Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of Human Papillomavirus Genotypes Among Women With High-Grade Cervical Lesions in Beijing, China

Abstract The aim of the study is to investigate the prevalence of high-risk human papillomavirus (hr-HPV) genotypes among Han women with high-grade cervical lesions in Beijing, China. Cervical cell specimens from patients with histopathologically confirmed cervical lesions at 7 hospitals in Beijing were examined with a validated HPV kit for 13 hr-HPV genotypes during the study period. The patients were divided into a low-grade cervical lesions group (cervical intraepithelial neoplasia grade 1, CIN1) and a high-grade cervical lesions group (CIN2+, including cervical intraepithelial neoplasia grade 2, CIN2; cervical intraepithelial neoplasia grade 3, CIN3; squamous cervical cancer, SCC; and adenocarcinoma of the cervix, ACC) based on the histopathology results. A total of 2817 eligible patients were enrolled, including 610 cases identified as CIN1 and 2207 as CIN2+. The hr-HPV positive rates in the CIN1 and CIN2+ groups were 78.2% (477/610) and 93.3% (2060/2207), respectively. The most frequently detected genotypes were HPV16, 58, 52 and18 in the CIN1 group and HPV16, 58, 33, and 52 in the CIN2+ group, in descending order of prevalence. In addition, the prevalence of HPV18 among the patients with ACC was 28.6% (14/49), significantly >7.2% (54/752) prevalence among the SCC patients (P < 0.001). Additionally, significantly more women in the CIN2+ group had multiple infections compared with those in the CIN1 group (38.1% and 24.9%, respectively; P < 0.001). However, as the cervical lesion grade increased, the prevalence of multiple hr-HPV infections gradually deceased to 44.2% in the CIN2 patients, 36.7% in the CIN3 patients, and 35.3% in the cervical cancer (CC) patients, which included SCC and ACC patients. In cases of multiple hr-HPV infections in the CIN2+ group, double infections accounted for ∼76.6%, and HPV16+58, HPV16+52, and HPV16+18 were the most common combinations, in descending order. The most frequent combination for triple infections was HPV16+58+31, with a rate of 4.2%. The highest positive rate occurred in the ⩽24 year-old group for all types of cervical lesions. The prevalence of HPV genotypes in the targeted population with high-grade cervical lesions differs from that of other countries. This information could be helpful for the prevention of CC in Beijing, China.
Hyphal Branching during Arbuscule Development Requires Reduced Arbuscular Mycorrhiza11[OPEN]

A plant transcription factor regulates the expression of genes necessary to enable arbuscular mycorrhizal fungi to develop branched hyphae in root cortical cells. During arbuscular mycorrhizal symbiosis, arbuscule development in the root cortical cell and simultaneous deposition of the plant periarbuscular membrane generate the interface for symbiotic nutrient exchange. The transcriptional changes that accompany arbuscule development are extensive and well documented. By contrast, the transcriptional regulators that control these programs are largely unknown. Here, we provide a detailed characterization of an insertion allele of Medicago truncatula Reduced Arbuscular Mycorrhiza1 (RAM1), ram1-3, which reveals that RAM1 is not necessary to enable hyphopodium formation or hyphal entry into the root but is essential to support arbuscule branching. In ram1-3, arbuscules consist only of the arbuscule trunk and in some cases, a few initial thick hyphal branches. ram1-3 is also insensitive to phosphate-mediated regulation of the symbiosis. Transcript analysis of ram1-3 and ectopic expression of RAM1 indicate that RAM1 regulates expression of EXO70I and Stunted Arbuscule, two genes whose loss of function impacts arbuscule branching. Furthermore, RAM1 regulates expression of a transcription factor Required for Arbuscule Development (RAD1). RAD1 is also required for arbuscular mycorrhizal symbiosis, and rad1 mutants show reduced colonization. RAM1 itself is induced in colonized root cortical cells, and expression of RAM1 and RAD1 is modulated by DELLAs. Thus, the data suggest that DELLAs regulate arbuscule development through modulation of RAM1 and RAD1 and that the precise transcriptional control essential to place proteins in the periarbuscular membrane is controlled, at least in part, by RAM1.
Performance of automated scoring of ER, PR, HER2, CK5/6 and EGFR in breast cancer tissue microarrays in the Breast Cancer Association Consortium

Breast cancer risk factors and clinical outcomes vary by tumour marker expression. However, individual studies often lack the power required to assess these relationships, and large‐scale analyses are limited by the need for high throughput, standardized scoring methods. To address these limitations, we assessed whether automated image analysis of immunohistochemically stained tissue microarrays can permit rapid, standardized scoring of tumour markers from multiple studies. Tissue microarray sections prepared in nine studies containing 20 263 cores from 8267 breast cancers stained for two nuclear (oestrogen receptor, progesterone receptor), two membranous (human epidermal growth factor receptor 2 and epidermal growth factor receptor) and one cytoplasmic (cytokeratin 5/6) marker were scanned as digital images. Automated algorithms were used to score markers in tumour cells using the Ariol system. We compared automated scores against visual reads, and their associations with breast cancer survival. Approximately 65–70% of tissue microarray cores were satisfactory for scoring. Among satisfactory cores, agreement between dichotomous automated and visual scores was highest for oestrogen receptor (Kappa = 0.76), followed by human epidermal growth factor receptor 2 (Kappa = 0.69) and progesterone receptor (Kappa = 0.67). Automated quantitative scores for these markers were associated with hazard ratios for breast cancer mortality in a dose‐response manner. Considering visual scores of epidermal growth factor receptor or cytokeratin 5/6 as the reference, automated scoring achieved excellent negative predictive value (96–98%), but yielded many false positives (positive predictive value = 30–32%). For all markers, we observed substantial heterogeneity in automated scoring performance across tissue microarrays. Automated analysis is a potentially useful tool for large‐scale, quantitative scoring of immunohistochemically stained tissue microarrays available in consortia. However, continued optimization, rigorous marker‐specific quality control measures and standardization of tissue microarray designs, staining and scoring protocols is needed to enhance results.
How Did I Get Here?: The Evolution of Social Network Position Within Firms

Volumes have been written on the subject of innovation, in academic literature as well as the popular press. Conventional wisdom would have one believe that innovation is the purview of the lone inventor at the workbench or the solo scientist huddled over the laboratory microscope. Yet a growing body of literature points to how relationships among actors - be they individuals, teams or entire companies - form the foundations of new knowledge (Hargadon & Sutton 1997; Powell, Koput & Smith-Doerr 1996; Uzzi & Spiro 2005). The most effective networks of relations are those that facilitate the exchange of unique information, often from distinct domains (Fleming 2002; Hargadon 2003). Within those networks, the people best situated to conduct such exchanges possess either large numbers of connections or, more typically, occupy positions as bridges between otherwise disconnected third parties (Burt 1992; Galaskiewicz 1979; Gould & Fernandez 1989). Despite the role social networks may play in fostering innovation, we do not well understand the processes by which actors come to occupy these positions. In this dissertation, I make use of a novel dataset to provide insight into how some people come to occupy certain preferential network position while others do not. Specifically, I study the work-flow network among software engineers at a large, West Coast technology company as defined by the writing and reviewing of lines of code. By following a sample of 804 new entrants to the firm over a period of three years, I am able to trace the evolution of their positions within the larger network and understand the influence of factors present at time of entry.The results of the analyses paint a consistent picture as to the determinants of position in the code review network for software engineers: one's team and one's job at time of entry play the strongest roles in determining one's subsequent centrality and autonomy. I find little to no evidence in support of a role for either intellectual endowment (educational attainment, years of previous work experience, coding ability) or social endowment (pre-employment relationships with other employees present at time of entry). Indeed, while non-significant, results were frequently opposite the hypothesized direction for individual attributes. The strong evidence on the influence of job- and team-related factors suggests that individuals have the greatest opportunity to shape their network positions when they choose their jobs and their managers, and thus their teams. One additional finding suggests that network activity also matters. That is, one can increase both centrality and autonomy through the brute force of writing a great deal of code.
The antecedents and consequences of socializees' adjustment during their organizational assimilation : an integrative study

Abstract of thesis entitled “The Antecedents and Consequences of Socializees' Adjustment During Their Organizational Assimilation: An Integrative Study”of thesis entitled “The Antecedents and Consequences of Socializees' Adjustment During Their Organizational Assimilation: An Integrative Study” Organizational assim ilation (OA) re fers to the process by which socia lizees or employees b ecome integrated into their em ployment or ganization following their organizational entry . Neglecting to assimilate socializees has substantial negativ e consequences, with socializees often poorl y adjusting to their job, role, cultural, and/or psychosocial systems, in turn leading to lower overall j ob satisfaction (OJS), poor overall job performance (OJP), a nd higher turnover intentions (TI). Given its importance, OA phenomenon has attracted the attention of scholars who use m ultiple approaches to address it. The use of m ultiple approaches and the lack of consistency in concept ualizing and m easuring OA adju stment have, ho wever, hampered the development of OA research and practice. This study proposed and tested a ne w mediation model of OA that posits that socializees’ success-related OA consequences (OJS, OJP , and TI) are f unctions of causal antecedents, including organizational socialization tactics (OST) an d core self-ev aluation (CSE), and mediators com prising task m astery, fitting in, standing out, role negotiation, and organizational identification. The study sought to explore and confirm the proposed OA adjustment dimensions from an integrative perspective, and to test the ef fects of the proposed antecedents on the consequences both directly and indirectly. A pilot study and a m ain study were conducted in which respondents filled out self-administered questio nnaires. Ei ght star -rated, m oderately priced, an d luxury hotels participated in the pilot study, yielding 481 usable questionnaire copies, and 19 star-rated luxury hotels participated in the m ain stud y, yielding 704 usa ble copies. Organizational tenures in the m ain stud y were between 1 m onth and 2 y ears. Bootstrap SEM (structural equation modeling) was employed across both samples to develop bot h m easurement and stru ctural m odels. Direct a nd indirect hypotheses among the latent proposed constructs were teste d based on the overall structural model of the main study. The study’s first contribution is the development of a new measurement model of OA adjustment dimensions from an integrative perspective, which contributes new
Browsing large‐scale cheminformatics data with dimension reduction

Visualization of large‐scale high dimensional data is highly valuable for data analysis facilitating scientific discovery in many fields. We present PubChemBrowse, a customized visualization tool for cheminformatics research. It provides a novel 3D data point browser that displays complex properties of massive data on commodity clients. As in Geographic Information System browsers for Earth and Environment data, chemical compounds with similar properties are nearby in the browser. PubChemBrowse is built around in‐house high performance parallel Multi‐dimensional scaling and Generative topographic mapping services and supports fast interaction with an external property database. These properties can be overlaid on 3D mapped compound space or queried for individual points. We prototype the integration with Chem2Bio2RDF system using SPARQL endpoint to access over 20 publicly accessible bioinformatics databases. We describe our design and implementation of the integrated PubChemBrowse application and outline its use in drug discovery. The same core technologies are generally applicable to develop high performance scientific data browsing systems for other applications. Copyright © 2011 John Wiley & Sons, Ltd.
Fast Computation of Electromagnetic Vibrations in Electrical Machines via Field Reconstruction Method and Knowledge of Mechanical Impulse Response

The main objective of this paper is to provide an efficient computational model for fast and accurate calculation of electromagnetically induced vibrations in electrical machines. Although a three-phase permanent-magnet synchronous machine has been used in this paper, the same methodology can be extended to other types of electric machinery. A brief comparison between the different methods for structural analysis in electrical machines is introduced. The method proposed in this paper uses finite-element analysis in order to extract the impulse responses that are used in calculating the vibration. A field reconstruction method is used for the electromagnetic field analysis.
Behavioral Inhibition and Effortful Control: Independent and Interactive Predictors of Child Externalizing Behavior

Externalizing symptoms, such as aggression, impulsivity and inattention, represent the most common forms of childhood maladjustment (Campbell et al., 2000). Mounting evidence and theory strongly suggest that temperament plays an important role in vulnerability to early externalizing symptoms (Muris & Ollendick, 2005). Two dimensions of temperament, behavioral inhibition (BI, Lengua, 2008) and effortful control (EC, Olson et al., 2005) have consistently emerged as predictors of early externalizing problems. However, there have been relatively few attempts to simultaneously examine the main, independent, and interactive contributions of multiple dimensions of temperament on early developing externalizing problems. (Eisenberg et al., 1997). In addition to temperament, several dimensions of parenting during early childhood have been linked to young children’s externalizing problems, both independently and in interaction with child attributes, such as BI and EC (Kiff, Lengua, & Zalewski, 2011). Thus, an additional goal of the current study was to test whether low levels of child BI and EC might amplify the positive association between harsh parenting and children’s later externalizing problems, and whether low levels of child BI and EC might attenuate the negative association between warm parenting and children’s later externalizing problems. Finally, the genetically-informed design of the Early Growth and Development Study also permits exploration of the intergenerational genetic continuity of EC and BI, both of which have shown moderate levels of heritability in prior research (Lemery-Chalfant et al., 2008). The results revealed that higher levels of harsh parenting were linked to higher levels of externalizing problems . In addition, higher levels of warm parenting were linked with lower levels of externalizing problems and on occasion, interactions between EC and BI and warm parenting were found in the development of toddler externalizing problems. Importantly, the current investigation provides support for the notion that parenting behavior assessed in the toddler period, when effects due to genes shared among biologically-related family members are removed, is associated with children’s subsequent externalizing problem behavior at 54 months.
A Scalable Distributed Graph Partitioner

We present Scalable Host-tree Embeddings for Efficient Partitioning (Sheep), a distributed graph partitioning algorithm capable of handling graphs that far exceed main memory. Sheep produces high quality edge partitions an order of magnitude faster than both state of the art offline (e.g., METIS) and streaming partitioners (e.g., Fennel). Sheep's partitions are independent of the input graph distribution, which means that graph elements can be assigned to processing nodes arbitrarily without affecting the partition quality. Sheep transforms the input graph into a strictly smaller elimination tree via a distributed map-reduce operation. By partitioning this tree, Sheep finds an upper-bounded communication volume partitioning of the original graph. We describe the Sheep algorithm and analyze its space-time requirements, partition quality, and intuitive characteristics and limitations. We compare Sheep to contemporary partitioners and demonstrate that Sheep creates competitive partitions, scales to larger graphs, and has better runtime.
Wave-induced drift and mixing

Over the past 10 years, several investigations have revealed that waves dramatically enhance the turbulent mixing near the surface (e.g. Agrawal et al., 1992). Besides, waves are known to have a non-zero mean motion in the direction of propagation: the Stokes drift. In a rotating frame, waves also induce a stress to the right of the direction of propagation: the Hasselmann force or "Stokes-Coriolis" effect. This effect is believed to compensate the Stokes drift by driving the mean flow in the opposite direction, and recent studies have proposed that it significantly modifies the profile of the Eulerian current near the surface (Lewis and Belcher, 2004). To embrace all these effects, a model of the ocean mixed layer is proposed. The motion is separated into a quasi-Eulerian mean flow and the wave-induced Stokes drift. Sigma coordinates are used to follow the surface motion (Mellor, 2003). This yields equations for the mean flow that are compatible to those of ocean-circulation models, with the wave part acting as a supplementary forcing. A 2.5 level turbulence closure scheme is used, in which dissipation of waves enhances turbulent kinetic energy near the surface. The different effects are investigated and the model is validated with measured profiles of turbulent kinetic energy (Terray et al., 1996), shear of Eulerian currents (Santala and Terray, 1992) and Lagrangian surface drifts. The model is generally consistent with all these observation, and suggests that surface drift observations, of the order of 3% of the wind speed, must be related to a strong surface shear that mainly comes from the shear of the Stokes drift. Essentially, a strong surface mixing is incompatible with large surface shears of the quasi-Eulerian velocity. Still, the model mean water velocities are only about 60% of observed drift velocities. The model also suggests a dependence of surface mixing and drift on the state of development of the waves that can be represented by a wave age parameter. It raises the question of the adequacy of parameterisations based on the wind only, as usual in ocean circulation models. We argue for a coupled wave-circulation model, particularly for fetch limited conditions often met in coastal areas, and estimate the likely impact on upwelling-type circulations.
Assistive strategies for people with fine motor skills impairments based on an analysis of sub-movements

Four studies describe the pointing performance of individuals with fine motor skills impairments. First, we describe the pointing performance of two individuals with Parkinsons disease via a sub-movement analysis and compare them with similar results found in the literature from young children and older able-bodied adults. The analysis suggests the need of an individual assessment of pointing difficulties and the personalization of the methods of assistance and motivates sub-sequent studies. Two experiments followed where we tested PointAssist, software that assists in pointing tasks by detecting difficulty through a sub-movement analysis and triggering help, with adjustments proposed to personalize the assistance provided. A within-subjects study with sixteen individuals with fine motor skills impairments resulted in statistically significant effects on accuracy using Friedman's test with (χ2(1) = 6.4, p = . 011) in favor of personalized PointAssist. A five week longitudinal study with three participants with Cerebral Palsy and other fine motor skills impairments shows the long term effects of PointAssist. The longitudinal study logged real-world use of pointing devices validating the results for real-world interactions. PointAssist had statistically significant effect of reduced sub-movement length and speed with p < . 00001 and p < . 0002 respectively for one of the participants. These results suggest better motor control near a target and statistically significant results on the sub-movement duration confirmed this. Finally, we designed, developed and tested a new assistive technology for individuals with severe motor skills impairments that we call the Reverse Funnel. Three participants, two with Cerebral Palsy and one with an undisclosed disability, participated and positive early results are presented as well as future developments of the newly developed strategy.