Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered intestinal microbiota and blood T cell phenotype are shared by patients with Crohn's disease and their unaffected siblings

Objective Crohn's disease (CD) is associated with intestinal dysbiosis, altered blood T cell populations, elevated faecal calprotectin (FC) and increased intestinal permeability (IP). CD-associated features present in siblings (increased risk of CD) but not in healthy controls, provide insight into early CD pathogenesis. We aimed to (1) Delineate the genetic, immune and microbiological profile of patients with CD, their siblings and controls and (2) Determine which factors discriminate between groups. Design Faecal microbiology was analysed by quantitative PCR targeting 16S ribosomal RNA, FC by ELISA, blood T cell phenotype by flow cytometry and IP by differential lactulose-rhamnose absorption in 22 patients with inactive CD, 21 of their healthy siblings and 25 controls. Subject's genotype relative risk was determined by Illumina Immuno BeadChip. Results Strikingly, siblings shared aspects of intestinal dysbiosis with patients with CD (lower concentrations of Faecalibacterium prausnitzii (p=0.048), Clostridia cluster IV (p=0.003) and Roseburia spp. (p=0.09) compared with controls). As in CD, siblings demonstrated a predominance of memory T cells (p=0.002) and elevated naïve CD4 T cell β7 integrin expression (p=0.01) compared with controls. FC was elevated (>50 μg/g) in 8/21 (38%) siblings compared with 2/25 (8%) controls (p=0.028); whereas IP did not differ between siblings and controls. Discriminant function analysis determined that combinations of these factors significantly discriminated between groups (χ2=80.4, df=20, p<0.001). Siblings were separated from controls by immunological and microbiological variables. Conclusions Healthy siblings of patients with CD manifest immune and microbiological abnormalities associated with CD distinct from their genotype-related risk and provide an excellent model in which to investigate early CD pathogenesis.
Viewstamped Replication Revisited

This paper presents an updated version of Viewstamped Replication, a replication technique that handles failures in which nodes crash. It describes how client requests are handled, how the group reorganizes when a replica fails, and how a failed replica is able to rejoin the group. The paper also describes a number of important optimizations and presents a protocol for handling reconfigurations that can change both the group membership and the number of failures the group is able to handle.
Structure and Function of the Plasma Membrane

The paucimolecular unit membrane model of the structure of the plasma membrane is critically reviewed in relation to current knowledge of the chemical and enzymatic composition of isolated plasma membranes, the properties of phospholipids, the chemistry of fixation for electron microscopy, the conformation of membrane proteins, the nature of the lipid-protein bonds in membranes, and possible mechanisms of transmembrane transport and membrane biosynthesis. It is concluded that the classical models, although not disproven, are not well supported by, and are difficult to reconcile with, the data now available. On the other hand, although a model based on lipoprotein subunits is, from a biochemical perspective, an attractive alternative, it too is far from proven. Many of the questions may be resolved by studies of membrane function and membrane biosynthesis rather than by a direct attack on membrane structure.
Long non-coding RNA XIST promotes cell growth and metastasis through regulating miR-139-5p mediated Wnt/β-catenin signaling pathway in bladder cancer

Bladder cancer is one of the most common urological malignancy all over the world. Recently, long non-coding RNA (lncRNA) XIST has been identified as an oncogenic gene in several type of cancers. However, the expression level and functional role of XIST in bladder cancer remain largely unknown. In the present study, we found that XIST was significantly up-regulated in bladder cancer tissues and cell lines, and was correlated with poor prognosis of bladder cancer patients. Furthermore, XIST knockdown significantly inhibited bladder cancer cell growth and metastasis in vitro and tumor growth in vivo. We also demonstrated that XIST acted as a competing endogenous RNA for miR-139-5p and repression of miR-139-5p could restore the inhibitory effects on bladder cancer cells induced by XIST shRNA. In addition, we identified that Wnt1 was a direct target of miR-139-5p, and XIST played the oncogenic role in bladder cancer by activating the Wnt/β-catenin signaling pathway. Taken together, our study suggested that lncRNA XIST may serve as a prognostic biomarker and a potential therapeutic target for bladder cancer.
Clues to NaCN formation.

Context ALMA is providing us essential information on where certain molecules form. Observing where these molecules emission arises from, the physical conditions of the gas, and how this relates with the presence of other species allows us to understand the formation of many species, and to significantly improve our knowledge of the chemistry that occurs in the space. Aims We studied the molecular distribution of NaCN around IRC +10216, a molecule detected previously, but whose origin is not clear. High angular resolution maps allow us to model the abundance distribution of this molecule and check suggested formation paths. Methods We modeled the emission of NaCN assuming local thermal equilibrium (LTE) conditions. These profiles were fitted to azimuthal averaged intensity profiles to obtain an abundance distribution of NaCN. Results We found that the presence of NaCN seems compatible with the presence of CN, probably as a result of the photodissociation of HCN, in the inner layers of the ejecta of IRC +10216. However, similar as for CH3CN, current photochemical models fail to reproduce this CN reservoir. We also found that the abundance peak of NaCN appears at a radius of 3 × 1015cm, approximately where the abundance of NaCl, suggested to be the parent species, starts to decay. However, the abundance ratio shows that the NaCl abundance is lower than that obtained for NaCN. We expect that the LTE assumption might result in NaCN abundances higher than the real ones. Updated photochemical models, collisional rates, and reaction rates are essential to determine the possible paths of the NaCN formation.
Skinfold Assessment: Accuracy and Application

Although not perfect, skinfolds (SK), or the measurement of fat under the skin, remains the most popular and practical method available to assess body composition on a large scale (Kuczmarski, Flegal, Campbell, & Johnson, 1994). Even for practitioners who have been using SK for years and are highly proficient at locating the correct anatomical sites and pinching the skin, the question remains—how accurate are the results? Creation of new SK equations using Dual Energy X-Ray Absorptiometry (DXA)technology as the criterion have improved the estimation accuracy achieved by SK. Practitioners are asked to recognize that the equations currently recommended by the American College of Sports Medicine underestimate body fatness by about 3% in both men and women. New equations, developed using DXA as the criterion, are prompting fitness and health professionals to reinterpret the meaning of the percentage of body fat standards for their clients. In summary, the accuracy of various SK assessments are reviewed and various principles of application are presented for the practitioner.
Cognitive Evaluation Theory: A meta-analytic review of the literature

Rewards have been shown to impair performance of a reinforced behavior. The work surrounding these detrimental effects of rewards has not been met with unanimous support. Does this phenomenon described in Deci’s cognitive evaluation theory concerning the detrimental effects of reward exist? Is Deci’s cognitive evaluation theory adequate to explain this phenomenon? A meta-analysis was employed to determine the existence of the detrimental effects of extrinsic rewards on intrinsic motivation. Results from this analysis showed that within strictly defined parameters the phenomenon defined by Deci exists. Implications from this analysis exemplify researchers’ need for closer supervision of the operationalization of variables based on the theoretical framework.
Hoxa2 knockdown in Xenopus results in hyoid to mandibular homeosis

The skeletal structures of the face and throat are derived from cranial neural crest cells (NCCs) that migrate from the embryonic neural tube into a series of branchial arches (BAs). The first arch (BA1) gives rise to the upper and lower jaw cartilages, whereas hyoid structures are generated from the second arch (BA2). The Hox paralogue group 2 (PG2) genes, Hoxa2 and Hoxb2, show distinct roles for hyoid patterning in tetrapods and fishes. In the mouse, Hoxa2 acts as a selector of hyoid identity, while its paralogue Hoxb2 is not required. On the contrary, in zebrafish Hoxa2 and Hoxb2 are functionally redundant for hyoid arch patterning. Here, we show that in Xenopus embryos morpholino‐induced functional knockdown of Hoxa2 is sufficient to induce homeotic changes of the second arch cartilage. Moreover, Hoxb2 is downregulated in the BA2 of Xenopus embryos, even though initially expressed in second arch NCCs, similar to mouse and unlike in zebrafish. Finally, Xbap, a gene involved in jaw joint formation, is selectively upregulated in the BA2 of Hoxa2 knocked‐down frog embryos, supporting a hyoid to mandibular change of NCC identity. Thus, in Xenopus Hoxa2 does not act redundantly with Hoxb2 for BA2 patterning, similar to mouse and unlike in fish. These data bring novel insights into the regulation of Hox PG2 genes and hyoid patterning in vertebrate evolution and suggest that Hoxa2 function is required at late stages of BA2 development. Developmental Dynamics 234:858–867, 2005. © 2005 Wiley‐Liss, Inc.
On the underlying mechanics of certain types of meaning change

Montagovian semantics treats word meanings in terms of intensions and extensions which are meant to capture speakers' ability to decide which words are to be used for what objects, properties, events, etc. The aim of the present paper is to refine this view in order to model facts about language change, acquisition, and knowledge of language. I will reconstruct intensions in terms of (a) given core referents, and (b) contextually determined ways to generalize these to full sets of (real or counterfactual) extensions. This reconstruction of word meanings is clarifying in several ways. It can explain how speakers can install the meanings of new words in a language on the basis of a limited set of intended referents, it makes clear how the limited knowledge of single speakers allows them to grasp the meaning of words in their language, and it allows to model certain types of historical meaning change and creative language use. The approach will finally be related to conceptual semantics, prototype theory, and classical truth value based semantics.
A Typology of Resilience: Rethinking Institutions for Sustainable Development

Under the general rubric of sustainability, societies are now struggling with the reconciliation of the demands of human systems and the health and continuation of the biosphere that supports them. Fundamental to coping with this challenge is the creation of decision-making and management approaches that possess an ability to operate in the face of pervasive risk and uncertainty In searching for clues to ways in which to meet the challenge, it would make sense to look to areas of human experience where change and the interaction of human and natural systems have been addressed before. We examine the intellectual areas of ecology and risk, and find that the attribute of resilience is a strong theme. A three-class typology of resilience (resistance to change; change at the margins; openness and adaptation), is developed to structure the discussion and clarify the issues. We argue that, whereas the nature of the problems facing humanity demands entertaining responses across this spectrum, current institutions and policy processes appear to be locked into "type 2"—change at the margins.
Transient and sustained effects of child-care attendance on hospital admission for gastroenteritis.

BACKGROUND There is evidence that children experience a transient increase in mild episodes of gastroenteritis when they start attending out-of-home child care. We assessed the transient and sustained effects of cumulative day-care attendance, age at first enrolment and type of child care facility attended on hospitalization rates for gastroenteritis. METHODS Cox proportional hazard models were used to estimate the risk of being hospitalized for gastroenteritis in two large cohorts of preschool (<6 years old) and elementary school-going (6-10 years old) children in Denmark. Day-by-day child-level registry data were used. Together, the two cohorts comprised 443,872 children, 21,038 hospitalizations and 1742,284 child-years (1994-2011). RESULTS From first day-care attendance until 12 months of cumulated attendance, preschool children attending day-care centres, but not those attending day-care homes, had an increased risk of hospitalization for gastroenteritis compared with children never attending registered day-care. Such increased risk was highest shortly after starting day-care attendance and then gradually declined. After 12 months of attendance, attending either day-care centres or day-care homes was associated with a lower risk for hospitalization. Such decreased risk was confined to children starting day-care attendance before the age of one year and extended throughout, but not beyond, their preschool years. CONCLUSIONS Attending day-care centres is associated with a higher risk for gastroenteritis hospitalization until completing 1 year of attendance. However, if children start attending day-care before the age of 1 year, they experience a lower risk of being hospitalized during their preschool years. This apparent protective effect does not last into the elementary school years.
Induction of Subacute Ruminal Acidosis Affects the Ruminal Microbiome and Epithelium

Subacute ruminal acidosis (SARA) negatively impacts the dairy industry by decreasing dry matter intake, milk production, profitability, and increasing culling rate and death loss. Six ruminally cannulated, lactating Holstein cows were used in a replicated incomplete Latin square design to determine the effects of SARA induction on the ruminal microbiome and epithelium. Experimental periods were 10 days with days 1–3 for ad libitum intake of control diet, followed by 50% feed restriction on day 4, and ad libitum access on day 5 to the basal diet or the basal diet with an additional 10% of a 50:50 wheat/barley pellet. Based on subsequent ruminal pH, cows were grouped (SARA grouping; SG) as Non-SARA or SARA based on time <5.6 pH (0 and 3.4 h, respectively). Ruminal samples were collected on days 1 and 6 of each period prior to feeding and separated into liquid and solid fractions. Microbial DNA was extracted for bacterial analysis using 16S rRNA gene paired-end sequencing on the MiSeq Illumina platform and quantitative PCR (qPCR). Ruminal epithelium biopsies were taken on days 1 and 6 before feeding. Quantitative RT-PCR was used to determine gene expression in rumen epithelium. Bray–Curtis similarity indicated samples within the liquid fraction separated by day and coincided with an increased relative abundance of genera Prevotella, Ruminococcus, Streptococcus, and Lactobacillus on day 6 (P < 0.06). Although Firmicutes was the predominant phyla in the solid fraction, a SG × day interaction (P < 0.01) indicated a decrease on day 6 for SARA cows. In contrast, phylum Bacteroidetes increased on day 6 (P < 0.01) for SARA cows driven by greater genera Prevotella and YRC22 (P < 0.01). Streptococcus bovis and Succinivibrio dextrinosolvens populations tended to increase on day 6 but were not affected by SG. In ruminal epithelium, CLDN1 and CLDN4 expression increased on day 6 (P < 0.03) 24 h after SARA induction and a tendency for a SG × day interaction (P < 0.10) was observed for CLDN4. Overall, results indicate more rapid adaptation to an induced bout of SARA in the solid fraction ruminal microbiome compared with ruminal epithelium.
El efecto de parpadeo atencional: influencia de las palabras negativas en una tarea de categorización de la valencia afectiva

Para estudiar en que medida las palabras emocionales modulan el efecto de Parpadeo Atencional(PA) administramos una tarea de Presentacion Serial Visual Rapida donde una palabra (objetivo O1) de valencia positiva, negativa o neutra, era seguida en la mitad de los ensayos por la palabra AGUA (objetivo O2) en alguna posicion posterior. La tarea incluia ensayos en los que solo debia detectarse si aparecia la palabra AGUA (O2) y ensayos de doble respuesta en los cuales ademas se debia categorizar la valencia del O1. Los resultados mostraron que la condicion de doble respuesta deterioraba la deteccion del O2 (PA) y este deterioro fue mayor despues de palabras negativas. A su vez, estos efectos fueron independientes de los niveles de ansiedad-rasgo de los participantes, lo cual sugiere la aparicion de un proceso generalizado de focalizacion de recursos cuando se hace saliente la valencia negativa de un estimulo. The attentional blink effect: Influence of negative words in an affective valence categorization task. In this study, we explored the emotional modulation of the Attentional Blink effect. In a Rapid Serial Visual Presentation procedure, a word (Target 1), either positive, negative or neutral, was followed by the word «WATER» (Target 2) in one half of the trials. The task included two conditions. In one of them, participants only had to detect the word “WATER”. In double-response trials, participants also categorized Target 1’s valence. Results showed that the detection of Target 2 was impaired in the doubleresponse condition, this impairment being greater when negative words appeared as Target 1, as compared to positive and neutral words. However these effects were independent on the Anxiety-Trait levels of participants. Overall, the pattern of data suggests that cognitive resources are focused on negative stimuli when their negative valence is emotionally salient enough.
International Schools and the International Baccalaureate

Elisabeth Fox traces the origins and development of the International Baccalaureate program as an outgrowth of continuing curriculum innovation in international schools. She describes its rapid expansion in North America, where many school systems are attracted by its challenging academic curriculum. Worldwide university recognition of the program is steadily increasing. Fox concludes by considering the prospects for future development, with particular emphasis on attempts to move the Baccalaureate beyond its Euro-centric origins.
Solvent Accessible Surface Representation in a Database System for Protein Docking

Protein docking is a new and challenging application for query processing in database systems. Our architecture for an efficient support of docking queries is based on the multistep query processing paradigm, a technique well-known from spatial database system. Along with physicochemical parameters, the geometry of the molecules plays a fundamental role for docking retrieval. Thus, 3D structures and 3D surfaces of molecules are basic objects in molecular databases. We specify a molecular surface representation based on topology, define a class of neighborhood queries, and sketch some applications with respect to the docking problem. We suggest a patch-based data structure called the TriEdge structure, first, to efficiently support topological query processing, and second, to save space in comparison to common planar graph representations such as the quad-edge structure. In analogy to the quad-edge structure, the TriEdge structure has an algebraic interface and is implemented via complex pointers. However, we achieve a reduction of the space requirement by a factor of four. Finally, we investigate the time performance of our prototype.
Order Effects in Personnel Decision Making

Research on primacy versus recency effects in personnel decision making was reconsidered within the framework of the belief-adjustment model of Hogarth and Einhorn (1992) in this article. The model posits that primacylrecency is a function of the interaction of various features of the judgment task. On the basis of this model, we predicted that recency effects will predominate in a simulated work sample, regardless of whether ratings are made after each work-sample exercise or only at the end of the process. One hundred seventeen university students received rater training and observed a candidate's performance in 2 role-play exercises. The conditions differed in terms of exercise order (positive-negative performance vs. negative-posi- tive performance) and response mode (step-by-step vs. end-of-sequence). Results were consistent with predictions. In addition, evidence was found for (within-target) contrast effects in the work-sample ratings. Implications of the model for selection and performance evaluat.
CT Morphometric Analysis to Determine the Anatomical Basis for the Use of Transpedicular Screws during Reconstruction and Fixations of Anterior Cervical Vertebrae

Background Accurate placement of pedicle screw during Anterior Transpedicular Screw fixation (ATPS) in cervical spine depends on accurate anatomical knowledge of the vertebrae. However, little is known of the morphometric characteristics of cervical vertebrae in Chinese population. Methods Three-dimensional reconstructions of CT images were performed for 80 cases. The anatomic data and screw fixation parameters for ATPS fixation were measured using the Mimics software. Findings The overall mean OPW, OPH and PAL ranged from 5.81 to 7.49 mm, 7.77 to 8.69 mm, and 33.40 to 31.13 mm separately, and SPA was 93.54 to 109.36 degrees from C3 to C6, 104.99 degrees at C7, whereas, 49.00 to 32.26 degrees from C4 to C7, 46.79 degrees at C3 (TPA). Dl/rSIP had an increasing trend away from upper endplate with mean value from 1.87 to 5.83 mm. Dl/rTIP was located at the lateral portion of the anterior cortex of vertebrae for C3 to C5 and ipsilateral for C6 to C7 with mean value from −2.70 to −3.00 mm, and 0.17 to 3.18 mm. The entrance points for pedicular screw insertion for C3 to C5 and C6 to C7 were recommended −2∼−3 mm and 0–4 mm from the median sagittal plane, respectively, 1–4 mm and 5–6 mm from the upper endplate, with TPA being 46.79–49.00 degrees and 40.89–32.26 degrees, respectively, and SPA being 93.54–106.69 degrees and 109.36–104.99 degrees, respectively. The pedicle screw insertion diameter was recommended 3.5 mm (C3 and C4), 4.0 mm (C5 to C7), and the pedicle axial length was 21–24 mm for C3 to C7 for both genders. However, the ATPS insertion in C3 should be individualized given its relatively small anatomical dimensions. Conclusions The data provided a morphometric basis for the ATPS fixation technique in lower cervical fixation. It will help in preoperative planning and execution of this surgery.
RACE AND ETHNIC DIFFERENCES IN THE EFFECTS OF RELIGIOUS ATTENDANCE ON SUBJECTIVE HEALTH

Religion and health research has not adequately addressed how the salutary benefits of participating in religious services differ among major racial and ethnic groups. This research uses data from the General Social Surveys to analyze differences in the effects of religious attendance upon subjective health among a sample of non-Latino White, non-Latino Black, and Latino adults. Modeled after a study by Levin and Markides (1986), first-order regressions of religious attendance on subjective health alternately controlled for social support, socioeconomic status, and subjective religiosity. The association between attendance and health tends to hold up among Whites and younger Black and Latino women, but controlling for subjective religiosity explained away bivariate associations among younger respondents in all three race/ethnic groups. Support for the socioeconomic status hypothesis was expected among Blacks and Latinos, but the results did not provide much evidence.