Miracle-dz/UniFAR-FTUs huggingface dataset:
Diminished supraspinal pain modulation in patients with mild traumatic brain injury

Background Chronic pain conditions are highly prevalent in patients with mild traumatic brain injury. Supraspinal diffuse axonal injury is known to dissociate brain functional connectivity in these patients. The effect of this dissociated state on supraspinal pain network is largely unknown. A functional magnetic resonance imaging study was conducted to compare the supraspinal pain network in patients with mild traumatic brain injury to the gender and age-matched healthy controls with the hypothesis that the functional connectivities of the medial prefrontal cortices, a supraspinal pain modulatory region to other pain-related sensory discriminatory and affective regions in the mild traumatic brain injury subjects are significantly reduced in comparison to healthy controls. Results The mild traumatic brain injury group (N = 15) demonstrated significantly (P < 0.01, cluster threshold > 150 voxels) less activities in the thalamus, pons, anterior cingulate cortex, insula, dorsolateral prefrontal cortex, and medial prefrontal cortices than the healthy control group (N = 15). Granger Causality Analyses (GCA) indicated while the left medial prefrontal cortices of the healthy control group cast a noticeable degree of outward (to affect) causality inference to multiple pain processing related regions, this outward inference pattern was not observed in the mild traumatic brain injury group. On the other hand, only patients’ bilateral anterior cingulate cortex received multiple inward (to be affected) causality inferences from regions including the primary and secondary somatosensory cortices and the inferior parietal lobe. Resting state functional connectivity analyses indicated that the medial prefrontal cortices of the mild traumatic brain injury group demonstrated a significantly (P < 0.01, F = 3.6, cluster size > 150 voxels) higher degree of functional connectivity to the inferior parietal lobe, premotor and secondary somatosensory cortex than the controls. Conversely, the anterior cingulate cortex of the healthy group demonstrated significantly (P < 0.01, F = 3.84, cluster size > 150 voxels) less degree of functional connectivities to the inferior parietal lobe and secondary somatosensory cortex than their mild traumatic brain injury counterparts. Conclusions In short, the current study demonstrates that patients with mild traumatic brain injury and headaches appear to have an altered state of supraspinal modulatory and affective functions related to pain perception.
FalconAO: Aligning Ontologies with Falcon

Falcon-AO is an automatic tool for aligning ontologies. There are two matchers integrated in Falcon-AO: one is a matcher based on linguistic matching for ontologies, called LMO; the other is a matcher based on graph matching for ontologies, called GMO. In Falcon-AO, GMO takes the alignments generated by LMO as external input and outputs additional alignments. Reliable alignments are gained through LMO as well as GMO according to the concept of reliability. The reliability is obtained by observing the linguistic comparability and structural comparability of the two ontologies being compared. We have performed Falcon-AO on tests provided by OAEI 2005 campaign and got some preliminary results. In this paper, we describe the architecture and techniques of Falcon-AO in brief and present our results in more details. Finally, comments about test cases and lessons learnt from the campaign will be presented.
SEASTAR: systematic evaluation of alternative transcription start sites in RNA

Abstract Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5′ Untranslated Regions (5′UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to identify the 5′ ends of transcripts. We developed a computational pipeline SEASTAR that identifies first exons from RNA-seq data alone then quantifies and compares alternative first exon usage across multiple biological conditions. The exons inferred by SEASTAR coincide with transcription start sites identified directly by CAGE experiments and bear epigenetic hallmarks of active promoters. To determine if differential usage of alternative first exons can yield insights into the mechanism controlling gene expression, we applied SEASTAR to an RNA-seq dataset that tracked the reprogramming of mouse fibroblasts into induced pluripotent stem cells. We observed dynamic temporal changes in the usage of alternative first exons, along with correlated changes in transcription factor expression. Using a combined sequence motif and gene set enrichment analysis we identified N-Myc as a regulator of alternative first exon usage in the pluripotent state. Our results demonstrate that SEASTAR can leverage the available RNA-seq data to gain insights into the control of gene expression and alternative transcript variation in eukaryotic transcriptomes.
IMMUNO-EFFECT OF RAW, GAMMA IRRADIATED, MICROWAVE TREATED AND FERMENTED WHEAT GERMS IN EXPERIMENTAL RATS.

In the present study on effect of feeding raw wheat germ, microwave treated wheat germ, gamma irradiated wheat germ and fermented wheat germ on Interferon gamma (IFN-γ ) and Interleukin 10 (IL-10) in serum of rats were investigated. The data indicated that treated and untreated wheat germ had significant increase in (IFNγ ) level in the serum of rats . Fermented wheat germ recorded the highest significant increase in this concept in comparison to control group. Wheat germ supplementation indicated significant changes of (IL-10) level in serum of rats in comparison to control group. Fermented wheat germ recorded the least significant decrease in (IL-10) level in serum of rats in comparison to control group. Treated and untreated wheat germ specially fermented wheat germ raised the immune system of experimental rats . On the other hand, the present study included the vitamins content (vitamins A, E, and C ) of raw ,microwave treated, gamma irradiated, and fermented wheat germ clarifying the role of each vitamin in raising the immune system.
Feeding Patterns of Potential West Nile Virus Vectors in South-West Spain

Background Mosquito feeding behaviour determines the degree of vector–host contact and may have a serious impact on the risk of West Nile virus (WNV) epidemics. Feeding behaviour also interacts with other biotic and abiotic factors that affect virus amplification and transmission. Methodology/Principal Findings We identified the origin of blood meals in five mosquito species from three different wetlands in SW Spain. All mosquito species analysed fed with different frequencies on birds, mammals and reptiles. Both ‘mosquito species’ and ‘locality’ explained a similar amount of variance in the occurrence of avian blood meals. However, ‘season of year’ was the main factor explaining the presence of human blood meals. The differences in diet resulted in a marked spatial heterogeneity in the estimated WNV transmission risk. Culex perexiguus, Cx. modestus and Cx. pipiens were the main mosquito species involved in WNV enzootic circulation since they feed mainly on birds, were abundant in a number of localities and had high vector competence. Cx. perexiguus may also be important for WNV transmission to horses, as are Cx. pipiens and Cx. theileri in transmission to humans. Estimates of the WNV transmission risk based on mosquito diet, abundance and vector competence matched the results of previous WNV monitoring programs in the area. Our sensitivity analyses suggested that mosquito diet, followed by mosquito abundance and vector competence, are all relevant factors in understanding virus amplification and transmission risk in the studied wild ecosystems. At some of the studied localities, the risk of enzootic circulation of WNV was relatively high, even if the risk of transmission to humans and horses was less. Conclusions/Significance Our results describe for first time the role of five WNV candidate vectors in SW Spain. Interspecific and local differences in mosquito diet composition has an important effect on the potential transmission risk of WNV to birds, horses and humans.
A MMSM-based Hybrid Method for Chinese MicroBlog Word Segmentation

After years of researches, Chinese word segmentation has achieved quite high precisions for formal style text. However, the performance of segmentation is not so satisfying for MicroBlog corpora. In this paper we describe a scheme for Chinese word segmentation for, MicroBlog which integrates the characterbased and word-based information in the directed graph generated by MMSM model. Word-level information is effective for analysis of known words, while character-level information is useful for analysis of unknown words. A multi-chain unequal states CRF model is proposed. The proposed multi-chain unequal states CRF has two state chains with unequal states which can recognize the POS tag simultaneously. The hybrid model was effective and adopted in real-world system.
Zero phase-lag synchronization through short-term modulations

Considering coupled phase model oscillator systems with non-identical time delays, we study the possibility of close-to-zero phase- lag synchronization (ZPS) without frequency depression (FD). FD refers to nearly vanishing frequencies of the synchronized oscillators (in com- parison to the intrinsic frequencies); its absence is crucial for interpreta- tions related to brain dynamics. Discussing an extension of the Kuramoto model, it is demonstrated that ZPS without FD may arise by allowing for dynamical parameters. Two models are presented: one is based on short- term modulation of the delays, while the other assumes static delays but short-term modulation of coupling strengths. We also speculate on possi- ble relevance of such mechanisms with respect to assembly formation by relating the frequency of the synchronized oscillation to recently proposed pattern frequency bands.
Creating secrets out of erasures

Current security systems often rely on the adversary's computational limitations. Wireless networks offer the opportunity for a different, complementary kind of security, which relies on the adversary's limited network presence (i.e., that the adversary cannot be located at many different points in the network at the same time). We present a system that leverages this opportunity to enable n wireless nodes to create a shared secret S, in a way that an eavesdropper, Eve, obtains very little information on S. Our system consists of two steps: (1) The nodes transmit packets following a special pattern, such that Eve learns very little about a given fraction of the transmitted packets. This is achieved through a combination of beam forming (from many different sources) and wiretap codes. (2) The nodes participate in a protocol that reshuffles the information known to each node, such that the nodes end up sharing a secret that Eve knows very little about. Our protocol is easily implementable in existing wireless devices and scales well with the number of nodes; these properties are achieved through a combination of public feedback, broadcasting, and network coding. We evaluate our system through a 5-node testbed. We demonstrate that a group of wireless nodes can generate thousands of new shared secret bits per second, with their secrecy being independent of the adversary's computational capabilities.
Journaling about stressful events: Effects of cognitive processing and emotional expression

The effects of two journaling interventions, one focusing on emotional expression and the other on both cognitive processing and emotional expression, were compared during 1 month of journaling about a stressful or traumatic event. One hundred twenty-two students were randomly assigned to one of three writing conditions: (a) focusing on emotions related to a trauma or stressor, (b) focusing on cognitions and emotions related to a trauma or stressor, or (c) writing factually about media events. Writers focusing on cognitions and emotions developed greater awareness of the positive benefits of the stressful event than the other two groups. This effect was apparently mediated by greater cognitive processing during writing. Writers focusing on emotions alone reported more severe illness symptoms during the study than those in other conditions. This effect appeared to be mediated by a greater focus on negative emotional expression during writing.
The relationship between nectaries and floral architecture: a case study in Geraniaceae and Hypseocharitaceae

Background and Aims Flowers of Geraniaceae and Hypseocharitaceae are generally considered as morphologically simple. However, previous studies indicated complex diversity in floral architecture including tendencies towards synorganization. Most of the species have nectar-rewarding flowers which makes the nectaries a key component of floral organization and architecture. Here, the development of the floral nectaries is studied and placed into the context of floral architecture. Methods Seven species from Geraniaceae and one from Hypseocharitaceae were investigated using scanning electron microscopy and light microscopy. Samples were prepared and processed using standard protocols. Key Results The development of the nectary glands follows the same trajectory in all species studied. Minor differences occur in the onset of nectarostomata development. The most striking finding is the discovery that a short anthophore develops via intercalary growth at the level of the nectary glands. This anthophore lifts up the entire flower apart from the nectary gland itself and thus plays an important role in floral architecture, especially in the flowers of Pelargonium. Here, the zygomorphic flowers show a particularly extensive receptacular growth, resulting in the formation of a spur-like receptacular cavity ('inner spur'). The nectary gland is hidden at the base of the cavity. Various forms of compartmentalization, culminating in the 'revolver flower' of Geranium maderense, are described. Conclusions Despite the superficial similarity of the flowers in Geraniaceae and Hypseocharitaceae, there is broad diversity in floral organization and floral architecture. While the receptacular origin of the spur-like cavity in Pelargonium had already been described, anthophore formation via intercalary growth of the receptacle in the other genera had not been previously documented. In the context of the most recent phylogenies of the families, an evolutionary series for the floral architecture is proposed, underscoring the importance of synorganization in these seemingly simple flowers.
BRAF and NRAS Locus-Specific Variants Have Different Outcomes on Survival to Colorectal Cancer

Purpose: Somatic mutation status at KRAS, BRAF, and NRAS is associated with prognosis in patients with advanced colorectal cancer (aCRC); however, it remains unclear whether there are intralocus, variant-specific differences in survival and other clinicopathologic parameters. Experimental Design: We profiled 2,157 aCRCs for somatic mutations in KRAS, BRAF, and NRAS and determined microsatellite instability status. We sought inter- and intralocus correlations between mutations and variant-specific associations with survival and clinicopathology. Results: KRAS mutations were rarely found together and those in codons 12 and 13 conferred poor prognosis [hazard ratio (HR), 1.44; 95% confidence interval (CI), 1.28–1.61; P = 6.4 × 10−10 and HR, 1.53; 95% CI, 1.26–1.86; P = 1.5 × 10−05, respectively]. For BRAF, more c.1781A>G (p.D594G) CRCs carried RAS mutations [14% (3/21)] compared with c.1799T>A (p.V600E) CRCs [1% (2/178), P = 9.0 × 10−03]. c.1799T>A (p.V600E) was associated with poor prognosis (HR, 2.60; 95% CI, 2.06–3.28; P = 1.0 × 10−15), whereas c.1781A>G (p.D594G) was not (HR, 1.30; 95% CI, 0.73–2.31; P = 0.37); this intralocus difference was significant (P = 0.04). More c.1799T>A (p.V600E) colorectal cancers were found in the right colon [47% (47/100)], compared with c.1781A>G (p.D594G) colorectal cancers [7% (1/15), P = 3.7 × 10−03]. For NRAS, 5% (3/60) of codon 61 mutant colorectal cancers had KRAS mutations compared with 44% (10/23) of codons 12 and 13 mutant colorectal cancers (P = 7.9 × 10−05). Codon 61 mutations conferred poor prognosis (HR, 1.47; 95% CI, 1.09–1.99; P = 0.01), whereas codons 12 and 13 mutations did not (HR, 1.29; 95% CI, 0.64–2.58; P = 0.48). Conclusions: Our data show considerable intralocus variation in the outcomes of mutations in BRAF and NRAS. These data need to be considered in patient management and personalized cancer therapy. Clin Cancer Res; 23(11); 2742–9. ©2016 AACR.
Prevalence of HPV in Adults Aged 18-69: United States, 2011-2014.

KEY FINDINGS Data from the National Health and Nutrition Examination Survey Human papillomavirus (HPV) is the most common sexually transmitted infection in the United States (1). Some HPV types can cause genital warts and are considered low risk, with a small chance for causing cancer. Other types are considered high risk, causing cancer in different areas of the body including the cervix and vagina in women, penis in men, and anus and oropharynx in both men and women (2). This report provides the most recent national estimates of oral HPV prevalence among adults aged 18-69 from the National Health and Nutrition Examination Survey (NHANES) 2011-2014, as well as prevalence of genital HPV among adults aged 18-59 from NHANES 2013-2014. Estimates of any HPV (37 types tested) as well as high-risk HPV (14 of the 37 types) are provided.
Aberrant functional network connectivity in psychopathy from a large (N = 985) forensic sample

Psychopathy is a personality disorder characterized by antisocial behavior, lack of remorse and empathy, and impaired decision making. The disproportionate amount of crime committed by psychopaths has severe emotional and economic impacts on society. Here we examine the neural correlates associated with psychopathy to improve early assessment and perhaps inform treatments for this condition. Previous resting‐state functional magnetic resonance imaging (fMRI) studies in psychopathy have primarily focused on regions of interest. This study examines whole‐brain functional connectivity and its association to psychopathic traits. Psychopathy was hypothesized to be characterized by aberrant functional network connectivity (FNC) in several limbic/paralimbic networks. Group‐independent component and regression analyses were applied to a data set of resting‐state fMRI from 985 incarcerated adult males. We identified resting‐state networks (RSNs), estimated FNC between RSNs, and tested their association to psychopathy factors and total summary scores (Factor 1, interpersonal/affective; Factor 2, lifestyle/antisocial). Factor 1 scores showed both increased and reduced functional connectivity between RSNs from seven brain domains (sensorimotor, cerebellar, visual, salience, default mode, executive control, and attentional). Consistent with hypotheses, RSNs from the paralimbic system—insula, anterior and posterior cingulate cortex, amygdala, orbital frontal cortex, and superior temporal gyrus—were related to Factor 1 scores. No significant FNC associations were found with Factor 2 and total PCL‐R scores. In summary, results suggest that the affective and interpersonal symptoms of psychopathy (Factor 1) are associated with aberrant connectivity in multiple brain networks, including paralimbic regions.
The association of plasma androgen levels with breast, ovarian and endometrial cancer risk factors among postmenopausal women

Although androgens may play an etiologic role in breast, ovarian and endometrial cancers, little is known about factors that influence circulating androgen levels. We conducted a cross‐sectional analysis among 646 postmenopausal women in the Nurses' Health Study to examine associations between adult risk factors for cancer, including the Rosner/Colditz breast cancer risk score, and plasma levels of testosterone, free testosterone, androstenedione, dehydroepiandrosterone (DHEA) and DHEA sulfate (DHEAS). All analyses were adjusted for age, laboratory batch and other cancer risk factors. Free testosterone levels were 79% higher among women with a body mass index of ≥30 vs. <22 kg/m2 (p‐trend <0.01) and 25% higher among women with a waist circumference of >89 vs. ≤74 cm (p‐trend = 0.02). Consuming >30 g of alcohol a day vs. none was associated with a 31% increase in DHEA and 59% increase in DHEAS levels (p‐trend = 0.01 and <0.01, respectively). Smokers of ≥25 cigarettes per day had 35% higher androstenedione and 44% higher testosterone levels than never smokers (p‐value, F‐test = 0.03 and 0.01, respectively). No significant associations were observed for height or time since menopause with any androgen. Testosterone and free testosterone levels were ∼30% lower among women with a hysterectomy vs. without (both p‐values < 0.01). Overall breast cancer risk was not associated with any of the androgens. Thus, several risk factors, including body size, alcohol intake, smoking and hysterectomy, were related to androgen levels among postmenopausal women, while others, including height and time since menopause, were not. Future studies are needed to clarify further which lifestyle factors modulate androgen levels.
Beyond Cooperative Robotics: The Central Role of Interdependence in Coactive Design

This article discusses that the concept of levels of autonomy is incomplete and insufficient as a model for designing complex human-machine teams, largely because it does not sufficiently account for the interdependence among their members. Building on a theory of joint activity, we introduce the notion of coactive design, an approach to human-machine interaction that takes interdependence as the central organizing principle among people and agents working together as a team.
Tangent linear superparameterization of convection in a 10 layer global atmosphere with calibrated climatology

This paper describes a new intermediate global atmosphere model in which synoptic and planetary dynamics including the advection of water vapor are explicit in 10 layers, the time‐mean flow is centered near a realistic state through the use of carefully calibrated time‐independent 3‐D forcings, and temporal anomalies of convective tendencies of heat and moisture in each column are represented as a linear matrix acting on the anomalous temperature and moisture profiles. Currently, this matrix is Kuang's [ ] linear response function (LRF) of a cyclic convection‐permitting model (CCPM) in equilibrium with specified atmospheric cooling (i.e., without radiation or WISHE interactions, so it conserves column moist static energy exactly). The goal of this effort is to cleanly test the role of convection's free‐tropospheric moisture sensitivity in tropical waves, without incurring large changes of mean climate that confuse the interpretation of experiments with entrainment parameters in the convection schemes of full‐physics GCMs. When the sensitivity to free‐tropospheric moisture is multiplied by a factor ranging from 0 to 2, the model's variability ranges from: (1) moderately strong convectively coupled Kelvin waves with speeds near 20 m s−1; to (0) similar but much weaker waves; to (2) similar but stronger and slightly faster waves as the water vapor field plays an increasingly important role. Longitudinal structure in the model's time‐mean tropical flow is not fully realistic, and does change significantly with matrix‐coupled variability, but further work on editing the anomaly physics matrix and calibrating the mean state could improve this class of models.