Miracle-dz/UniFAR-FTUs huggingface dataset:
ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2

Mechanisms regulating mammalian meiotic progression are poorly understood. Here we identify mouse YTHDC2 as a critical component. A screen yielded a sterile mutant, “ketu”, caused by a Ythdc2 missense mutation. Mutant germ cells enter meiosis but proceed prematurely to aberrant metaphase and apoptosis, and display defects in transitioning from spermatogonial to meiotic gene expression programs. ketu phenocopies mutants lacking MEIOC, a YTHDC2 partner. Consistent with roles in post-transcriptional regulation, YTHDC2 is cytoplasmic, has 3′ → 5′ RNA helicase activity in vitro, and has similarity within its YTH domain to an N6-methyladenosine recognition pocket. Orthologs are present throughout metazoans, but are diverged in nematodes and, more dramatically, Drosophilidae, where Bgcn is descended from a Ythdc2 gene duplication. We also uncover similarity between MEIOC and Bam, a Bgcn partner unique to schizophoran flies. We propose that regulation of gene expression by YTHDC2-MEIOC is an evolutionarily ancient strategy for controlling the germline transition into meiosis.
The response of male broiler chicks to a corn-soy diet supplemented with L-methionine, L-cystine, choline, sulfate, and vitamin B12.

Six experiments with male broiler chicks were conducted to study responses to dietary supplements of L-methionine, L-cystine, choline, sulfate, and vitamin B12. A corn-soy-poultry oil-based diet calculated to contain . 38% methionine, . 74% total sulfur containing amino acids, 23% protein, 3,265 kcal metabolizable energy/kg, and 1.39 mg/g of choline was fed. Analysis indicated an average of . 38% Methionine (.35 to .45) . 77% Methionine + Cysteine (.72 TO .92), and 1.23 mg choline/g feed (.99 to 1.56) in the basal diet. Chicks fed the basal diets gained an average of 508 g in 21 days and had average feed conversion ratios (FCR) of 1.55. Chicks fed diets supplemented with . 2% L-methionine gained significantly more (P less than .05) than those fed the basal diet in each experiment (average gain = 551 g; FCR = 1.44). Chicks fed choline-supplemented diets gained as well as those fed L-methionine in five of six experiments (P greater than .05) (average gain = 541 g; FCR = 1.48). Chicks fed sodium sulfate-supplemented diets gained as well as those fed L-methionine in two of four experiments when adequate sodium was fed (average gain = 536; FCR = 1.50). Chicks fed choline and sulfate supplements together did no better than those fed choline supplements only, with adequate sodium levels in the basal diet. The same basal diet was fed in the last two experiments. In one trial, a response to vitamin B12 was observed; in the other there was no response. (ABSTRACT TRUNCATED AT 250 WORDS)
Issues in dietary intake assessment of children and adolescents

Studies of food habits and dietary intakes face a number of unique respondent and observer considerations at different stages from early childhood to late adolescence. Despite this, intakes have often been reported as if valid, and the interpretation of links between intake and health has been based, often erroneously, on the assumption of validity. However, validation studies of energy intake data have led to the widespread recognition that much of the dietary data on children and adolescents is prone to reporting error, mostly through under-reporting. Reporting error is influenced by body weight status and does not occur systematically across different age groups or different dietary survey techniques. It appears that the available methods for assessing the dietary intakes of children are, at best, able to provide unbiased estimates of energy intake only at the group level, while the food intake data of most adolescents are particularly prone to reporting error at both the group and the individual level. Moreover, evidence for the existence of subject-specific responding in dietary assessments challenges the assumption that repeated measurements of dietary intake will eventually obtain valid data. Only limited progress has been made in understanding the variables associated with misreporting in these age groups, the associated biases in estimating nutrient intakes and the most appropriate way to interpret unrepresentative dietary data. Until these issues are better understood, researchers should exercise considerable caution when evaluating all such data.
Factors affecting cleanliness of continously cast steel

Optimal steel cleanliness resulted from a comprehensive programme of plant trials. Improvements were measured using total oxygen and nitrogen pickup of the steel melt, tundish slag chemistry, visual inspection of final coils, and trials of experimental coils on a canmaking line. The plant trials included the evaluation of BOF steelmaking practices, ladle shrouding, ladle opening practices, tundish flow control devices, tundish fluxes, and submerged entry nozzle change practices.
Trajectory-driven Influential Billboard Placement

In this paper we propose and study the problem of trajectory-driven influential billboard placement: given a set of billboards $\ur$ (each with a location and a cost), a database of trajectories $\td$ and a budget $\budget$, find a set of billboards within the budget to influence the largest number of trajectories. One core challenge is to identify and reduce the overlap of the influence from different billboards to the same trajectories, while keeping the budget constraint into consideration. We show that this problem is NP-hard and present an enumeration based algorithm with $(1-1/e)$ approximation ratio. However, the enumeration should be very costly when $|\ur|$ is large. By exploiting the locality property of billboards' influence, we propose a partition-based framework \psel. \psel partitions $\ur$ into a set of small clusters, computes the locally influential billboards for each cluster, and merges them to generate the global solution. Since the local solutions can be obtained much more efficient than the global one, \psel should reduce the computation cost greatly; meanwhile it achieves a non-trivial approximation ratio guarantee. Then we propose a \bbsel method to further prune billboards with low marginal influence, while achieving the same approximation ratio as \psel. Experiments on real datasets verify the efficiency and effectiveness of our methods.
Hypoxia and transforming growth factor‐beta1 pathway activation promote Chinese Hamster Ovary cell aggregation

Suspension cultivation is the preferred mode of operation for the large‐scale production of many biologics. Chinese Hamster Ovary (CHO) cells are anchorage‐dependent in origin, but they have been widely adapted to suspension culture. In suspension culture, formation of CHO cell aggregates is a common phenomenon and compromises cell culture performance in multiple ways. To better understand the underlying mechanisms that regulate cell aggregation, we utilized CHO‐specific transcriptome profiling as a screening tool and demonstrated that many genes encoding extracellular matrix (ECM) proteins were upregulated in the cultures with increased cell aggregation. Significantly, hypoxia was identified to be a cause for promoting CHO cell aggregation, and transforming growth factor beta1 (TGFβ1) pathway activation served as an intermediate step mediating this biological cascade. These transcriptomics findings were confirmed by cell culture experiments, and it was further demonstrated that adding recombinant TGFβ1 to the culture significantly increased ECM protein fibronectin expression and cell aggregation. The results of this study emphasize the importance of adequate mixing and oxygen supply for suspension cultures from a new angle, and regulating the TGFβ1 pathway is proposed as a new strategy for mitigating cell aggregation to improve cell culture performance.
Field experience and the long-term durability of reinforced concrete structures

For reinforced concrete structures the conventional wisdom is that after some years of exposure to marine conditions reinforcement corrosion is inevitable. Much attention is paid in the literature to the rate of ingress of chlorides through the concrete cover to the reinforcing bars and to ensuring highly impermeable cover and/or deeper cover, to try top prevent chloride-induced or carbonation-induced corrosion initiation. Actual field experience shows that there are many reinforced concrete structures that have survived remarkably well for many decades despite having very high chloride concentrations next to the reinforcing bars. Even with very modest concrete cover by modern standards, exhumation often finds bars free from corrosion. Detailed investigations of a number of such cases showed no corrosion if the concrete pH levels are above about 9. On the other hand, very severe reinforcement corrosion was observed in the few cases where the concrete had cracked right through the cover to the bars. Often there was no external evidence or signs of interior corrosion, including longitudinal cracking. The implications of these findings for practice are discussed.
Proteomic analysis of red blood cells and the potential for the clinic: what have we learned so far?

ABSTRACT Introduction: Red blood cells (RBC) are the most abundant host cells in the human body. Mature erythrocytes are devoid of nuclei and organelles and have always been regarded as circulating ‘bags of hemoglobin’. The advent of proteomics has challenged this assumption, revealing unanticipated complexity and novel roles for RBCs not just in gas transport, but also in systemic metabolic homeostasis in health and disease. Areas covered: In this review we will summarize the main advancements in the field of discovery mode and redox/quantitative proteomics with respect to RBC biology. We thus focus on translational/clinical applications, such as transfusion medicine, hematology (e.g. hemoglobinopathies) and personalized medicine. Synergy of omics technologies – especially proteomics and metabolomics – are highlighted as a hallmark of clinical metabolomics applications for the foreseeable future. Expert commentary: The introduction of advanced proteomics technologies, especially quantitative and redox proteomics, and the integration of proteomics data with omics information gathered through orthogonal technologies (especially metabolomics) promise to revolutionize many biomedical areas, from hematology and transfusion medicine to personalized medicine and clinical biochemistry.
Plasticity in the Macromolecular-Scale Causal Networks of Cell Migration

Heterogeneous and dynamic single cell migration behaviours arise from a complex multi-scale signalling network comprising both molecular components and macromolecular modules, among which cell-matrix adhesions and F-actin directly mediate migration. To date, the global wiring architecture characterizing this network remains poorly defined. It is also unclear whether such a wiring pattern may be stable and generalizable to different conditions, or plastic and context dependent. Here, synchronous imaging-based quantification of migration system organization, represented by 87 morphological and dynamic macromolecular module features, and migration system behaviour, i.e., migration speed, facilitated Granger causality analysis. We thereby leveraged natural cellular heterogeneity to begin mapping the directionally specific causal wiring between organizational and behavioural features of the cell migration system. This represents an important advance on commonly used correlative analyses that do not resolve causal directionality. We identified organizational features such as adhesion stability and adhesion F-actin content that, as anticipated, causally influenced cell migration speed. Strikingly, we also found that cell speed can exert causal influence over organizational features, including cell shape and adhesion complex location, thus revealing causality in directions contradictory to previous expectations. Importantly, by comparing unperturbed and signalling-modulated cells, we provide proof-of-principle that causal interaction patterns are in fact plastic and context dependent, rather than stable and generalizable.
Dietary interaction of phosphorus with sodium from either chloride or bicarbonate affects laying hen performance.

Experimental diets consisting of two levels of total phosphorus (.30 and .75%) and three different treatments of supplemental sodium (.35% NaCl, 1.40% NaCl, and .35% NaCl plus 1.50% NaHCO3) were fed in a 2 X 3 factorial arrangement to laying hens for 16 weeks. The latter two treatments of sodium were designed to supply the same level of sodium (.55%) from different chemical forms. Hens fed . 30% phosphorus laid significantly (P less than .01) less eggs than those fed . 75% phosphorus. A highly significant (P less than .01) interaction was found between phosphorus and sodium treatments. The high level of sodium from either chloride or bicarbonate decreased egg production at the lower level of phosphorus and increased it when the higher level of phosphorus was fed. Sodium bicarbonate affected egg production more strongly than sodium chloride did. There were no significant treatment effects on egg weight and egg shell weight. Addition of sodium bicarbonate to the low phosphorus diet significantly (P less than .05) decreased feed consumption of the hen. Supplemental sodium bicarbonate with either level of dietary phosphorus significantly (P less than .05) increased percent nitrogen retention of the hen, but excessive sodium chloride did not.
Tags are not metadata, but "just more content" - to some people

The authoring of tags ‐ unlike the authoring of traditional metadata ‐ is highly popular among users. This harbours unprecedented opportunities for organizing content. However, tags are still poorly understood. What do they “mean”, in what senses are they similar to or dierent from metadata? Dierent tags support dierent communities, but how exactly do they reflect the plurality of opinions,what is the relation to individual dierences in authoring and reading? In this paper, we oer a definition and empirical evidence for the claim that “tags are not metadata, but just more content”. The analysis rests on a multi-annotator classification of a blog corpus using the WordNet domain labels system (WND), the development of a system of text-classification methods using WordNet and WND, and a quantitative and qualitative comparative analysis of these classifications. We argue that the notion of a “gold standard” may be meaningless in social media, and we outline possible consequences for labelling and search-engine development.
A leucocytopenia induced in chickens by dietary ochratoxin A.

Ochratoxin A was fed (0, .5, 1.0, 2.0, 4.0, and 8.0 microgram/g) to broiler chickens from day-old to three weeks of age when the birds were bled and total leucocyte and differential counts were performed. Ochratoxin A significantly (P less than .05) reduced leucocyte counts at every dose level of ochratoxin A administered. The leucocytopenia was characterized by an increase in the relative concentration of heterophils and decrease in the relative concentration of lymphocytes. From total leucocyte and differential leucocyte counts the number of circulating cells was calculated for each type of leucocyte. The total number of circulating lymphocytes of blood decreased significantly (P less than .05) at every dose level of ochratoxin A administered, and the number of monocytes decreased at 2.0 microgram/g and above. However, the number of circulating heterophils was not altered. These data demonstrated that ochratoxin A induced a severe leucocytopenia (lympocytopenia primarily and monocytopenia to a lesser extent) and implied that the functioning of the immune system might be altered.
Peripheral B-Cell Subset Distribution in Primary Antiphospholipid Syndrome

Background: B-cell differentiation and B-cell tolerance checkpoints may be different in antiphospholipid syndrome (APS) from systemic lupus erythematosus (SLE) and can help to understand differences between them. Our aim was to define alterations of B-cell subsets in patients with primary APS (pAPS) and to compare them with SLE patients and healthy controls (HC). Methods: Cross-sectional study including three study groups: 37 patients with pAPS, 11 SLE patients, and 21 age- and gender-matched HC. We determined the frequencies of different B-cell subsets in peripheral blood naïve and memory compartments. In addition, we measured serum B cell-activating factor (BAFF) levels and circulating pro-inflammatory cytokines, such as IL-6, by commercial ELISA and CBA, respectively. Results: Patients with pAPS showed a lower percentage of immature and naïve B cells than patients with SLE (p = 0.013 and p = 0.010, respectively) and a higher percentage of non-switched memory B cells than patients with SLE (p = 0.001). No differences either in the percentage of switched memory cells or plasma cells were found among the different groups. Serum BAFF levels were higher in SLE patients than in healthy controls and pAPS patients (p = 0.001 and p = 0.017, respectively). A significant increase in the serum BAFF levels was also observed in pAPS patients compared to HC (p = 0.047). Circulating IL-6 levels were higher in SLE and pAPS patients than HC (p = 0.036 and p = 0.048, respectively). A positive correlation was found between serum BAFF and IL-6 levels in patients with SLE but not in pAPS (p = 0.011). Conclusions: Our characterization of peripheral blood B-cell phenotypes in pAPS demonstrates different frequencies of circulating B cells at different stages of differentiation. These differences in the naïve B-cell repertoire could explain the higher number and variety of autoantibodies in SLE patients in comparison to pAPS patients, especially in those with obstetric complications.
Effects of Multimethod Intervention on Bedside Report Compliance and Patient Satisfaction

Miscommunication is a large contributing factor to hospital sentinel events. Communication with nurses is a component of the Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) survey. The HCAHPS survey not only assesses patient satisfaction but also impacts how hospitals are reimbursed. A literature review reveals that nursing bedside shift positively impacts patient satisfaction and nurse communication. There is limited research on how to implement bedside report as well as what to include during report. A pilot study evaluated an educational intervention and its impact on nurses' compliance with bedside report. The study also evaluated whether bedside report compliance affected HCAHPS scores. A test of independent proportions showed that overall compliance scores increased significantly from period 1 (46%) to period 3 (81%), z = 2.23, P = −. 017, one-tailed. HCAHPS scores for nursing communication went from 69.9% in quarter 1 of 2015 to 73.8% in quarter 4 of 2016, but there was no statistically significant change.
A New Semidefinite Programming Relaxation for the Quadratic Assignment Problem and Its Computational Perspectives

Recent progress in solving quadratic assignment problems QAPs from the QAPLIB Quadratic Assignment Problem Library test set has come from mixed-integer linear or quadratic programming models that are solved in a branch-and-bound framework. Semidefinite programming SDP bounds for QAPs have also been studied in some detail, but their computational impact has been limited so far, mostly because of the restrictive size of the early relaxations. Some recent progress has been made by studying smaller SDP relaxations and by exploiting group symmetry in the QAP data. In this work, we introduce a new SDP relaxation, where the matrix variables are only of the order of the QAP dimension, and we show how one may exploit group symmetry in the problem data for this relaxation. We also provide a detailed numerical comparison with related bounds from the literature. In particular, we compute the best-known lower bounds for two QAPLIB instances.
The airborne microflora of poultry houses.

Two experiments were conducted to compare effects of housing temperatures and bird density on the airborne microflora of poultry houses. Temperatures of 15.6 and 26.7 C were used with birds housed at densities of . 42 or . 84 m3 per bird. Air samples were taken using a New Brunswick STA 200 microbiological air sampler. Numbers of aerobic, anaerobic, coliform and lactic acid bacteria, and molds were determined by plate counts with numbers of Escherichia coli and Staphylococcus aureus determined by most probable numbers procedures. Microorganisms were identified by picking representative colonies from plates and inoculating into differential media for biochemical tests. Higher bird density (.42 m3/bird) resulted in greater numbers of airborne microorganisms in both experiments. Fifteen genera of bacteria were identified with two or more species identified for eight genera. Among the most commonly identified aerobic genera were Bacillus, Micrococcus, Proteus, Pseudomonas and Staphylococcus, while four species of Clostridia were the most frequently identified anaerobes. Nine genera of molds were identified with over one-half of all isolates being either Aspergillus or Penicillium. Microorganisms represented only a small fraction of the airborne particulate matter in the study.
Self-selection of calcium during the rearing and early laying periods of White Leghorn pullets.

The ability of pullets to selectively consume calcium to meet the requirements of the rearing and early laying period was studied in White Leghorns. In the first of two experiments, 456 pullets were fed either an . 89% calcium rearing diet (control) or a . 35% calcium diet in combination with a separate source of 38% calcium chick-sized grit (calcium self-selection) from 35 to 126 days of age. Twenty-four pullets from each of these rearing treatments were selected for the second experiment at 112 days of age and were housed in individual laying cages. Rearing treatments were continued until 176 days of age with mash and grit consumption recorded daily for each pullet. From 177 to 225 days of age these pullets were fed a 3.50% calcium diet containing either ground limestone or oyster shell as a calcium source or a . 35% calcium diet fed in combination with a separate source of oyster shell. Pullet calcium intake reflected the requirements for growth during the rearing period, calcium storage in the medullary bone 19 days prior to lay, and egg shell formation during the laying period; average calcium intake for these periods was 1.18, 2.08, and greater than 3.50%, respectively. Pullets also demonstrated the ability to compensate for rearing deficiencies by increased calcium consumption when fed oyster shell on an ad lib basis. Calcium consumption was found to be significantly higher on days when an oviposition occurred than when no eggs were laid. Mash consumption during the early laying period also reflected the reproductive status of the hen with the highest consumption on days when both oviposition and ovulation occurred, intermediate consumption when either oviposition or ovulation occurred, and lowest consumption when neither oviposition nor ovulation was detected.