Miracle-dz/UniFAR-FTUs huggingface dataset:
WordRank: Learning Word Embeddings via Robust Ranking

Embedding words in a vector space has gained a lot of attention in recent years. While state-of-the-art methods provide efficient computation of word similarities via a low-dimensional matrix embedding, their motivation is often left unclear. In this paper, we argue that word embedding can be naturally viewed as a ranking problem due to the ranking nature of the evaluation metrics. Then, based on this insight, we propose a novel framework WordRank that efficiently estimates word representations via robust ranking, in which the attention mechanism and robustness to noise are readily achieved via the DCG-like ranking losses. The performance of WordRank is measured in word similarity and word analogy benchmarks, and the results are compared to the state-of-the-art word embedding techniques. Our algorithm is very competitive to the state-of-the- arts on large corpora, while outperforms them by a significant margin when the training set is limited (i.e., sparse and noisy). With 17 million tokens, WordRank performs almost as well as existing methods using 7.2 billion tokens on a popular word similarity benchmark. Our multi-node distributed implementation of WordRank is publicly available for general usage.
Motor and cognitive outcome in patients with Parkinson's disease 8 years after subthalamic implants

Deep brain stimulation of the subthalamic nucleus represents the most important innovation for treatment of advanced Parkinson’s disease. Prospective studies have shown that although the beneficial effects of this procedure are maintained at 5 years, axial motor features and cognitive decline may occur in the long term after the implants. In order to address some unsolved questions raised by previous studies, we evaluated a series of 20 consecutive patients who received continuous stimulation for 8 years. The overall motor improvement reported at 5 years (55.5% at Unified Parkinson’s Disease Rating Scale—motor part, P50.001 compared with baseline) was only partly retained 3 years later (39%, P50.001, compared with baseline; 16.5%, P50.01, compared with 5 years), with differential effects on motor features: speech did not improve and postural stability worsened (P50.05). The preoperative levodopa equivalent daily dose was reduced by 58.2% at 5 years and by 60.3% at 8 years. In spite of subtle worsening of motor features, a dramatic impairment in functional state (56.6% at Unified Parkinson’s Disease Rating Scale—Activities of Daily Living, P50.01) emerged after the fifth year of stimulation. The present study did not reveal a predictive value of preoperative levodopa response, whereas few single features at baseline (such as gait and postural stability motor scores and the preoperative levodopa equivalent daily dose) could predict long-term motor outcome. A decline in verbal fluency (slightly more pronounced than after 5 years) was detected after 8 years. A significant but slight decline in tasks of abstract reasoning, episodic memory and executive function was also found. One patient had developed dementia at 5 years with further progression at 8 years. Executive dysfunction correlated significantly with postural stability, suggesting interplay between axial motor deterioration and cognition. Eight years after surgery, no significant change was observed on scales assessing depression or anxiety when compared with baseline. At 8 years, there was no significant increase of side-effects when compared with 5-year follow-up. In conclusion, deep brain stimulation of the subthalamic nucleus is a safe procedure with regard to cognitive and behavioural morbidity over long-term follow-up. However, the global benefit partly decreases later in the course of the disease, due to progression of Parkinson’s disease and the appearance of medication- and stimulation-resistant symptoms.
Elemental micro-imaging and quantification of human substantia nigra using synchrotron radiation based x-ray fluorescence—in relation to Parkinson’s disease

Synchrotron radiation based x-ray fluorescence (SRXRF) was applied to the quantitative evaluation of elemental changes in substantia nigra pars compacta (SNc) in Parkinson’s disease (PD) in the framework of a study on the role of chemical elements in the pathophysiology of PD. The analysis was carried out for dopaminergic nerve cells and extraneuronal spaces. The mass fractions of P, S, Cl, K, Ca, Fe, Cu, Zn, Br and Rb were determined. The application of standard samples developed especially for the determination of elemental mass fractions in thin tissue sections using the SRXRF technique is presented. Two-dimensional maps of elemental distribution show that the location of nerve cells in SNc sections is precisely visualized by the high levels of most elements. It was found that statistically significant differences between control and PD neurons are observed for S (p = 0.04), Cl (p = 0.02), Ca (p = 0.08), Fe (p = 0.04) and Zn (p = 0.04). The mass fractions of P (p = 0.08), S (p = 0.07), Cl (p = 0.04), Zn (p = 0.08) and Rb (p = 0.08) in areas outside the nerve cell bodies differed significantly between PD and control groups. A clear cluster separation between the PD nerve cells and neurons representing the control group was noticed. It was found that Cl, Fe, Ca and Zn are the most significant elements in the general discrimination between PD nerve cells and the control. The comparison between the extraneuronal spaces showed that Cl, Fe and Cu differentiate the PD and control group the most. The evident contribution of chemical elements to the pathophysiology of PD was shown.
In Silico Transitions to Multicellularity Ricard Solé

SFI WORKING PAPER: 2014-04-006 SFI Working Papers contain accounts of scientific work of the author(s) and do not necessarily represent the views of the Santa Fe Institute. We accept papers intended for publication in peer-reviewed journals or proceedings volumes, but not papers that have already appeared in print. Except for papers by our external faculty, papers must be based on work done at SFI, inspired by an invited visit to or collaboration at SFI, or funded by an SFI grant. ©NOTICE: This working paper is included by permission of the contributing author(s) as a means to ensure timely distribution of the scholarly and technical work on a non-commercial basis. Copyright and all rights therein are maintained by the author(s). It is understood that all persons copying this information will adhere to the terms and constraints invoked by each author's copyright. These works may be reposted only with the explicit permission of the copyright holder. www.santafe. edu
Influence of thermal parameters on the dendritic arm spacing and the microhardness of Al-5.5wt.%Sn alloy directionally solidified

As ligas Al-Sn sao amplamente utilizados em aplicacoes tribologicas. Nesse estudo, analises termica, microestrutural e dureza (HV) foram realizadas ao longo de um lingote da liga Al-5,5%Sn, obtido por solidificacao direcional horizontal transitoria. Os principais parâmetros analisados incluem a velocidade de deslocamento da isoterma liquidus (VL) e a taxa de resfriamento (TR). Esses parâmetros termicos desempenham um papel fundamental na formacao da microestrutura. A microestrutura dendritica foi caracterizada atraves dos espacamentos dentriticos primarios (λ1), os quais foram determinados, experimentalmente, e correlacionados com VL, e TR. O comportamento apresentado pela liga Al- 5,5% Sn, durante a solidificacao,e semelhante ao de outras ligas de aluminio, isto e, observa-se rede dendritica mais grosseira com a diminuicao da taxa de resfriamento, indicando que a imiscibilidade entre o aluminio e estanho nao tem um efeito significativo sobre o relacao entre o espacamento dendritico primario e taxa de resfriamento. A dependencia da microdureza em VL, TR e no λ1 foi tambem analisada. Verificaram-se menores valores de HV para maiores TR. Por outro lado, os valores HV aumentam com valores crescentes de λ1.
Dynamic Modelling of Heart Rate Response Under Different Exercise Intensity

Heart rate is one of the major indications of human cardiovascular response to exercises. This study investigates human heart rate response dynamics to moderate exercise. A healthy male subject has been asked to walk on a motorised treadmill under a predefined exercise protocol. ECG, body movements, and oxygen saturation (SpO2) have been reliably monitored and recorded by using non-invasive portable sensors. To reduce heart rate variation caused by the influence of various internal or external factors, the designed step response protocol has been repeated three times. Experimental results show that both steady state gain and time constant of heart rate response are not invariant when walking speed is faster than 3 miles/hour, and time constant of offset exercise is noticeably longer than that of onset exercise.
The Role of M2 Macrophages in the Progression of Chronic Kidney Disease following Acute Kidney Injury

Introduction Acute kidney injury (AKI) is a major risk factor in the development of chronic kidney disease (CKD). However, the mechanisms linking AKI to CKD remain unclear. We examined the alteration of macrophage phenotypes during an extended recovery period following ischemia/reperfusion injury (IRI) and determine their roles in the development of fibrosis. Methods The left renal pedicle of mice was clamped for 40 min. To deplete monocyte/macrophage, liposome clodronate was injected or CD11b-DTR and CD11c-DTR transgenic mice were used. Results Throughout the phase of IRI recovery, M2-phenotype macrophages made up the predominant macrophage subset. On day 28, renal fibrosis was clearly shown with increased type IV collagen and TGF-β. The depletion of macrophages induced by the liposome clodronate injection improved renal fibrosis with a reduction of kidney IL-6, type IV collagen, and TGF-β levels. Additionally, the adoptive transfer of the M2c macrophages partially reversed the beneficial effect of macrophage depletion, whereas the adoptive transfer of the M1 macrophages did not. M2 macrophages isolated from the kidneys during the recovery phase expressed 2.5 fold higher levels of TGF-β than the M1 macrophages. The injection of the diphtheria toxin into CD11b or CD11c-DTR transgenic mice resulted in lesser depletion or no change in M2 macrophages and had little impact on renal fibrosis. Conclusion Although M2 macrophages are known to be indispensible for short-term recovery, they are thought to be main culprit in the development of renal fibrosis following IRI.
Protocol compliance and time management in blunt trauma resuscitation

Objectives: To study advanced trauma life support (ATLS) protocol adherence prospectively in trauma resuscitation and to analyse time management of daily multidisciplinary trauma resuscitation at a level 1 trauma centre, for both moderately and severely injured patients. Patients and methods: All victims of severe blunt trauma were consecutively included. Patients with a revised trauma score (RTS) of 12 were resuscitated by a “minor trauma” team and patients with an RTS of less than 12 were resuscitated by a “severe trauma” team. Digital video recordings were used to analyse protocol compliance and time management during initial assessment. Results: From 1 May to 1 September 2003, 193 resuscitations were included. The “minor trauma” team assessed 119 patients, with a mean injury severity score (ISS) of 7 (range 1–45). Overall protocol compliance was 42%, ranging from 0% for thoracic percussion to 93% for thoracic auscultation. The median resuscitation time was 45.9 minutes (range 39.7–55.9). The “severe team” assessed 74 patients, with a mean ISS of 22 (range 1–59). Overall protocol compliance was 53%, ranging from 4% for thoracic percussion to 95% for thoracic auscultation. Resuscitation took 34.8 minutes median (range 21.6–44.1). Conclusion: Results showed the current trauma resuscitation to be ATLS-like, with sometimes very low protocol compliance rates. Timing of secondary survey and radiology and thus time efficiency remains a challenge in all trauma patients. To assess the effect of trauma resuscitation protocols on outcome, protocol adherence needs to be improved.
Conflict management and job characteristics of nurses in South African public hospitals

This study sought to determine whether job demands and job resources predicted conflict handling styles among nurses within South African public hospitals. A convenience sample of 205 nurses were included (males = 10.7%; age range 46 to 60 years = 38.5%, experience of 5 years and more = 70.8%, African = 92.2%). They completed Rahim's Organisational Conflict Inventory – II (ROCI–II: Rahim, 1986) and a job characteristics measure developed for this study. Data were analysed to assess which job demands and resources predicted which conflict handling styles. From the results, time demands, crisis management and colleague support predicted the use of an avoiding style, whereas workload, time demands, job security, feedback and colleague support predict the use of the integrating style. Time demands and payment predicted the use of the obliging style, while workload, crisis management and payment predicted the use of the dominating style. The compromising style was predicted by colleague support. It seems from the findings that conflict is frequently predicted by time demands.
CD8+ T Cells Are Required for Inflammation and Destruction in Cigarette Smoke-Induced Emphysema in Mice1

Increased numbers of T lymphocytes are observed in the lungs of patients with chronic obstructive pulmonary disease, but their role in the disease process is not known. We investigated the role of CD8+ T cells in inflammatory cell recruitment and lung destruction in a cigarette smoke-induced murine model of emphysema. In contrast to wild-type C57BL/6J mice that displayed macrophage, lymphocyte, and neutrophil recruitment to the lung followed by emphysema in response to cigarette smoke, CD8+ T cell-deficient (CD8−/−) mice had a blunted inflammatory response and did not develop emphysema when exposed to long-term cigarette smoke. Further studies supported a pathogenetic pathway whereby the CD8+ T cell product, IFN-γ-inducible protein-10, induces production of macrophage elastase (matrix metalloproteinase 12) that degrades elastin, both causing lung destruction directly and generating elastin fragments that serve as monocyte chemokines augmenting macrophage-mediated lung destruction. These studies demonstrate a requirement for CD8+ T cells for the development of cigarette smoke-induced emphysema and they provide a unifying pathway whereby CD8+ T cells are a central regulator of the inflammatory network in chronic obstructive pulmonary disease.
New CO observations and simulations of the NGC 4438/NGC 4435 system

NGC 4438 is a highly perturbed spiral with a stellar tidal tail and extraplanar molecular gas, now very HI deficient, crossing the center of the Virgo cluster at high speed. Various authors have attributed the perturbed appearance to the ram pressure of the intracluster medium, the tidal interaction with NGC 4435, and an ISM-ISM collision between the ISM of NGC 4438 and NGC 4435. We present new CO observations covering virtually all of NGC 4438 and the center of NGC 4435 and detailed simulations including all of the above effects. For the first time CO is detected in NGC 4435. In NGC 4438 we find double line profiles at distances up to 40" to the west and south-west and redshifted lines with respect to galactic rotation in the south of the center. The lack of gas to the North and East coupled with the large gaseous extent to the West and the redshifted and double line profiles can only be reproduced with a ram pressure wind. NGC 4438 is most probably on its first passage through the cluster center and has been stripped of its HI only over the past 100 Myr. While an ISM-ISM collision between NGC 4435 and NGC 4438 may occur, the effect is not significant compared to ram pressure and tidal forces, not surprising for the passage of an S0 galaxy 5-10 kpc from the center of NGC 4438. We also detect narrow CO lines, in the absence of detected HI, in the northern tidal arm some 15 kpc from the center of NGC 4438. This can be understood from the simulations assuming a few percent of the gas is too dense to experience the ram pressure wind. NGC 4438 has changed greatly over the past 100 Myr due to its plunge through the center of the Virgo cluster and the interaction with the S0 NGC 4435.
The Bacterial Intimins and Invasins: A Large and Novel Family of Secreted Proteins

Background Gram-negative bacteria have developed a limited repertoire of solutions for secreting proteins from the cytoplasmic compartment to the exterior of the cell. Amongst the spectrum of secreted proteins are the intimins and invasins (the Int/Inv family; TC# 1.B.54) which are characterized by an N-terminal β-barrel domain and a C-terminal surface localized passenger domain. Despite the important role played by members of this family in diseases mediated by several species of the Enterobacteriaceae, there has been little appreciation for the distribution and diversity of these proteins amongst Gram-negative bacteria. Furthermore, there is little understanding of the molecular events governing secretion of these proteins to the extracellular milieu. Principal Findings In silico approaches were used to analyze the domain organization and diversity of members of this secretion family. Proteins belonging to this family are predominantly associated with organisms from the γ-proteobacteria. Whilst proteins from the Chlamydia, γ-, β- and ε-proteobacteria possess β-barrel domains and passenger domains of various sizes, Int/Inv proteins from the α-proteobacteria, cyanobacteria and chlorobi possess only the predicted β-barrel domains. Phylogenetic analyses revealed that with few exceptions these proteins cluster according to organismal type, indicating that divergence occurred contemporaneously with speciation, and that horizontal transfer was limited. Clustering patterns of the β-barrel domains correlate well with those of the full-length proteins although the passenger domains do so with much less consistency. The modular subdomain design of the passenger domains suggests that subdomain duplication and deletion have occurred with high frequency over evolutionary time. However, all repeated subdomains are found in tandem, suggesting that subdomain shuffling occurred rarely if at all. Topological predictions for the β-barrel domains are presented. Conclusion Based on our in silico analyses we present a model for the biogenesis of these proteins. This study is the first of its kind to describe this unusual family of bacterial adhesins.
Competition for Light and Nutrients in Layered Communities of Aquatic Plants

Dominance of free-floating plants poses a threat to biodiversity in many freshwater ecosystems. Here we propose a theoretical framework to understand this dominance, by modeling the competition for light and nutrients in a layered community of floating and submerged plants. The model shows that at high supply of light and nutrients, floating plants always dominate due to their primacy for light, even when submerged plants have lower minimal resource requirements. The model also shows that floating-plant dominance cannot be an alternative stable state in light-limited environments but only in nutrient-limited environments, depending on the plants’ resource consumption traits. Compared to unlayered communities, the asymmetry in competition for light—coincident with symmetry in competition for nutrients—leads to fundamentally different results: competition outcomes can no longer be predicted from species traits such as minimal resource requirements ( rule) and resource consumption. Also, the same two species can, depending on the environment, coexist or be alternative stable states. When applied to two common plant species in temperate regions, both the model and field data suggest that floating-plant dominance is unlikely to be an alternative stable state.
Burden of Malaria and Health Service Utilization in a Tribal Community of West Bengal State, India

There is an urgent need for updating key socio-economic-cultural indictors and scientific understanding on Malaria for suitable control strategies among tribal populations. The study was conducted to find risk correlates of Malaria among tribal groups. A community based analytical cross-sectional study was done among tribals of a district of West Bengal in eastern India by interview technique using standardized tool. The study participants were predominantly males (81.50% %), between 45-60 years (65.87%),one in ten had no formal education; more than half of them were associated with agriculture. One fourth of the participants reported their source of knowledge on Malaria from Newspaper/ Radio/ TV while one fourths became knowledgeable while suffering from Malaria. Majority recognized mosquito bite as basic issue (71.63%), bite at night (96.64%), breed in stagnant water (79.57%). Yet, only one fourth correctly responded that mosquitoes, after biting a Malaria patient, can transmit the disease;. Half of them identified common malarial symptom of fever with shivering and indoor dark resting place of mosquitoes during daytime. Malaria is caused by Plasmodium parasite was correctly known to very few (1.44%). Regarding health seeking behaviour, 40.63% preferred hospital treatment; still disease condition was deciding factor to seek formal care by 95.67%; incidentally their expectation of treatment was limited to chloroquine (84.62). Bed nets was practiced as the commonest protective method followed by draining of stagnant water. Among users using bed nets only 85(70.83%) reported using Insecticide treated nets. The present study findings could provide baseline information to design effective and sustainable Malaria control strategies suited to local conditions in the near future as unsatisfactory knowledge about Malaria among the tribals is significant risk.
Predictability and stability of laser-assisted subepithelial keratectomy with mitomycin C for the correction of high myopia

Abstract The purpose of this study was to evaluate the predictability and stability of laser-assisted subepithelial keratectomy (LASEK) with mitomycin C (MMC) in correction of high myopia (⩽−6.0 diopters [D]) as compared to low-to-moderate myopia (>−6.0 D). This is a retrospective, comparative, cohort study which included 43 eyes of 43 consecutive patients who underwent LASEK with MMC in a private hospital in Hong Kong by a single surgeon. Twenty-five eyes had high myopia (mean spherical equivalent [SE] = −8.53 ± 1.82 D) and 18 eyes had low-to-moderate myopia (mean SE = −3.99 ± 1.37 D) before surgery. In terms of refractive predictability, mean SE was significantly better in eyes with preoperative low-to-moderate myopia than high myopia at 6 months (0.04 ± 0.23 vs 0.31 ± 0.52 D, P = .035). In terms of refractive stability, between 1 and 3 months, both groups had mean absolute change of SE of around 0.25 D. Between 3 and 6 months, preoperative low-to-moderate myopia group had significantly less absolute change of SE compared to high myopia group (0.07 vs 0.23 D, P = .003). More eyes with preoperative high myopia changed SE by more than 0.25 D than those with low-to-moderate myopia between 3 and 6 months (32.0% vs 5.6%, P = .057). In conclusion, LASEK with MMC is more unpredictable and unstable in correction of high myopia than low-to-moderate myopia. The refractive outcome of most low-to-moderate myopia correction stabilizes at 3 months. Stability is not achieved until after 6 months in high myopia correction.
One hundred neuroblastomas detected through a mass screening system in Japan

Background. In Japan, a nationwide mass screening (MS) program for preclinical detection of neuroblastoma in infants was done by measuring urinary vanillylmandelic acid and homovanillic acid at the age of 6 months. In this study, clinical, histopathologic, and biologic features of 100 neuroblastomas detected through the Japanese MS are presented.