Miracle-dz/UniFAR-FTUs huggingface dataset:
Construction and Analysis of Siberian Tiger Bacterial Artificial Chromosome Library with Approximately 6.5-Fold Genome Equivalent Coverage

Bacterial artificial chromosome (BAC) libraries are extremely valuable for the genome-wide genetic dissection of complex organisms. The Siberian tiger, one of the most well-known wild primitive carnivores in China, is an endangered animal. In order to promote research on its genome, a high-redundancy BAC library of the Siberian tiger was constructed and characterized. The library is divided into two sub-libraries prepared from blood cells and two sub-libraries prepared from fibroblasts. This BAC library contains 153,600 individually archived clones; for PCR-based screening of the library, BACs were placed into 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 116.5 kb, representing approximately 6.46 genome equivalents of the haploid genome and affording a 98.86% statistical probability of obtaining at least one clone containing a unique DNA sequence. Screening the library with 19 microsatellite markers and a SRY sequence revealed that each of these markers were present in the library; the average number of positive clones per marker was 6.74 (range 2 to 12), consistent with 6.46 coverage of the tiger genome. Additionally, we identified 72 microsatellite markers that could potentially be used as genetic markers. This BAC library will serve as a valuable resource for physical mapping, comparative genomic study and large-scale genome sequencing in the tiger.
Assessment the effects of land use changes on soil physicochemical properties in Jafarabad of Golestan province, Iran

Land use changes from natural ecosystems into managed ecosystems resulted in negative effects on soil structure and quality. The main objective of this study was to determine the effects of different land-use types on physicochemical properties of soils in Jafarabad region, Northern Iran. Land use systems including natural forest, pastureland and agriculture were identified. Twenty seven of soil samples were collected from the 0-30 cm depth of three different adjacent land uses. The eleven soil physicochemical properties of soil were measured. Land use changes from forest to agriculture resulted in significant decreases in silt contents, aggregate stability, N, P, K and organic matter and with this change, bulk density, sand content and pH was increased significantly. There was no significant change in EC and clay among studied land use types. The results of study showed that forest clearing and subsequently cultivation and tillage practices resulted in the decline of the soil quality and these changes affects on soil sensitivity to degradation and erosion.
Novel flower-shaped albumin particles as controlled-release carriers for drugs to penetrate the round-window membrane

Controlled-release carriers for local drug delivery have attracted increasing attention for inner-ear treatment recently. In this paper, flower-shaped bovine serum albumin (FBSA) particles were prepared by a modified desolvation method followed by glutaraldehyde or heat denaturation. The size of the FBSA particles varied from 10 μm to 100 μm, and most were 50–80 μm. Heat-denatured FBSA particles have good cytocompatibility with a prolonged survival time for L929 cells. The FBSA particles were utilized as carriers to investigate the release behaviors of the model drug – rhodamine B. Rhodamine B showed a sustained-release effect and penetrated the round-window membrane of guinea pigs. We also confirmed the attachment of FBSA particles onto the round-window membrane by microscopy. The FBSA particles, with good biocompatibility, drug-loading capacity, adhesive capability, and biodegradability, may have potential applications in the field of local drug delivery for inner-ear disease treatment.
Flat plate for OAM generation in the millimeter band

The use of electromagnetic waves carrying orbital angular momentum in the radio frequency range is a growing subject, and so is the design of antennas able to produce such waves. The aim of this paper is to present a new type of antenna (a flat plate) in order to generate an electromagnetic wave carrying orbital angular momentum in the millimeter frequency band.
The long-time dynamics of Dirac particles in the Kerr-Newman black hole geometry

We consider the Cauchy problem for the massive Dirac equation in the non-extreme Kerr-Newman geometry outside the event horizon. We derive an integral representation for the Dirac propagator involving the solutions of the ODEs which arise in Chandrasekhar’s separation of variables. It is proved that for initial data in L 1 near the event horizon with L 2 decay at infinity, the probability of the Dirac particle to be in any compact region of space tends to zero as t goes to infinity. This means that the Dirac particle must either disappear in the black hole or escape to infinity.
Doppler Ultrasound

In the typical 2-D echocardiographic image, blood flow is not imaged (cavities and vessels are black; the exception being the spontaneous echo contrast in low flow states). The reason is that the red blood cells are very small and do not offer a reflective surface; instead, they scatter the ultrasound, like the fog is scattering the light. Imaging of blood flow is possible with Doppler ultrasound. The clinical applications of Doppler ultrasound are numerous and very important for the understanding of the circulation physiology and for the evaluation of cardiovascular hemodynamics.
Macro and Micro Paradata for Survey Assessment

At present we typically assess quality by relying heavily on summary process measures or macro paradata that is a by-product of sample selection and survey administration (e.g., item and unit nonresponse rates, response variances, sampling and coverage errors). These measures are an outgrowth of the randomization-based approach to survey sampling that triumphed in government agencies around the world in the two decades after the seminal 1934 paper of Neyman. When most of our present measures were developed, therefore, nonsampling error problems, like nonresponse, were less serious or less well understood. Now there is a widespread belief that the randomization paradigm needs to be replaced by a more explicitly model-based approach that continues to incorporate features like random selection. In this paper we will illustrate how the current macro paradata measures might be revised or reinterpreted in the light of the concerns just mentioned. The changing partnership between data producers and data analyzers also increases the need for a greatly expanded use of micro paradata – i.e., process details known on each case (such as how many attempts it took to get an interview, whether the interview was in English or Spanish, etc.) To illustrative the paper will employ novel macro paradata summaries of coverage and unit nonresponse, plus micro paradata measures of response variation. The examples will all be taken from the National Survey of America’s Families (NSAF) but we believe the perspective we advocate would be actionable in other settings too.
Insulin-mediated GLUT4 Translocation Is Dependent on the Microtubule Network*

The GLUT4 facilitative glucose transporter is recruited to the plasma membrane by insulin. This process depends primarily on the exocytosis of a specialized pool of vesicles containing GLUT4 in their membranes. The mechanism of GLUT4 vesicle exocytosis in response to insulin is not understood. To determine whether GLUT4 exocytosis is dependent on intact microtubule network, we measured insulin-mediated GLUT4 exocytosis in 3T3-L1 adipocytes in which the microtubule network was depolymerized by pretreatment with nocodazole. Insulin-mediated GLUT4 translocation was inhibited by more than 80% in nocodazole-treated cells. Phosphorylation of insulin receptor substrate 1 (IRS-1), activation of IRS-1 associated phosphatidylinositide 3-kinase, and phosphorylation of protein kinase B/Akt-1 were not inhibited by nocodazole treatment indicating that the microtubule network was not required for proximal insulin signaling. An intact microtubule network is specifically required for insulin-mediated GLUT4 translocation since nocodazole treatment did not affect insulin-mediated GLUT1 translocation or adipsin secretion. By using in vitro microtubule binding, we demonstrated that both GLUT4 vesicles and IRS-1 bind specifically to microtubules, implicating microtubules in both insulin signaling and GLUT4 translocation. Vesicle binding to microtubules was not mediated through direct binding of GLUT4 or insulin-responsive aminopeptidase to microtubules. A model microtubule-dependent translocation of GLUT4 is proposed.
Charged-particle distributions in s=13 TeV pp interactions measured with the ATLAS detector at the LHC

Charged-particle distributions are measured in proton–proton collisions at a centre-of-mass energy of 13 TeV, using a data sample of nearly 9 million events, corresponding to an integrated luminosity of 170 μb − 1 , recorded by the ATLAS detector during a special Large Hadron Collider ﬁll. The charged- particle multiplicity, its dependence on transverse momentum and pseudorapidity and the dependence of the mean transverse momentum on the charged-particle multiplicity are presented. The measurements are performed with charged particles with transverse momentum greater than 500 MeV and absolute pseudorapidity less than 2.5, in events with at least one charged particle satisfying these kinematic requirements. Additional measurements in a reduced phase space with absolute pseudorapidity less than 0.8 are also presented, in order to compare with other experiments. The results are corrected for detector effects, presented as particle-level distributions and are compared to the predictions of various Monte Carlo event generators. © 2016 CERN for the beneﬁt of the ATLAS Collaboration. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Funded by SCOAP 3 .
CHILD ADULTS / ADULT CHILDREN: GROWING UP IN KZN.

Although it is acknowledged in the Southern African literature that children living in conditions of poverty have always assumed more household responsibilities, the AIDS epidemic has exacerbated this and significantly changed the nature of childhood as an increasing number of children face life without parents. The study sought to gain insight into the experiential lives of six “child” heads of households and their siblings and to explore, in particular, how they construct their sense of self and family. For the purposes of the study a child-headed household was deemed a household in which a child of 18 or under or still in school was the household head in the absence of any other dependable, permanent adult figure. The study used a narrative approach and thematic analysis and the results emerging from the children‟s accounts of themselves were focused around the core themes of adult responsibility in the absence of adult status and relationships with adults in the extended family and wider community. The idea of children or adolescents competently running households, taking responsibility for themselves and their futures and adopting a more democratic and shared means of decision making, further challenges conventional conceptions of the „borders‟ between childhood and adulthood and family structure that have been contested and shifting through history. However, being on the front line of social change comes at a cost. Challenging society‟s popular understanding of children as passive, dependent and innocent positions these young people outside of the norm and what they report is that they feel alone, unheard and victimised. The findings are discussed within the context of Burman‟s critique of psychology‟s traditional theoretical notions of universal and innately driven development and a re-conceptualisation of children‟s experiences in terms of the context in which they live, and Crossley‟s perspective on narrative which emphasises agency grounded within cultural forms of sense-making. A new way of discussing these unconventionally structured families is also presented through the reconfiguration of relationships between family members, recognising connections that span generations and across different household spaces.
Trauma exposure, posttraumatic stress, and preventive health behaviours: a systematic review

ABSTRACT Psychological trauma has implications for many aspects of physical health, including preventive health behaviours (PHBs). However, whether trauma exposure additionally contributes to PHBs above and beyond the effects of posttraumatic stress disorder (PTSD) symptoms remains unclear. In this systematic review, 32 studies were analysed to characterise: (1) the relationships between trauma exposure and PHBs, (2) the relationships between PTSD symptoms and PHBs, (3) the unique associations between trauma exposure and PHBs, independent of PTSD symptoms, and (4) the unique associations between PTSD symptoms and PHBs, independent of trauma exposure. Findings were variable across the three examined PHBs (physical activity, diet, medical screening) when only trauma exposure or PTSD symptoms were taken into account. Clearer relationships emerged between trauma exposure and PHBs when PTSD symptoms were taken into account, demonstrating that trauma exposure is related to PHB engagement above and beyond the effects of PTSD symptoms. Additionally, PTSD symptoms shared unique associations with physical activity and screening frequency, which were not explained by trauma exposure. Our review reveals that teasing apart the effects of trauma exposure and PTSD symptoms on PHBs brings greater clarity to the strength and direction of these associations.
Investigations of Backscattering Effects in Optical Fibers and Their Influences on the Link Monitoring

In this paper, first, we employed the coupled-mode theory to investigate the backscattering power characteristics of Rayleigh backscattering (RB) and stimulated Brillouin scattering (SBS) both synchronously and precisely. We discovered how the RB and SBS power changed with pump powers and fiber lengths. The scattering power curves with different pump powers could be divided into three regions. The first was called “the linear region of RB,” in which the pump power was mainly converted into RB and the RB power grew linearly with pump powers. The second region was called “the stimulation region of Brillouin scattering,” in which the power was mainly converted into SBS. In “the gain-saturated region,” when the pump power was much higher than the SBS threshold, both the RB and SBS power were gain-saturated. We also obtained the power curves with different fiber lengths. The power curves were helpful to set up proper launch powers in practical engineering applications, such as optical time-dome reflectometry systems and distributed fiber sensors. Then, we verified our theoretical results by experiments. Finally, according to the measurements and numerical solutions of the coupled-mode equations, we discussed the application of backscattering and gave advice for pump power selections in different fiber link monitoring systems.
MALT: distributed data-parallelism for existing ML applications

Machine learning methods, such as SVM and neural networks, often improve their accuracy by using models with more parameters trained on large numbers of examples. Building such models on a single machine is often impractical because of the large amount of computation required. We introduce MALT, a machine learning library that integrates with existing machine learning software and provides data parallel machine learning. MALT provides abstractions for fine-grained in-memory updates using one-sided RDMA, limiting data movement costs during incremental model updates. MALT allows machine learning developers to specify the dataflow and apply communication and representation optimizations. Through its general-purpose API, MALT can be used to provide data-parallelism to existing ML applications written in C++ and Lua and based on SVM, matrix factorization and neural networks. In our results, we show MALT provides fault tolerance, network efficiency and speedup to these applications.
Teachers Caught in the Action: Professional Development That Matters

In their newest volume, Lieberman and Miller enlist a stellar group of contributors to offer - once again - the best of what is known and practiced about professional development in schools. What is the purpose of staff development? What ends does it seek? To answer these often overlooked questions, the editors turn to the distinguished Maxine Greene, Carl D. Glickman, Derrick P. Aldridge, Judith Warren Little, Marilyn Cochran-Smith, and Susan L. Lytle. In opening chapters they remind us that it is essential to tie what we do in staff development to larger goals. Because what we do in staff development can best be understood in terms of Contexts, Strategies, and Structures, the remainder of the book features distinguished educators who write from their own unique experiential and theoretical stances. Jacqueline Ancess describes how teachers in New York City secondary schools increase their own learning while improving student outcomes * Milbrey W. McLaughlin and Joel Zarrow demonstrate how teachers learn to use data to improve their practice and meet educational standards * Lynne Miller presents a case study of a long-lived school-university partnership * Beverly Falk recounts stories of teachers working together to develop performance assessments, to understand their student's learning, to re-think their curriculum, and much more * Laura Stokes analyzes a school that successfully uses inquiry groups. There are further contributions (including some from novice teachers) by Anna Richert Ershler, Ann Lieberman, Diane Wood, Sarah Warshauer Freedman, and Joseph P. McDonald. These powerful exemplars from practice provide a much-needed overview of what matters and what really works in professional development today.
Distinct and separable roles for EZH2 in neurogenic astroglia

The epigenetic mechanisms that enable specialized astrocytes to retain neurogenic competence throughout adult life are still poorly understood. Here we show that astrocytes that serve as neural stem cells (NSCs) in the adult mouse subventricular zone (SVZ) express the histone methyltransferase EZH2. This Polycomb repressive factor is required for neurogenesis independent of its role in SVZ NSC proliferation, as Ink4a/Arf-deficiency in Ezh2-deleted SVZ NSCs rescues cell proliferation, but neurogenesis remains defective. Olig2 is a direct target of EZH2, and repression of this bHLH transcription factor is critical for neuronal differentiation. Furthermore, Ezh2 prevents the inappropriate activation of genes associated with non-SVZ neuronal subtypes. In the human brain, SVZ cells including local astroglia also express EZH2, correlating with postnatal neurogenesis. Thus, EZH2 is an epigenetic regulator that distinguishes neurogenic SVZ astrocytes, orchestrating distinct and separable aspects of adult stem cell biology, which has important implications for regenerative medicine and oncogenesis. DOI: http://dx.doi. org/10.7554/eLife.02439. 001
Expansion of the antimicrobial peptide repertoire in the invasive ladybird Harmonia axyridis

The harlequin ladybird beetle Harmonia axyridis has emerged as a model species in invasion biology because of its strong resistance against pathogens and remarkable capacity to outcompete native ladybirds. The invasive success of the species may reflect its well-adapted immune system, a hypothesis we tested by analysing the transcriptome and characterizing the immune gene repertoire of untreated beetles and those challenged with bacteria and fungi. We found that most H. axyridis immunity-related genes were similar in diversity to their counterparts in the reference beetle Tribolium castaneum, but there was an unprecedented expansion among genes encoding antimicrobial peptides and proteins (AMPs). We identified more than 50 putative AMPs belonging to seven different gene families, and many of the corresponding genes were shown by quantitative real-time RT–PCR to be induced in the immune-stimulated beetles. AMPs with the highest induction ratio in the challenged beetles were shown to demonstrate broad and potent activity against Gram-negative bacteria and entomopathogenic fungi. The invasive success of H. axyridis can therefore be attributed at least in part to the greater efficiency of its immune system, particularly the expansion of AMP gene families and their induction in response to pathogens.
Genome-wide association analysis with matched samples discloses additional novel risk loci

Genome-wide association studies have identified many candidate causal variants associated with common complex diseases and traits, but most of them have been drawn from nonrandomized case/control designs. In nonrandomized experiments, the results drawn from two different groups can be misleading because the units exposed to one group generally differ systematically from the units exposed to the other group. Propensity score is widely used to group case and control units for a more direct and significant comparison even with nonrandomized experiments. This propensity score matching can help with prioritizing additional uncovered variants on disease risk via sub-group analysis in genome-wide association studies. The aim of this work is to propose a post-hoc association test based on the subsets of samples. For that purpose, this paper presents a new paradigm for a post-hoc genome-wide association test when the sample size of controls are larger than that of cases: selecting control samples by equating the distribution of covariates in the case and control groups and re-performing association analysis upon these matched samples. We demonstrated the feasibility of this approach by applying it to 2752 type II diabetes patients in 8842 Korean population. Genome-wide association approach with matched samples is able to disclose 9 additional novel variants and 7 out of 9 have not identified from the association test of whole control samples. The process described here can successfully be combined with other types of case/control studies with large covariate information. This indicates that there a possibility of obtaining additional candidate causal variants responsible for common diseases through genome-wide association analysis with matched samples.
Cooperative Strategies for Improving the Tourism Industry in Remote Geographic Regions: An Addition to Trust and Commitment Theory with one Key Mediating Construct

The success of cooperative relationships is influenced by interorganizational commitment, which is a long‐run goal of networks. Our research examined cooperative relationships in the tourism industry to better understand what makes them successful. The study is an extension of previous empirical research on commitment. The overall research questions were: “What factors lead to interorganizational commitment in remote tourism destinations? ” and “What are the relationships between the factors? ” A literature search was conducted to identify factors related to organizational commitment. Search findings suggested a model proposing that interpersonal commitment mediates the effect of trust and reciprocity on interorganizational commitment. Data for the model was collected from a sample of tourism firms in successful cooperative networks. The theoretical model was purified based on convergent, nomological and discriminant validity as well as construct reliability. Our findings demonstrated that the relationship between trust and interorganizational commitment is in fact mediated by interpersonal commitment. We confirmed that reciprocity is directly related to interorganizational commitment, and is not mediated by interpersonal commitment. Thus, tourism firms should develop cooperative strategies in their networks by focusing on enhancing interpersonal commitment through trust, thereby ultimately helping to strengthen interorganizational commitment.