Miracle-dz/UniFAR-FTUs huggingface dataset:
More than 9,000,000 Unique Genes in Human Gut Bacterial Community: Estimating Gene Numbers Inside a Human Body

Background Estimating the number of genes in human genome has been long an important problem in computational biology. With the new conception of considering human as a super-organism, it is also interesting to estimate the number of genes in this human super-organism. Principal Findings We presented our estimation of gene numbers in the human gut bacterial community, the largest microbial community inside the human super-organism. We got 552,700 unique genes from 202 complete human gut bacteria genomes. Then, a novel gene counting model was built to check the total number of genes by combining culture-independent sequence data and those complete genomes. 16S rRNAs were used to construct a three-level tree and different counting methods were introduced for the three levels: strain-to-species, species-to-genus, and genus-and-up. The model estimates that the total number of genes is about 9,000,000 after those with identity percentage of 97% or up were merged. Conclusion By combining completed genomes currently available and culture-independent sequencing data, we built a model to estimate the number of genes in human gut bacterial community. The total number of genes is estimated to be about 9 million. Although this number is huge, we believe it is underestimated. This is an initial step to tackle this gene counting problem for the human super-organism. It will still be an open problem in the near future. The list of genomes used in this paper can be found in the supplementary table.
Y-Balance Test Performance Following a Competitive Field Hockey Season: A Pretest-Posttest Study.

CONTEXT The Y-Balance Test (YBT) is a dynamic balance assessment used as a preseason musculoskeletal screen to determine injury risk. While the YBT has demonstrated excellent test-retest reliability, it is unknown if YBT performance changes following participation in a competitive athletic season. OBJECTIVE Determine if a competitive athletic season affects YBT performance in field hockey players. DESIGN Pretest-posttest. SETTING Laboratory. PARTICIPANTS 20 NCAA Division I women's field hockey players (age = 19.55 ± 1.30 y; height = 165.10 ± 5.277 cm; mass = 62.62 ± 4.64 kg) from a single team volunteered. Participants had to be free from injury throughout the entire study and participate in all athletic activities. INTERVENTIONS Participants completed data collection sessions prior to (preseason) and following the athletic season (postseason). Between data collections, participants competed in the fall competitive field hockey season, which was ~3 months in duration. During data collection, participants completed the YBT bilaterally. MAIN OUTCOME MEASURES The independent variable was time (preseason, postseason) and the dependent variables were normalized reach distances (anterior, posteromedial, posterolateral, composite) and between-limb symmetry for each reach direction. Differences between preseason and postseason were examined using paired t tests (P ≤ .05) as well as Bland-Altman limits of agreement. RESULTS 4 players sustained a lower extremity injury during the season and were excluded from analysis. There were no significant differences between preseason and postseason reach distances for any reach directions on either limb (P ≥ .31) or in the between-limb symmetries (P ≥ .52). The limits of agreement analyses determined there was a low mean bias across measurements (≤1.67%); however, the 95% confidence intervals indicated there was high variability within the posterior reach directions over time (±4.75 to ± 14.83%). CONCLUSION No changes in YBT performance were identified following a competitive field hockey season in Division I female athletes. However, the variability within the posterior reach directions over time may contribute to the limited use of these directions for injury risk stratification.
Use of transgenic mice reveals cell-specific transformation by a simian virus 40 T-antigen amino-terminal mutant

We have used the multifunctional transforming protein, simian virus 40 T antigen, as a probe to study the mechanisms of cell growth regulation in the intact organism. T antigen appears to perturb cell growth, at least in part, by stably interacting with specific cellular proteins that function to maintain normal cell growth properties. Experiments in cultured cells indicate that at least three distinct regions of simian virus 40 T antigen have roles in transformation. Two regions correlate with the binding of known cellular proteins, p53, pRB, and p107. A third activity, located near the amino terminus, has been defined genetically but not biochemically. By targeting expression of wild-type and mutant forms of T antigen to distinct cell types in transgenic mice, we have begun to systematically determine which activities play a role in tumorigenesis of each cell type. In this study, we sought to determine the role of the amino-terminal transformation function with such an analysis of the T-antigen mutant dl1135. This protein, which lacks amino acids 17 to 27, retains the p53-, pRB-, and p107-binding activities yet fails to transform cells in culture. To direct expression in transgenic mice, we used the lymphotropic papovavirus transcriptional signals that are specific for B and T lymphocytes and the choroid plexus epithelium of the brain. We show here that although defective in cell culture, dl1135 specifically induced the development of thymic lymphomas in the mouse. Expression of the protein was routinely observed in B- and T-lymphoid cells, although B-cell abnormalities were not observed. Choroid plexus tumors were observed only infrequently; however, dl1135 was not consistently expressed in this tissue. Within a given transgenic line, the penetrance of T-cell tumorigenesis was 100% but appeared to require secondary events, as judged from the clonal nature of the tumors. These experiments suggest that the amino-terminal region of T antigen has a role in the transformation of certain cell types (such as fibroblasts in culture and B lymphocytes) but is dispensable for the transformation of T lymphocytes.
Memory-Optimized Hybrid Decoding Method for Multi-Rate Turbo Codes

To provide near-optimal error-correcting performance for multi-rate turbo codes and minimize the size of additional memory, a new decoding method is proposed in this paper. The proposed decoding is based on two methods: hybrid sliding window and dynamic metric encoding. The new window scheme combines dummy metric calculation and border metric storing methods to halve the border metric memory and improve the error-correcting performance for multi-rate codes. The dynamic encoding of metrics also significantly reduces the border metric memory without degrading the performance. Employing the two proposed methods reduces the conventional border metric memory by 83%. In addition, the superb error-correcting performance of the proposed method is verified for various code rates by conducting intensive simulations for 3GPP LTE codes.
Vehicular Communications: Survey and Challenges of Channel and Propagation Models

Vehicular communication is characterized by a dynamic environment, high mobility, and comparatively low antenna heights on the communicating entities (vehicles and roadside units). These characteristics make vehicular propagation and channel modeling particularly challenging. In this article, we classify and describe the most relevant vehicular propagation and channel models, with a particular focus on the usability of the models for the evaluation of protocols and applications. We first classify the models based on the propagation mechanisms they employ and their implementation approach. We also classify the models based on the channel properties they implement and pay special attention to the usability of the models, including the complexity of implementation, scalability, and the input requirements (e.g., geographical data input). We also discuss the less-explored aspects in vehicular channel modeling, including modeling specific environments (e.g., tunnels, overpasses, and parking lots) and types of communicating vehicles (e.g., scooters and public transportation vehicles). We conclude by identifying the underresearched aspects of vehicular propagation and channel modeling that require further modeling and measurement studies.
Training is an investment with return in temporary workers: A social exchange perspective

Purpose – The purpose of this paper is to analyse whether a social exchange relationship between temporary workers and organizations is possible. The authors aim to consider whether, when training is perceived by an employee as an organizational practice that promotes his or her employability, this entails a social exchange relationship.Design/methodology/approach – Surveys from 240 call centre workers were analyzed using correlation and multiple regression to explore relationships between training to promote employability, perceived organizational support (POS) and affective commitment.Findings – The data support the idea that social exchange theories are useful frameworks in explaining temporary workers' affective commitment towards organisations. Organisational investment in training was positively related to the affective commitment of these temporary workers. However, employees attributed greater importance to the fact that training increased their employability than to the number of training hours r.
The Relationship between Personality Traits, Goal Orientation, and Preferred Paths to Value Creation: The Case of Latent Entrepreneurs.

This study examined the relationship between personality and the preferences expressed by latent entrepreneurs amongst different ways of creating value. Latent entrepreneurs are individuals who would prefer to be an entrepreneur rather than a salaried employee. Latent entrepreneurs take all the first time decisions on entering entrepreneurship and their entry choices have been linked in the literature to their expressed preferences. The study addressed the personality-value creation relationship through two goals. The first addressed the personality-value creation preference relationship directly. Value creation was operationalized using the Competing Values Model (Quinn & Rohrbaugh, 1983). Each approach to value creation was regressed on hypothesized personality traits. It was found that a different, hypothesized, personality trait was associated primarily with each of the personality-value creation relationships. The second goal, based on theoretical insights by Schneider et al. (1995) and Schein (2004) tested the role of goal orientation as a possible mediator of the personality-value creation relationship. Three of the four goal orientations of contemporary goal orientation theory (Elliot & McGregor, 2001) were found to mediate the different personality-value creation relationships. The study represents a break with traditional personality research in entrepreneurship, which focuses on the entrepreneur rather than on the venture the entrepreneur creates. The theoretical and practical implications of this different approach are discussed. THE RELATIONSHIP BETWEEN PERSONALITY TRAITS, GOAL ORIENTATION, AND PREFERRED .
Social Exclusion in Great Britain

Towards an empirical operationalization of social exclusion The operationalization of social exclusion: theoretical and policy approaches Developing a set of quantitative indicators of social exclusion for Great Britain Investigating the multi-dimensional nature of social exclusion in Great Britain Investigating the longitudinal nature of social exclusion in Great Britain Identifying social exclusion in Great Britain during the 1990s Social exclusion in Europe: comparing the UK to other European Union Member States Operationalizing social exclusion: implications for research and policy Bibliography Appendices Index.
Collagenase chemonucleolysis versus percutaneous endoscopic discectomy for extraforaminal lumbar disc herniations

Objective: To compare the advantages and disadvantages of collagenase chemonucleolysis and percutaneous endoscopic discectomy (PED) in the management of extraforaminal lumbar disc herniation. Methods: In this non-randomized controlled clinical trial, a total of 49 patients who were diagnosed with extraforaminal lumbar disc herniation were assigned to undergo either PED (n=22) or collagenase chemonucleolysis (n=27). The primary outcomes were pain improvements (VAS scores), therapeutic efficacy (improved MacNab criteria) and the incidence of complications within 6 months after operation; and the secondary outcomes included intraoperative pain symptoms, operation duration, the time for postoperative bed rest and the costs for hospitalization. Results: The preoperative basic information was similar among the patients in both groups (P>0.05). Besides, no significant differences in postoperative Visual Analogue Scale (VAS) score at two weeks, three months, and six months, as well as in the postoperative therapeutic efficacy at six months respectively were found between both groups (P>0.05). Neither groups had severe complications (P>0.05). The patients with collagenase chemonucleolysis had longer bed rest duration, but fewer costs for hospitalization, shorter operation time, less intraoperative pain compared with the PED patients (P<0.001). Conclusion: Collagenase chemonucleolysis is safe and effective for extraforaminal lumbar disc herniations, and has the advantages of immediate relief of intraoperative pain, reduced costs for hospitalization, and simpler operation.
2 Microcircuit of the Superior Colliculus A Neuronal Machine that Determines Timing and Endpoint of Saccadic Eye Movements

The superior colliculus (SC) plays a key role in controlling the timing and endpoints of saccadic eye movements. Although the activity of collicular neurons in awake animals and anatomical connection with other CNS structures have been intensively studied, information processing in the local circuits of the superior colliculus is only poorly understood. During the last decade, however, whole-cell patch clamp recording techniques have been introduced in slice preparation in combination with intracellular staining technique as a powerful tool for studying the intrinsic circuitry and biophysical properties of neurons in the local circuits of the SC. Ongoing in vitro studies are giving us definitive descriptions on the operation of the local circuits, which could never be obtained by conventional techniques. In this chapter, we summarize the current status of in vitro approaches to the SC functions and speculate about how research that combines the in vitro and in vivo preparations will facilitate further understanding of the oculomotor control.
The role of women in decision-making positions: the case of Israeli sport organisations

This thesis analyses discourses about the roles and barriers to access for women to decision-making positions in Israeli sport organisations. In particular it focuses on the exploration of discourses of masculinity and femininity that underpin the relatively recent construction of Israel society and the institutions of sport within it. It is observed that for the most part, Israeli sport organisations are governed by men and have served the interests of forms of hegemonic masculinity. In order to understand and explore the social construction of these gendered discourses in Israeli sport, two innovative and significant policy initiatives toward gender equity in sport were explored through the perceptions and discourses of key actors. These include the establishment of a Volleyball Academy for Young Talented Girls (VAYTG) and the creation of the National Project for Women and Sport (NPWS). The theoretical framework for this thesis is informed by poststructuralist feminism, which provided an alternative way to understand and analyse voices of the (predominantly female) 'other' and thus to explore the historical contextual construction of current discourses of masculinity within Israeli sport organisations and society as a whole. The process of narrative revisions and production of gendered knowledge revealed how discourses produce and reinforce gender inequities in Israeli society, such as the discourse of militarisation or the unique political affiliation system in the sporting arena which continue to implicitly exclude women (and some men) from gaining access to leadership positions in sport organisations. Within this theoretical frame, Critical Discourse Analysis was employed as a methodological approach to analyse how female and male interviewees, all considered to be 'insiders' within their organisations, explained the process of the construction of gendered roles and barriers. Included in the interview data was also the auto-ethnographical accounts of the author, who was a primary actor in the process of developing policy in the two case study initiatives addressed. Dominant discourses of femininity (such as the discourse of sisterhood and of the processes of mentoring), and of masculinity (and how these promote uniformity) were identified as mechanisms for reproducing the gendered reality of sport leadership in Israel. The implication of a critical theoretical approach is that it should be emancipatory in its ambitions and impact, and the study is intended to contribute to enhancing the understanding of how discourse not only reflects but also creates barriers and opportunities so that the construction of such barriers can be challenged in progressive policy discourses.
Chemical Blocking of Zinc Ions in CNS Increases Neuronal Damage Following Traumatic Brain Injury (TBI) in Mice

Background Traumatic brain injury (TBI) is one of the leading causes of disability and death among young people. Although much is already known about secondary brain damage the full range of brain tissue responses to TBI remains to be elucidated. A population of neurons located in cerebral areas associated with higher cognitive functions harbours a vesicular zinc pool co-localized with glutamate. This zinc enriched pool of synaptic vesicles has been hypothesized to take part in the injurious signalling cascade that follows pathological conditions such as seizures, ischemia and traumatic brain injury. Pathological release of excess zinc ions from pre-synaptic vesicles has been suggested to mediate cell damage/death to postsynaptic neurons. Methodology/Principal Findings In order to substantiate the influence of vesicular zinc ions on TBI, we designed a study in which damage and zinc movements were analysed in several different ways. Twenty-four hours after TBI ZnT3-KO mice (mice without vesicular zinc) were compared to littermate Wild Type (WT) mice (mice with vesicular zinc) with regard to histopathology. Furthermore, in order to evaluate a possible neuro-protective dimension of chemical blocking of vesicular zinc, we treated lesioned mice with either DEDTC or selenite. Our study revealed that chemical blocking of vesicular zinc ions, either by chelation with DEDTC or accumulation in zinc-selenium nanocrystals, worsened the effects on the aftermath of TBI in the WT mice by increasing the number of necrotic and apoptotic cells within the first 24 hours after TBI, when compared to those of chemically untreated WT mice. Conclusion/Significance ZnT3-KO mice revealed more damage after TBI compared to WT controls. Following treatment with DEDTC or selenium an increase in the number of both dead and apoptotic cells were seen in the controls within the first 24 hours after TBI while the degree of damage in the ZnT3-KO mice remained largely unchanged. Further analyses revealed that the damage development in the two mouse strains was almost identical after either zinc chelation or zinc complexion therapy.
An integrated global model of present‐day plate motions and plate boundary deformation

SUMMARY In this paper we present a global model (GSRM-1) of both horizontal velocities on the Earth’s surface and horizontal strain rates for almost all deforming plate boundary zones. A model strain rate field is obtained jointly with a global velocity field in the process of solving for a global velocity gradient tensor field. In our model we perform a least-squares fit between model velocities and observed geodetic velocities, as well as between model strain rates and observed geological strain rates. Model velocities and strain rates are interpolated over a spherical Earth using bi-cubic Bessel splines. We include 3000 geodetic velocities from 50 different, mostly published, studies. Geological strain rates are obtained for central Asia only and they are inferred from Quaternary fault slip rates. For all areas where no geological information is included a priori constraints are placed on the style and direction (but not magnitude) of the model strain rate field. These constraints are taken from a seismic strain rate field inferred from (normalized) focal mechanisms of shallow earthquakes. We present a global solution of the second invariant of the model strain rate field as well as strain rate solutions for a few selected plate boundary zones. Generally, the strain rate tensor field is consistent with geological and seismological data. With the assumption of plate rigidity for all areas other than the plate boundary zones we also present relative angular velocities for most plate pairs. We find that in general there is a good agreement between the present-day plate motions we obtain and longterm plate motions, but a few significant differences exist. The rotation rates for the Indian, Arabian and Nubian plates relative to Eurasia are 30, 13 and 50 per cent slower than the NUVEL1A estimate, respectively, and the rotation rate for the Nazca Plate relative to South America is 17 per cent slower. On the other hand, Caribbean‐North America motion is 76 per cent faster than the NUVEL-1A estimate. While crustal blocks in the India‐Eurasia collision zone move significantly and self-consistently with respect to bounding plates, only a very small motion is predicted between the Nubian and Somalian plates. By integrating plate boundary zone deformation with the traditional modelling of angular velocities of rigid plates we have obtained a model that has already been proven valuable in, for instance, redefining a no-net-rotation model of surface motions and by confirming a global correlation between seismicity rates and tectonic moment rates along subduction zones and within zones of continental deformation.
Elegant : a flexible SDDS-compliant code for accelerator simulation.

ELEGANT (ELEctron Generation ANd Tracking) is the principle accelerator simulation code used at the Advanced Photon Source (APS) for circular and one-pass machines. Capabilities include 6-D tracking using matrices up to third order, canonical integration, and numerical integration. Standard beamline elements are supported, as well as coherent synchrotron radiation, wakefields, rf elements, kickers, apertures, scattering, and more. In addition to tracking with and without errors, ELEGANT performs optimization of tracked properties, as well as computation and optimization of Twiss parameters, radiation integrals, matrices, and floor coordinates. Orbit/trajectory, tune, and chromaticity correction are supported. ELEGANT is fully compliant with the Self Describing Data Sets (SDDS) file protocol, and hence uses the SDDS Toolkit for pre- and post-processing. This permits users to prepare scripts to run the code in a flexible and automated fashion. It is particularly well suited to multistage simulation and concurrent simulation on many workstations. Several examples of complex projects performed with ELEGANT are given, including top-up safety analysis of the APS and design of the APS bunch compressor.