Cells Show Features of Dysfunctional Activation During Fatal Sepsis.xlsx

Field: Medicine (Health Sciences)

<p>Sepsis and septic shock remain leading causes of morbidity and mortality for patients in the intensive care unit. During the early phase, immune cells produce various cytokines leading to prompt activation of the immune system. Polymorphonuclear leukocytes (PMNs) respond to different signals producing inflammatory factors and executing their antimicrobial mechanisms, resulting in the engulfment and elimination of invading pathogens. However, excessive activation caused by various inflammatory signals produced during sepsis progression can lead to the alteration of PMN signaling and subsequent defects in their functionality. Here, we analyzed samples from 34 patients in septic shock, focusing on PMNs gene expression and proteome changes associated with septic shock. We revealed that, compared to those patients who survived longer than five days, PMNs from patients who had fulminant sepsis were characterized by a dysfunctional hyper-activation, show altered metabolism, and recent exit from the cell cycle and signs of cellular lifespan. We believe that this multi-omics approach, although limited, pinpoints the alterations in PMNs’ functionality, which may be rescued by targeted treatments.</p>
Unsupervised robotic sorting: Towards autonomous decision making robots

Field: Computer Science (Physical Sciences)

Autonomous sorting is a crucial task in industrial robotics which can be very challenging depending on the expected amount of automation. Usually, to decide where to sort an object, the system needs to solve either an instance retrieval (known object) or a supervised classification (predefined set of classes) problem. In this paper, we introduce a new decision making module, where the robotic system chooses how to sort the objects in an unsupervised way. We call this problem Unsupervised Robotic Sorting (URS) and propose an implementation on an industrial robotic system, using deep CNN feature extraction and standard clustering algorithms. We carry out extensive experiments on various standard datasets to demonstrate the efficiency of the proposed image clustering pipeline. To evaluate the robustness of our URS implementation, we also introduce a complex real world dataset containing images of objects under various background and lighting conditions. This dataset is used to fine tune the design choices (CNN and clustering algorithm) for URS. Finally, we propose a method combining our pipeline with ensemble clustering to use multiple images of each object. This redundancy of information about the objects is shown to increase the clustering results.
The use of fluorescent probes to assess viability of the plant pathogenic bacterium Clavibacter michiganensis subsp. michiganensis by flow cytometry

Field: Agricultural and Biological Sciences (Life Sciences)

Determination of the viability of bacteria by the conventional plating technique is a time-consuming process. Methods based on enzyme activity or membrane integrity are much faster and may be good alternatives. Assessment of the viability of suspensions of the plant pathogenic bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) using the fluorescent probes Calcein acetoxy methyl ester (Calcein AM), carboxyfluorescein diacetate (cFDA), and propidium iodide (PI) in combination with flow cytometry was evaluated. Heat-treated and viable (non-treated) Cmm cells labeled with Calcein AM, cFDA, PI, or combinations of Calcein AM and cFDA with PI, could be distinguished based on their fluorescence intensity in flow cytometry analysis. Non-treated cells showed relatively high green fluorescence levels due to staining with either Calcein AM or cFDA, whereas damaged cells (heat-treated) showed high red fluorescence levels due to staining with PI. Flow cytometry also allowed a rapid quantification of viable Cmm cells labeled with Calcein AM or cFDA and heat-treated cells labeled with PI. Therefore, the application of flow cytometry in combination with fluorescent probes appears to be a promising technique for assessing viability of Cmm cells when cells are labeled with Calcein AM or the combination of Calcein AM with PI.
Recent results from b-baryon decays at LHCb

Field: Physics and Astronomy (Physical Sciences)

Recent measurements of b-baryon decays using 3$fb^{-1}$ proton-proton collision data collected by the LHCb experiment are presented. Measurements of the branching fractions of $\\Lambda_{b}^{0} \\rightarrow J/\\psi p \\pi$, $\\Lambda_{b}^{0}\\rightarrow \\Lambda_{c}^{+}D_{s}^{-}$, $\\Lambda_{b}^{0}\\rightarrow \\Lambda_{c}^{+}D^{-}$, and $\\Lambda_{b}^{0}\\rightarrow \\Lambda_{c}^{+}\\pi^{-}$ decays have been made, as well as precise measurements of the mass and lifetime of the $\\Xi^0_{b}$ baryon. In addition, the $p_{T}$ and $\\eta$ dependence of the ratio of $\\Lambda_{b}^{0}$ to $B^{0}$ production fractions has been measured.
Beyond Static and Dynamic Risk Factors

Field: Psychology (Social Sciences)

Both desistance research and strengths-based approaches to offender rehabilitation suggest that attempts to reduce sex offender recidivism should attend to an offender’s release environment. Recent research has demonstrated that better quality release planning is associated with reduced recidivism; however, whether release planning contributes significant incremental validity in predicting recidivism over and above static and dynamic risk factors is unclear. In the present study, release planning was retrospectively assessed for a sample of child molesters ( n = 196) who had been released into the community following completion of a prison-based treatment program and its relative contribution to recidivism risk prediction was investigated. The average follow-up period was 11.08 years, during which 13.3% of the sample were convicted of a new sexual offence. Hierarchical Cox regression analyses showed that release planning contributed additional predictive validity for sexual recidivism after controlling for static and dynamic risk factors. Findings suggest that assessment of release planning might improve accuracy of sex offender risk assessments and that improved release planning should contribute to reductions in recidivism.
Effects of a Tai Chi/Qigong Intervention on Body Composition, Sleep Quality, and Emotional Eating in Midlife and Older Women

Field: Health Professions (Health Sciences)

abstract: Weight gain and unfavorable body composition are prevalent among midlife and older women; shifts in these characteristics can have detrimental implications on emotional and physical health and longevity. Efforts to attenuate weight-related factors detailing the potential development of obesity are traditionally driven by manipulation of nutrition and/or physical activity; however, sustained results are limited. Novel and integrative approaches are needed to reduce the burden of adverse changes in weight and associated consequences. \n\n This dissertation is built around a model of effects of Tai Chi/Qigong in body composition and a pilot test of this intervention and model factors in a group of midlife/older women (N = 36). Three resulting manuscripts include: 1) a proposed biobehavioral model detailing how a Tai Chi/Qigong intervention may improve weight-related outcomes through psychological, behavioral, and physiological pathways, 2) a paper examining pre- to post- intervention differences in the primary outcomes of percent body fat, sleep quality, and emotional eating and the exploratory outcomes of perceived stress, mood state, mindfulness, self-compassion and body awareness; and 3) an exploratory analysis examining correlations between primary (sleep quality, emotional eating), exploratory (perceived stress, mood state, mindfulness, self-compassion and body awareness), and neurophysiological (heart rate variability) outcomes of interest—further, regression models were conducted to explore the predictive value of the independent variables on the dependent variables and associated changes. \n\n In manuscript two, dependent t-tests were used to assess pre/post-differences (percent body fat and survey measures); this single group study (8-weeks of Tai Chi/Qigong) did not have a control group. Results of manuscript two demonstrate significant changes in sleep quality (p = .04), perceived stress (p = .05), and body awareness (p = .01). Findings of manuscript three indicate changes in the dependent variable of sleep quality were partially explained by perceived stress (adjusted R2 = 13.4%) and changes in the dependent variable of emotional eating were significantly explained by self-compassion (adjusted R2 = 42.1%). In the context of weight gain and unfavorable body composition in midlife/older women, results of this pilot study, using a standardized Tai Chi/Qigong intervention, indicate that select psycho-emotional factors may be important to explore further.
Prison Visiting Policies and Practices

Field: Social Sciences (Social Sciences)

Based on empirical evidence that visiting is significantly related to parole success, correctional administrators have begun to view family visits as one component of the rehabilitation process. Several authorities have encouraged correctional institutions to maximize visiting opportunities. Previous studies have noted geographical and architectural limits to such maximization. This article reports the results of a national survey of visiting policies and draws comparisons with surveys reported in 1978 and 1954 to determine the extent to which prisons have increased efforts to make visiting a priority.