Miracle-dz/UniFAR-FTUs huggingface dataset:
A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas

Cortical activity has distinct features across scales, from the spiking statistics of individual cells to global resting-state networks. We here describe the first full-density multi-area spiking network model of cortex, using macaque visual cortex as a test system. The model represents each area by a microcircuit with area-specific architecture and features layer- and population-resolved connectivity between areas. Simulations reveal a structured asynchronous irregular ground state. In a metastable regime, the network reproduces spiking statistics from electrophysiological recordings and cortico-cortical interaction patterns in fMRI functional connectivity under resting-state conditions. Stable inter-area propagation is supported by cortico-cortical synapses that are moderately strong onto excitatory neurons and stronger onto inhibitory neurons. Causal interactions depend on both cortical structure and the dynamical state of populations. Activity propagates mainly in the feedback direction, similar to experimental results associated with visual imagery and sleep. The model unifies local and large-scale accounts of cortex, and clarifies how the detailed connectivity of cortex shapes its dynamics on multiple scales. Based on our simulations, we hypothesize that in the spontaneous condition the brain operates in a metastable regime where cortico-cortical projections target excitatory and inhibitory populations in a balanced manner that produces substantial inter-area interactions while maintaining global stability.
Clinical Significance of Autoantibody Expression in Allogeneic Stem-Cell Recipients

Background. The occurrence of autoantibodies has been reported in allogeneic stem-cell recipients, but the association of this occurrence with chronic graft-versus-host disease (cGVHD) or survival remains uncertain. Methods. A total of 121 consecutive patients who underwent allogeneic stem-cell transplantation from November 2001 to March 2008 and survived at least 3 months after transplantation were included in this study. Results. Forty-seven patients (38.8%) expressed at least one of various autoantibodies after transplantation. Antinuclear antibody was positive in 22 patients (18.2%), antidouble stranded DNA in seven (5.8%), antismooth muscle antibody in six (5%), rheumatoid factor in 17 (14.0%), and a positive Coombs test recorded for 12 patients (9.9%). cGVHD was more commonly diagnosed in the patients with autoantibody expression (61.7% vs. 43.2%, P=0.048). The patients expressing autoantibodies had a better 5-year overall survival than those without any autoantibody expression: 70.2% and 47.9% for the autoantibody-positive and autoantibody-negative patients, respectively (P=0.002). The cumulative incidence of relapse was 21.5% and 39.3% for the autoantibody-positive and autoantibody-negative patients, respectively (P=0.023). In particular, the patients expressing autoantibodies without cGVHD had a better overall survival (100%) than the patients in the other groups: 63.1% for the autoantibody- and cGVHD-positive patients, 59.6% for the autoantibody-negative and cGVHD-positive patients, and 36.6% for the autoantibody- and cGVHD-negative patients. The multivariate analysis identified autoantibody expression as a good prognostic factor regarding survival (hazard ratio=0.378, 95% confidence interval=0.185–0.775, P=0.008). Conclusion. The occurrence of autoantibodies after allogeneic stem-cell transplantation was found to be related to cGVHD, and patients expressing autoantibodies had a better survival.
Taming parallel I/O complexity with auto-tuning

We present an auto-tuning system for optimizing I/O performance of HDF5 applications and demonstrate its value across platforms, applications, and at scale. The system uses a genetic algorithm to search a large space of tunable parameters and to identify effective settings at all layers of the parallel I/O stack. The parameter settings are applied transparently by the auto-tuning system via dynamically intercepted HDF5 calls. To validate our auto-tuning system, we applied it to three I/O benchmarks (VPIC, VORPAL, and GCRM) that replicate the I/O activity of their respective applications. We tested the system with different weak-scaling configurations (128, 2048, and 4096 CPU cores) that generate 30 GB to 1 TB of data, and executed these configurations on diverse HPC platforms (Cray XE6, IBM BG/P, and Dell Cluster). In all cases, the auto-tuning framework identified tunable parameters that substantially improved write performance over default system settings. We consistently demonstrate I/O write speedups between 2× and 100× for test configurations.
Measuring article quality in wikipedia: models and evaluation

Wikipedia has grown to be the world largest and busiest free encyclopedia, in which articles are collaboratively written and maintained by volunteers online. Despite its success as a means of knowledge sharing and collaboration, the public has never stopped criticizing the quality of Wikipedia articles edited by non-experts and inexperienced contributors. In this paper, we investigate the problem of assessing the quality of articles in collaborative authoring of Wikipedia. We propose three article quality measurement models that make use of the interaction data between articles and their contributors derived from the article edit history. Our B<scp>asic</scp> model is designed based on the mutual dependency between article quality and their author authority. The P<scp>eer</scp>R<scp>eview</scp> model introduces the review behavior into measuring article quality. Finally, our P<scp>rob</scp>R<scp>eview</scp> models extend P<scp>eer</scp>R<scp>eview</scp> with partial reviewership of contributors as they edit various portions of the articles. We conduct experiments on a set of well-labeled Wikipedia articles to evaluate the effectiveness of our quality measurement models in resembling human judgement.
Runtime optimization of IEEE 802.11 wireless LANs performance

IEEE 802.11 is the standard for wireless local area networks (WLANs) promoted by the Institute of Electrical and Electronics Engineers. Wireless technologies in the LAN environment are becoming increasingly important and the IEEE 802.11 is the most mature technology to date. Previous works have pointed out that the standard protocol can be very inefficient and that an appropriate tuning of its congestion control mechanism (i.e., the backoff algorithm) can drive the IEEE 802.11 protocol close to its optimal behavior. To perform this tuning, a station must have exact knowledge of the network contention level; unfortunately, in a real case, a station cannot have exact knowledge of the network contention level (i.e., number of active stations and length of the message transmitted on the channel), but it, at most, can estimate it. We present and evaluate a distributed mechanism for contention control in IEEE 802.11 wireless LANs. Our mechanism, named asymptotically optimal backoff (AOB), dynamically adapts the backoff window size to the current network contention level and guarantees that an IEEE 802.11 WLAN asymptotically achieves its optimal channel utilization. The AOB mechanism measures the network contention level by using two simple estimates: the slot utilization and the average size of transmitted frames. These estimates are simple and can be obtained by exploiting information that is already available in the standard protocol. AOB can be used to extend the standard 802.11 access mechanism without requiring any additional hardware. The performance of the IEEE 802.11 protocol, with and without the AOB mechanism, is investigated through simulation. Simulation results indicate that our mechanism is very effective, robust, and has traffic differentiation potentialities.
Does imitation act as an oxytocin nebulizer in autism spectrum disorder?

Sir, There is a growing interest in using oxytocin to improve the social and emotional impairments of individuals with autistic spectrum disorder (ASD). In an elegant paper recently published in Brain , oxytocin was shown to enhance both the score of correct inferences and the low autistic brain activity in the right anterior insula when inferring the emotions and beliefs of others (Aoki et al. , 2014). Using a revisited version of the Sally-Anne Task, Aoki and colleagues suggest that reduced activity of the right anterior insula is a potential neural marker of autistic deficit in social inferences. Oxytocin may target this abnormal insula activity. Children and adults with ASD are described as lacking empathy, affiliative behaviour and social overture. Several studies have suggested that oxytocin has therapeutic effects on autistic deficits in social responses and the understanding of emotion in others (Andari et al. , 2010; Striepens et al. , 2012). More generally, literature on human and non-human primates presents converging evidence of oxytocin’s positive effects on prosocial behaviour (Guastela and MacLeod, 2012; Chang and Platt, 2014). Recently, 7- to 14-day-old macaques where found to increase their facial gesturing at a human caregiver after oxytocin nebulization (Simpson et al. , 2014). Moreover, being imitated predicted oxytocin-associated increases in affiliative behaviours. Even without nebulization, newborn macaques are shown to display more affiliation toward humans who imitate them; they look longer at imitators, spend more time in their proximity and prefer exchanging tokens with them (Paukner et al. , 2009). Such results promote the idea that an empathic connection results from behavioural matching. Indeed, our own research with low-functioning children with ASD similarly assessed the affiliative role of being imitated; children come in close proximity, smile, look at the unacquainted experimenter, touch or kiss the experimenter and decrease self-injuring …
On the Convergence of the Self-Consistent Field Iteration in Kohn-Sham Density Functional Theory

It is well known that the self-consistent field (SCF) iteration for solving the Kohn--Sham (KS) equation often fails to converge, yet there is no clear explanation. In this paper, we investigate the SCF iteration from the perspective of minimizing the corresponding KS total energy functional. By analyzing the second-order Taylor expansion of the KS total energy functional and estimating the relationship between the Hamiltonian and the part of the Hessian which is not used in the SCF iteration, we are able to prove global convergence from an arbitrary initial point and local linear convergence from an initial point sufficiently close to the solution of the KS equation under the assumptions that the gap between the occupied states and unoccupied states is sufficiently large and the second-order derivatives of the exchange correlation functional are uniformly bounded from above. Although these conditions are very stringent and are almost never satisfied in reality, our analysis is interesting in the sense th.
Myocardial and microvascular inflammation/infection in patients with HIV-associated pulmonary artery hypertension

Background:Right ventricle compromise affects survival of patients with HIV-associated pulmonary artery hypertension (PAH). Design:Myocardial histology with viral assessment may clarify the mechanism of right ventricular deterioration and provide clues on PAH origin. Methods:Fifteen patients with HIV infection, PAH and right ventricular dysfunction underwent cardiac magnetic resonance, catheterization, coronary with ventricular angiography and biventricular endomyocardial biopsy. Endothelial expression of HLA-DR, ICAM-1, E-selectin and VCAM-1 was semi-quantitatively evaluated. PCR for HIV, hepatitis C virus, human herpes virus-6, human herpes virus-8, Epstein–Barr virus, adenovirus, cytomegalovirus, enterovirus, influenza A/B and parvovirus B19 was performed. In PCR-positive hearts, viral protein adenovirus-1 and TORDJI-22 were assessed by immunohistology. Results:New York Heart Association class was 2.4 ± 0.5, mean pulmonary artery pressure 49.93 ± 10.15 mmHg and wedge pressure 9.5 ± 2.19 mmHg. Coronaries were normal with slow flow. Left ventricular and/or right ventricular micro-aneurysms were seen in eight patients. Cardiac magnetic resonance documented increased right ventricular end-diastolic volume with reduced ejection fraction, normal left ventricular end-diastolic volume and left ventricular ejection fraction. Subepicardial/mesocardial oedema and delayed enhancement in the inter-ventricular junction and/or left ventricular inferolateral wall was detected in eight patients. Histology showed active lymphocytic myocarditis in 12 patients, with microvasculitis in three. Endothelial adhesion molecules were over-expressed in all patients. PCR was positive in four patients for hepatitis C virus and in two for adenovirus, and viruses localized both in cardiomyocytes and endothelial cells. Conclusions:Inflammation/infection of myocardium and intramural vessels is detectable in patients with HIV-associated PAH. It may adversely affect right ventricular function and have a role in the compromised pulmonary circulation.
Circumventing IP-address pseudonymization

This paper presents an attack that circumvents anonymization of IP addresses in IP network traffic data in O(n) time, or O(n) time under certain circumstances. The attack is based on packet injection, and circumvents all anonymization techniques that assign a static and unique pseudonym to an IP address. It turns out that the packet injection itself, as well as the extraction of the corresponding anonymized header data, are the most time-consuming steps.
Addition of Interleukin-21 for Expansion of T-Cells for Adoptive Immunotherapy of Murine Melanoma

We previously demonstrated that interleukin (IL)-7/15 was superior to IL-2 for expansion of T cells in vitro for adoptive immunotherapy. We sought to ascertain whether IL-21 would further improve yield and therapeutic efficacy of T cells in culture. Naïve T cell receptor (TcR) transgenic splenocytes or antigen-sensitized lymph node cells were harvested from PMEL-1 mice and exposed to bryostatin-1 and ionomycin (B/I) for 18 h. Cells were then cultured in IL-2, IL-21, IL-7/15 or IL-7/15/21 for six days. Harvested cells were analyzed by flow cytometry and used to treat C57Bl/6 mice injected intravenously with B16 melanoma. Lungs were harvested and metastases counted 14 days after treatment. Culturing lymphocytes in IL-7/15/21 increased expansion compared to IL-2 or IL-7/15. IL-21 and IL-7/15/21 increased CD8+ cells compared to IL-2 or IL-7/15. IL-21 preferentially expanded a CD8+CD44−CD62L+ T “naïve” population, whereas IL-7/15/21 increased CD8+CD44+CD62Lhigh central-memory T cells. T cells grown in IL-7/15/21 were more effective at reducing metastases than IL-2. The addition of IL-21 to IL-7/15 induced greater expansion of lymphocytes in culture and increased the yield of CD8+ T central-memory cells vs. IL-7/15 alone. This may have significant impact on future clinical trials of adoptive immunotherapy, particularly for generating adequate numbers of lymphocytes for treatment.
Tracking the Evolution of Social Emotions: A Time-Aware Topic Modeling Perspective

Many of today's online news websites have enabled users to specify different types of emotions (e.g., Angry and shocked) they have after reading news. Compared with traditional user feedbacks such as comments and ratings, these specific emotion annotations are more accurate for expressing users' personal emotions. In this paper, we propose to exploit these users' emotion annotations for online news in order to track the evolution of emotions, which plays an important role in various online services. A critical challenge is how to model emotions with respect to time spans. To this end, we propose a time-aware topic modeling perspective for solving this problem. Specifically, we first develop a model named emotion-Topic over Time (eToT), in which we represent the topics of news as a Beta distribution over time and a multinomial distribution over emotions. Whilee ToT can uncover the latent relationship among news, emotion and time directly, it cannot capture the dynamics of topics. Therefore, we further develop another model named emotion based Dynamic Topic Model (eDTM), where we explore the state space model for tracking the dynamics of topics. In addition, we demonstrate that both eToT and eDTM could enable several potential applications, such as emotion prediction, emotion-based news recommendations and emotion anomaly detections. Finally, we validate the proposed models with extensive experiments with a real-world data set.
Implications of Genotype and Climate Variability on Phenolic Compounds of Grain: a Sorghum Case Study

It has been predicted that the global temperature will continue to rise in the future, which means crops including sorghum will likely be grown under higher temperatures than those currently, and consequently this may affect the nutritional properties of the grain. This chapter reports how genotype and growth temperature affected polyphenol and antioxidant activity and in vitro iron availability in sorghum grains. Six sorghum genotypes (CCH1, CCH2, AQL33/QL36, Ai4, PI563516 and IS 8525) were grown in a controlled growth chamber under two day/night temperature regimes, 32/21 °C (optimum temperature, OT) and 38/21 °C (high temperature, HT). The effects of temperature regimes on physical characteristics (hardness, weight and diameter) were also investigated. Additionally, the effects of the two growth temperatures on tannin, phytate, mineral, and in vitro iron availability of raw and cooked grains (as porridge) of the six sorghum genotypes were also determined. The results indicated that the weight and diameter of the sorghum kernels significantly increased in almost all genotypes (except for CCH1) with the higher growing temperature. Genotype had a
ASPECTS on CTA Source Images Versus Unenhanced CT: Added Value in Predicting Final Infarct Extent and Clinical Outcome

Background and Purpose— The Alberta Stroke Program Early CT Score (ASPECTS) is a grading system to assess ischemic changes on CT in acute ischemic stroke. CT angiography–source images (CTA-SI) predict final infarct volume. We examined whether the final infarct ASPECTS and clinical outcome were more related to acute CTA-SI ASPECTS than to the acute noncontrast CT (NCCT) ASPECTS. Methods— ASPECTS was assigned by 2 raters on the acute NCCT, CTA-SI, and follow-up imaging. The mean baseline ASPECTS of acute NCCT and CTA-SI was compared with the follow-up ASPECTS. Rate ratios (RRs) were used to quantify the relationship between the dichotomized baseline ASPECTS (categorized as 0 to 7 versus 8 to 10) and favorable patient outcome. Results— Thirty-nine patients were recruited. Proximal occlusion (internal carotid artery or middle cerebral artery) was seen in 62%, M2 occlusion in 18%, and no occlusion was seen in 20% of patients. The median time between symptom onset and imaging was 1.9 (1.2 to 2.5) hours. There was a significantly larger difference of 1.4 between the mean baseline NCCT and CTA-SI ASPECTS in patients who had more ischemic changes (follow-up ASPECTS=0 to 3) than a difference of 0.6 in patients who had near-to-normal CT scans (follow-up ASPECTS=8 to 10). The rate of favorable outcome for acute NCCT ASPECTS of 8 to 10 was 51.8% versus 25.0% for 0 to 7 (RR, 2.1, 95% CI: 0.7 to 5.9, P=0.12). For acute CTA-SI ASPECTS of 8 to 10, the rate of favorable outcome was 58.8% versus 31.8% for 0 to 7 (RR, 1.8, 95% CI: 0.9 to 3.8, P=0.09). Conclusions— CTA-SI ASPECTS provides added information in the prediction of final infarct size.
DIVERSITY AND DISTRIBUTION OF MICROFUNGI FROM DIPTEROCARP FORESTS IN SARAWAK, BORNEO ISLAND (MALAYSIA)

South-east Asian dipterocarp forests contain plant species that are vulnerable and at risk of extinction. Microfungi, as important decomposers and sources of useful metabolites, have not been well studied in regards to their diversity and distribution in the South-east Asian dipterocarp forests. This study reports the microfungal species associated with dominant and vulnerable plant species in two dipterocarp forests, namely Gunung Gading and Kubah National Parks, in Sarawak on the Borneo Island. Green leaves and litters of five host plants, namely Baccaurea sp. , Macaranga triloba (Thunb.) Mull.Arg. , Macaranga sp. , Shorea macrophylla (de Vr.) Ashton and Syzygium sp. , were incubated on water agar and malt extract agar. A total of 171 fungal taxa were recorded on the five host plants, during two visits, each to both forests. Syzygium sp. had the highest microfungal diversity of 84 taxa followed by 80 taxa on Macaranga sp. , 53 taxa on Baccaurea sp. , 43 taxa on M. triloba and the lowest, 35 taxa, on Shorea macrophylla. Pestalotiopsis spp. , Oidiodendron spp. , Graphium spp. , and Mycelia sterilia were the most frequently isolated microfungal species from all the five host plants. There was a high microfungal similarity between Syzygium sp. and Macaranga sp. with 34 taxa common to both plants. The lowest similarity was recorded between S. macrophylla, M. triloba and Baccaurea sp. with only 13 taxa common between them. This is the first report on microfungi associated with dominant and vulnerable plant species in South-east Asian dipterocarp forests; an important record of the fungal diversity on these plants and an exposition on microfungi in Sarawak, Borneo Island, Malaysia.Keywords: Microfungi, Macaranga, Shorea, Baccaurea, Syzygium
On the effectiveness of Robot-Assisted Language Learning

Abstract This study introduces the educational assistant robots that we developed for foreign language learning and explores the effectiveness of robot-assisted language learning (RALL) which is in its early stages. To achieve this purpose, a course was designed in which students have meaningful interactions with intelligent robots in an immersive environment. A total of 24 elementary students, ranging in age from ten to twelve, were enrolled in English lessons. A pre-test/post-test design was used to investigate the cognitive effects of the RALL approach on the students’ oral skills. No significant difference in the listening skill was found, but the speaking skills improved with a large effect size at the significance level of 0.01. Descriptive statistics and the pre-test/post-test design were used to investigate the affective effects of RALL approach. The result showed that RALL promoted and improved students’ satisfaction, interest, confidence, and motivation at the significance level of 0.01.
The Mass Profile of the Coma Galaxy Cluster

We use a new redshift survey complete to mR≃15.4 within 4. °25 from the center of the Coma cluster to measure the mass profile of the cluster to r~5.5 h-1 Mpc. We extend the profile to r~10 h-1 Mpc with a further sample complete to mR=15.4 in 42% of the area within a 10° radius and to m=15.5 in the remaining area. Galaxies within this region are falling onto the cluster on moderately radial orbits and thus do not satisfy virial equilibrium. Nonetheless, identification of the caustics in redshift space provides an estimate of the gravitational potential at radius r and hence of the system mass, M(≤10 h-1 Mpc)=(1.65±0.41)×1015 h-1 M (1 σ error). Previous mass estimates derived from optical and X-ray observations are limited to r≤2.5 h-1 Mpc. Our mass profile is consistent with these estimates but extends to distances 4 times as large. Over the entire range, the mass increases with r at the rate expected for a Navarro, Frenk, & White density profile.