Miracle-dz/UniFAR-FTUs huggingface dataset:
Leveraging heterogeneous network embedding for metabolic pathway prediction

Metabolic pathway reconstruction from genomic sequence information is a key step in predicting regulatory and functional potential of cells at the individual, population and community levels of organization. Although the most common methods for metabolic pathway reconstruction are gene-centric e.g. mapping annotated proteins onto known pathways using a reference database, pathway-centric methods based on heuristics or machine learning to infer pathway presence provide a powerful engine for hypothesis generation in biological systems. Such methods rely on rule sets or rich feature information that may not be known or readily accessible. Here, we present pathway2vec, a software package consisting of six representational learning based modules used to automatically generate features for pathway inference. Specifically, we build a three layered network composed of compounds, enzymes, and pathways, where nodes within a layer manifest inter-interactions and nodes between layers manifest betweenness interactions. This layered architecture captures relevant relationships used to learn a neural embedding-based low-dimensional space of metabolic features. We benchmark pathway2vec performance based on node-clustering, embedding visualization and pathway prediction using MetaCyc as a trusted source. In the pathway prediction task, results indicate that it is possible to leverage embeddings to improve pathway prediction outcomes. Availability and implementation The software package, and installation instructions are published on github.com/pathway2vec Contact shallam@mail.ubc. ca
An empirical analysis of research paradigms within international human resource management: The need for more diversity

The goal of this article is to provide a fine-grained analysis of international human resource management research that addresses the different perspectives applied in that research. We coded 203 peer-reviewed international human resource management articles published between 2011 and 2018 with content analytical methods guided by the compass of management research developed by Sieben, which is rooted in critical management research. We were particularly attentive to the various discursive orientations international human resource management scholars have adopted, including ideologically critical, poststructuralist, functionalist and interpretive perspectives. We further examined which methods, theoretical perspectives and topics were common within and across different perspectives. This analysis indicated that critical research intending to politicize and question existing structures and ways of organizing is still marginal. Along with the dominance of functionalist and interpretive studies, papers in our dataset commonly use a strategic human resource perspective, are predominantly interested in the human resource management–performance link and focus rather narrowly on multinational corporations and expatriates. Furthermore, while international human resource management scholars increasingly account for the contextual embeddedness of organizations through macro-level theories, they mainly apply institutional perspectives that view organizations as adapting to institutional constraints. We propose a more diverse and reflexive approach – inspired by ideologically critical and poststructuralist perspectives – that may help to overcome these blind spots. Such an approach might, for instance, look at types of organizations other than multinational corporations and individuals other than highly skilled expatriates and might explicitly bring multiple, external stakeholders into the picture. We conclude by suggesting that international human resource management research and practice would benefit from more research diversity which enables more holistic analyses of phenomena, more innovative research and resultant insights, and more space for meta-theoretical reflections.
Asymmetric relationships between El Niño/La Niña and floods/droughts in the following summer over Chongqing, China

ABSTRACT This study presents a detailed analysis of the asymmetric relationships between the warm/cold phase of the El Niño–Southern Oscillation and the typical flood/drought years in summer over Chongqing. Furthermore, its underpinning mechanisms are also explored. The results show that: (1) El Niño and La Niña have an asymmetric influence on summer precipitation in the following year over Chongqing. Generally, the composite atmospheric circulation anomalies for El Niño years are consistent with the composite results for typical flood years in summer over Chongqing, which indicates a tight link between typical flood years in summer over Chongqing and El Niño events. However, the relationship between typical drought years in summer over Chongqing and La Niña events is not significant. (2) From winter to the following summer, the extent of positive SST anomalies in the equatorial eastern Pacific associated with typical flood years in summer over Chongqing shrinks, whereas in the tropical Indian Ocean, the extent slightly expands. This trend indicates that the impact of El Niño on typical flood years in summer over Chongqing is maintained through the ‘relay effect’ of SSTs in the tropical Indian Ocean, which is the result of a lagged response of positive SST anomalies in the tropical Indian Ocean to El Niño events in winter. GRAPHICAL ABSTRACT
Komplikationen bei rheumachirurgischen Eingriffen der Schulter

Zusammenfassung Das Schultergelenk ist bei der rheumatoiden Arthritis häufig mitbefallen. Aufgrund seines komplexen Aufbaus führt der rheumatische Befall früh zu Funktionsstörungen, die aber subjektiv oft erst spät empfunden werden. Arthroskopische Eingriffe weisen eine geringe Komplikationsrate auf. Rotatorenmanschettenrekonstruktionen führen aufgrund der rheumatisch bedingten Veränderungen des Muskel- und Sehnengewebes häufig zu Rerupturen. Die endoprothetische Versorgung wird bei der rheumatisch stark veränderten Schulter durch die entzündlichen Gewebsveränderungen erschwert. Periprothetische Frakturen treten aufgrund der verminderten Knochenqualität auf und sind nur erschwert osteosynthetisch zu versorgen. Multipler Gelenkersatz erfordert hierbei mitunter individuelle Lösungsmöglichkeiten. Protheseninfekte an der Schulter sind schwerwiegende Komplikationen und bedürfen einer frühzeitigen Diagnosestellung und operativer Revision.
Soil Available Phosphorus Loss Caused by Periodical Understory Management Reduce Understory Plant Diversity in a Northern Subtropical Pinus massoniana Plantation Chronosequence

Clearing of understory plants is a common management method in plantation forests, but its long-term impact on soil properties and understory plant diversity is still poorly understood. In order to uncover the potential relationship between understory diversity and soil properties, we categorized understory plants into herbs and shrubs, and took soil depth into consideration. We measured the soil variables and investigated the understory plant diversity in four stand age-classes (9-year-old for young, 18-year-old for intermediate, 28-year-old for near-mature, and 48-year-old for mature) in a Pinus massoniana plantation. We aimed to examine how the diversity of herbs and shrubs changed with stand succession and to determine which of the three soil depths (0–10 cm, 10–20 cm, 20–40 cm) had the strongest explanation for the understory plant diversity. Furthermore, structural equation modeling (SEM) was performed to assess the direct and indirect effect of understory clearing and stand age on understory diversity. We found that understory clearing influenced the trend of diversity of herbs and shrubs with stand age, and understory diversity showed a strong correlation with soil physical properties in all three soil layers. The soil properties in the 10–20 cm soil layer related with the diversity of herbs and shrubs most, while the 20–40 cm soil layer properties related with them the least. Understory clearing reduced soil available phosphorus (AP). Understory clearing and stand age were found to benefit understory plant diversity directly and decreased the understory diversity indirectly via AP. Consequently, to improve our understanding of the impact of understory clearing and stand age on biodiversity, we should take into account its direct and indirect effects.
Kardiochirurgia wad wrodzonych Transfusion-free anatomical correction of transposition of the great arteries (dTGA) in a 4.4-kg neonate

Operacje na otwartym sercu bez u¿ycia preparatów krwiopochodnych s1 przeprowadzane z powodzeniem u doros3ych od lat 60. poprzedniego stulecia [1]. Jednak¿e taka procedura u noworodka nadal stanowi wyzwanie dla zespo3u podejmuj1cego siê korekcji z3o¿onej wady serca, wymagaj1cej u¿ycia kr1¿enia pozaustrojowego (CPB) i w wielu przypadkach koñczy siê podaniem preparatu krwi po zakoñczeniu CPB [2, 3]. Szczególna trudnoœæ dotyczy tych wad serca, których ca3kowita korekcja wi1¿e siê z du¿1 œródi pooperacyjn1 utrat1 krwi. Czynnikami zwiêkszaj1cymi to ryzyko s1 m.in. d3ugi czas CPB, koniecznoœæ przeprowadzenia korekcji w pierwszych dniach ¿ycia bez mo¿liwoœci uprzedniego przygotowania pacjenta oraz niska masa operowanego dziecka [4]. Efektem mo¿e byæ nadmierna hemodylucja, a nastêpnie zwiêkszenie ryzyka krwawieñ pooperacyjnych, obni¿enia ciœnienia onkotycznego krwi z zatrzymaniem p3ynu w przestrzeni pozanaczyniowej oraz powik3ania neurologiczne [5]. Do wad serca obarczonych wieloma czynnikami ryzyka krwawienia œródi pooperacyjnego nale¿y prze3o¿enie wielkich naczyñ (dTGA). Korekcja ca3kowita tej wady wi1¿e siê z podaniem preparatów krwiopochodnych (koncentratu krwinek czerwonych, pe3nej krwi), nie tylko do primingu CPB, ale równie¿ pooperacyjnie, w celu utrzymania odpowiednio wysokiego ciœnienia krwi, a u 1/5 pacjentów, ze wzglêdu na wysokie ryzyko krwawienia, zachodzi równie¿ potrzeba podania koncentratu krwinek p3ytkowych [6]. Mimo wielu niebezpieczeñstw, jakie niesie za sob1 wykonanie korekcji wady serca u noworodka bez u¿ycia preparatów krwiopochodnych, œwiadomoœæ skutków ubocznych stosowania transfuzji krwi oraz przekonania religijne, Streszczenie
Circuito Cuántico Shor Qiskit

Quantum computing is a dynamic and exciting field of research that brings together the knowledge of various disciplines, including quantum physics, computer science and the classical theory of complexity. During the 1980s, David Deutsch's work helped define the theory of quantum computing. Currently, IBM has a real quantum computer. In this article, the IBM QISK platforms were used to implement the Shor algorithm from scratch. This algorithm allows primary factorization. This algorithm was taken as a reference, because it has been highly criticized in the literature for showing the supposed intractability of the factorization and the universal applicability of the theory of classical complexity, in addition to questioning the non-reversible safety of current encryption methods.
Exploring victims’ interactions with the criminal justice system. A literature review.

This project brings together a body of evidence on best practices that help to increase victim satisfaction, enhance victim wellbeing and encourage victims to participate in, or stay involved with, the criminal justice process. It is hoped that the review will provide stakeholders with a deeper understanding of victim interactions with the criminal justice system and an evidence base that can be used to enhance victims’ experiences within the criminal justice system. The review will also constitute a valuable resource for researchers and act as a springboard for future empirical research on best practice in this area.
Assessment of Joint Parameters in a Kinect Sensor Based Rehabilitation Game

A Kinect sensor based basketball game is developed for delivering post-stroke exercises in association with a newly developed elbow exoskeleton. Few interesting features such as audio-visual feedback and scoring have been added to the game platform to enhance patient’s engagement during exercises. After playing the game, the performance score has been calculated based on their reachable points and reaching time to measure their current health conditions. During exercises, joint parameters are measured using the motion capture technique of Kinect sensor. The measurement accuracy of Kinect sensor is validated by two comparative studies where two healthy subjects were asked to move elbow joint in front of Kinect sensor wearing the developed elbow exoskeleton. In the first study, the joint information collected from Kinect sensor was compared with the exoskeleton based sensor. In the next study, the length of upperarm and forearm measured by Kinect were compared with the standard anthropometric data. The measurement errors between Kinect and exoskeleton are turned out to be in the acceptable range; 1% for subject 1 and 0.44% for subject 2 in case of joint angle; 5.55% and 3.58% for subject 1 and subject 2 respectively in case of joint torque. The average errors of Kinect measurement as compared to the anthropometric data of the two subjects are 16.52% for upperarm length and 9.87% for forearm length. It shows that Kinect sensor can measure the activity of joint movement with a minimum margin of error.
Estimation of causal continuous‐time autoregressive moving average random fields

We estimate model parameters of Lévy‐driven causal continuous‐time autoregressive moving average random fields by fitting the empirical variogram to the theoretical counterpart using a weighted least squares (WLS) approach. Subsequent to deriving asymptotic results for the variogram estimator, we show strong consistency and asymptotic normality of the parameter estimator. Furthermore, we conduct a simulation study to assess the quality of the WLS estimator for finite samples. For the simulation, we utilize numerical approximation schemes based on truncation and discretization of stochastic integrals and we analyze the associated simulation errors in detail. Finally, we apply our results to real data of the cosmic microwave background.
Changes in the Gait Pattern of Hemiparetic Patients with Subacute Basal Ganglia Stroke: a Retrospective Study

Objectives: This study observed changes in gait pattern according to the motor grade of the paretic lower limb in patients with basal ganglia stroke who are in the subacute phase. Methods: We used the Manual Muscle Test (MMT) to evaluate the motor grade of the paretic lower limb of 21 patients with subacute basal ganglia stroke and then divided them into two groups based on the MMT results. Stroke patients with a motor grade above Gr. III were put in group I (15 people) and those with a grade less than Gr. III in group II (6 people). We also estimated spatiotemporal factors using treadmill gait analysis equipment. The values were gait velocity, step length, step time, double support phase, and cadence. The first measure was conducted during the early period of admission and the second was between four and five weeks after admission. Results: In Group I, the gait velocity and step length of both legs significantly increased. In Group II, the step length and step time of the paretic side and the gait velocity tended to decrease, but not significantly. The step length of the paretic side in Group II was significantly longer than that in Group I at the first measure. The step time of the paretic side in Group I was significantly shorter than that in Group II and gait velocity and cadence in Group I were significantly higher than in Group II at the second measure. Conclusions: The gait parameters of all stroke patients improved in terms of time. In addition, the changes in gait pattern were different depending on the motor grade of the paretic lower limb.
Actual role of ERCP in a diagnostic and therapeutically algorithm in a in some biliary tract disease

Жлъчнокаменната болест е сред най-често срещаните заболявания у човека. Лечението й включва холецистектомия с отстраняване на жлъчния мехур и всички конкременти, вкл. и тези в билиарния тракт. 10-25% от случаите на холелитиаза се съпътстват от холедохолитиаза. Навлизането на лапароскопската холецистектомия изисква надежден метод за преоперативна идентификация на болните с холедохолитиаза. Конкременти, задържани в жлъчните пътища след холецистектомия са чест проблем. Индикациите за ендоскопската ретроградна холангиопанкреатография /EРХПГ/ след холецистекомия включват съмнение за некоригирана дуктална патология (камък или папиларна стеноза), ятрогенна увреда на жлъчни пътища или неоткрит процес (напр. панкреасен тумор). EРХПГ с екстракция на конкремент са ефикасни в 90% от случаите с холедохолитиаза след холецистектомия и затова са предпочитан метод. Билиарните неоплазми са честа причина за иктер. EРХПГ осигурява информация относно необходимостта от отворена хирургична намеса или палиативна ендоскопска интервенция (протезиране). При пациенти с холангит EРХПГ идентифицира причините за обструкция и дава възможност за интервенционално лечение. При болни с ампуларни стенози EРХПГ помага за прецизиране на анатомията на жлъчните пътища и установяване на допълнителни фактори, напр. холангиолитиаза или други заболявания. При повечето случаи методът позволява дефинитивна диагноза. Сфинктеротомия при такива пациенти преодолява стенозата и най-често води до подобряване на клиничната симптоматика.
Criterios de éxito y fracaso en implantes dentales Óseointegrados

espanolActualmente los implantes dentales oseointegrados constituyen una alternativa terapeutica para la restauracion de los dientes perdidos por diferentes causas. La aparicion de multiples sistemas de implantes y su uso en la poblacion hace necesario el empleo de un grupo de criterios para poder predecir el exito o fracaso de las restauraciones implantosoportadas. Cada paciente debe conocer los riesgos y beneficios del procedimiento asi como una prediccion del tiempo de vida de la restauracion implantosoportada. La aplicacion clinica de algunos parametros e indices dan sustento a la utilizacion adecuada de los criterios de exito y fracaso. EnglishAt the moment osseointegrated dental implants constitute a therapeutic alternative for the restoration of the lost teeth by different causes. The appearance of multiple systems of dental implants and its use in the population makes the use necessary of a group of criteria to be able to predict the success or failure of the implant-supported restorations. Each patient must know the risks and benefits the procedure as well as a weather forecast of life of the implant-supported restoration. The clinical application of some parameters and indices gives to sustenance to the suitable use of the success criteria and failure.
Temporal changes in distributions and the species atlas: How can British and Irish plant data shoulder the inferential burden?

Species distribution atlases often rely on volunteer effort to achieve their desired coverage, an activity now typically discussed, at least in academia, under the general theme of “citizen science”. Such data, however, are rarely without complex biases, particularly with respect to the estimation of trends in species’ distributions over many decades. The data of the Botanical Society of Britain and Ireland (BSBI) are no exception to this, and both careful thought in data aggregation (spatial, temporal, and taxonomic) and appropriate modelling procedures are required to overcome these challenges. We discuss these issues, with a primary focus on the statistical models that have been put forward to adjust for such biases. Such models include the Telfer method, various “reporting rate” approaches based on generalised linear models, the frequency scaling using local occupancy (“Frescalo”) model, occupancy models, and spatial smoothing methods. In each case the strengths and limitations in relation to estimating trends from distribution data with important time-varying biases are assessed. Various properties of BSBI data, in particular the increasing numbers of records at fine spatial and temporal scales over the past century, coupled with a general lack of re-visits to sites at such finer scales and the time-varying biases previously mentioned, imply that methods that can be sensibly applied at coarser levels are likely to be most appropriate for estimating accurate long-term trends in distributions. We conclude that Frescalo, which can be seen as a type of occupancy model where an adjustment for overlooked species is made in relation to spatial rather than temporal replication, whilst simultaneously adjusting for variable regional effort, is currently the most sophisticated tool for achieving this. Although recording community-accepted adjustments to data collection practices may allow for a greater application of occupancy modelling or other approaches in the future, methods that seek accurate trends over the long-term are necessarily limited either to scales at which various properties of the data in hand are most likely to be unbiased, or at which the biases are well enough understood to be modelled accurately.
Perspectives of teachers, children, and parents on the transition to first grade

This research is a case study of a school that sought to ascertain what is required for the optimal adjustment of children to first grade from the perspective of each partner in the education triad – children, parents, and the teaching staff (teachers and assistant teachers). The research tools adapted to the participants are open-ended questionnaires to elicit the perspectives of the parents and teaching staff, and interviews of the children following their creation of a metaphorical collage to elicit their perspectives. Participants were three first-grade teachers, the assistant first-grade teacher, ten children from one of the first-grade classes, and twelve parents of these children. All the children attend a regional primary school and come from [cooperative Israeli settlements in central Israel. The findings indicate that the emotional climate of the school was regarded as positive by all the respondents. Although all respondents expressed a desire for more inter-personal communication with each other, the expectations of parents and teachers differed with respect to the desired frequency and setting limits on the communication between them. The paper also describes changes instituted to improve communication between the school and the parents in light of the research findings.