Miracle-dz/UniFAR-FTUs huggingface dataset:
Familial hemiplegic migraine and autosomal dominant arteriopathy with leukoencephalopathy (CADASIL)

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a recently described familial cerebrovascular disorder shown to map to chromosome 19q12. Familial hemiplegic migraine has also been shown in some families to map close to the CADASIL locus. The fully developed CADASIL phenotype consists of recurrent strokes developing in the fourth decade, progressing to a pseudobulbar palsy, spastic quadriparesis, and subcortical dementia. In an Irish family 15 members were fully investigated by magnetic resonance scanning; 10 had typical magnetic resonance features of CADASIL. Five members of this family had familial hemiplegic migraine and 4 of these had magnetic resonance evidence of CADASIL. Two other members had migraine with and without aura as a presenting clinical symptom of CADASIL. This disorder has been shown by linkage analysis to map to the CADASIL locus at chromosome 19. The phenotype at presentation of CADASIL in this family was variable and age related and included familial hemiplegic migraine, migraine with and without aura, transient ischemic attacks, strokes, and spinal cord infarction. This family study increases our understanding of the spectrum of clinical manifestations of this underrecognized familial cerebrovascular disorder.
Camera model identification with the use of deep convolutional neural networks

In this paper, we propose a camera model identification method based on deep convolutional neural networks (CNNs). Unlike traditional methods, CNNs can automatically and simultaneously extract features and learn to classify during the learning process. A layer of preprocessing is added to the CNN model, and consists of a high pass filter which is applied to the input image. Before feeding the CNN, we examined the CNN model with two types of residuals. The convolution and classification are then processed inside the network. The CNN outputs an identification score for each camera model. Experimental comparison with a classical two steps machine learning approach shows that the proposed method can achieve significant detection performance. The well known object recognition CNN models, AlexNet and GoogleNet, are also examined.
Effects of the Built Environment on Childhood Obesity: The Case of Urban Recreational Trails and Crime

We study the effects of urban environment on childhood obesity by concentrating on the effects of walking trails and crime close to children's homes on their BMI and obesity status. We use a unique dataset, which combines information on recreational trails in Indianapolis with data on violent crimes and anthropomorphic and diagnostic data from children's clinic visits between 1996 and 2005. We find that having a trail near a home reduces children's weight. However, the effect depends on the amount of nearby violent crimes. Significant reductions occur only in low crime areas and trails could have opposite effects on weight in high crime areas. These effects are primarily among boys, older children, and children who live in higher income neighborhoods. Evaluated at the mean length of trails this effect for older children in no crime areas would be a reduction of 2 lb of the body weight. Falsification tests using planned trails instead of existing trails, show that trails are more likely to be located in areas with heavier children, suggesting that our results on effects of trails represent a lower bound.
Serum netrin-1 in relation to gadolinium-enhanced magnetic resonance imaging in early multiple sclerosis

Background Netrin-1, a secreted laminin-related protein, is known to regulate not only axonal guidance and neuronal cell migration, but also blood–brain barrier integrity and inflammation. Two preliminary studies reported altered serum netrin-1 levels in multiple sclerosis; however, associations with longitudinal clinical and magnetic resonance imaging activity have not been investigated. Objectives We aimed to assess serum netrin-1 in multiple sclerosis and controls with respect to disease activity and its temporal dynamics. Methods Serum netrin-1 was assessed by enzyme-linked immunosorbent assay in 79 patients with clinically isolated syndrome or multiple sclerosis, and 30 non-inflammatory neurological disease controls. In patients, serum samples were collected immediately prior to gadolinium-enhanced 3 T magnetic resonance imaging at two time points (initial contrast-enhancing gadolinium+ n = 47, non-enhancing gadolinium– n = 32; reference gadolinium– n = 70; median time-lag 1.4, interquartile range 1.0–2.3 years). Results Serum netrin-1 levels were similar in clinically isolated syndrome, multiple sclerosis and controls, and gadolinium+ and gadolinium– patients. Among gadolinium+ patients, serum netrin-1 was decreased in clinically active (n = 8) vs non-active patients (n = 39; p = 0.041). Serum netrin-1 showed no temporal dynamics in multiple sclerosis and was unrelated to clinical data. Conclusions Serum netrin-1 levels show no multiple sclerosis specific changes and are not sensitive for detection of subclinical disease activity. Netrin-1 changes during relapses may deserve further examination.
Rapidly Mixing Gibbs Sampling for a Class of Factor Graphs Using Hierarchy Width

Gibbs sampling on factor graphs is a widely used inference technique, which often produces good empirical results. Theoretical guarantees for its performance are weak: even for tree structured graphs, the mixing time of Gibbs may be exponential in the number of variables. To help understand the behavior of Gibbs sampling, we introduce a new (hyper)graph property, called hierarchy width. We show that under suitable conditions on the weights, bounded hierarchy width ensures polynomial mixing time. Our study of hierarchy width is in part motivated by a class of factor graph templates, hierarchical templates, which have bounded hierarchy width-regardless of the data used to instantiate them. We demonstrate a rich application from natural language processing in which Gibbs sampling provably mixes rapidly and achieves accuracy that exceeds human volunteers.
Factors associated with damage accrual in patients with systemic lupus erythematosus: results from the Systemic Lupus International Collaborating Clinics (SLICC) Inception Cohort

Background and aims We studied damage accrual and factors determining development and progression of damage in an international cohort of systemic lupus erythematosus (SLE) patients. Methods The Systemic Lupus International Collaborating Clinics (SLICC) Inception Cohort recruited patients within 15 months of developing four or more 1997 American College of Rheumatology (ACR) criteria for SLE; the SLICC/ACR damage index (SDI) was measured annually. We assessed relative rates of transition using maximum likelihood estimation in a multistate model. The Kaplan–Meier method estimated the probabilities for time to first increase in SDI score and Cox regression analysis was used to assess mortality. Results We recruited 1722 patients; mean (SD) age 35.0 (13.4) years at cohort entry. Patients with damage at enrolment were more likely to have further worsening of SDI (SDI 0 vs ≥1; p<0.001). Age, USA African race/ethnicity, SLEDAI-2K score, steroid use and hypertension were associated with transition from no damage to damage, and increase(s) in pre-existing damage. Male gender (relative transition rates (95% CI) 1.48 (1.06 to 2.08)) and USA Caucasian race/ethnicity (1.63 (1.08 to 2.47)) were associated with SDI 0 to ≥1 transitions; Asian race/ethnicity patients had lower rates of new damage (0.60 (0.39 to 0.93)). Antimalarial use was associated with lower rates of increases in pre-existing damage (0.63 (0.44 to 0.89)). Damage was associated with future mortality (HR (95% CI) 1.46 (1.18 to 1.81) per SDI point). Conclusions Damage in SLE predicts future damage accrual and mortality. We identified several potentially modifiable risk factors for damage accrual; an integrated strategy to address these may improve long-term outcomes.
An attempt to independently verify the utility of the Van Nuys Prognostic Index for ductal carcinoma in situ

The Van Nuys Prognostic Index (VNPI) purports to predict the risk of ipsilateral breast tumor recurrence (IBTR) after excision of ductal carcinoma in situ (DCIS). It is a simple scoring scheme based on a retrospective evaluation of data from a single group of investigators. Various versions of VNPI have been proposed using clinical and pathologic features including tumor size, tumor grade, margin width, and patient age. Despite common use of VNPI in the clinical management of patients with DCIS, independent validation is lacking.
An Approach to Mine Business Rule Intents from Domain-specific Documents

An enterprise system enables business by providing various services that are guided by set of well-defined processes, and adhere to certain business rules and constraints. The business rules are usually written using English in operating procedures, terms and conditions, and various other supporting documents. For implementing the business rules in a software system, or expressing them as UML use-case specifications, analysts manually interpret the documents, leading to potential discrepancies, ambiguities, and quality issues in the software system that can be resolved only after testing. To minimize such errors, we propose a novel method to mine the documents automatically to extract the fundamental atomic facts in every sentence - called as business rule intents. We adopt dependency tree parser to parse the rule sentences and extract rule intents from them. Our experiments using few publicly available sample documents in the financial domain yielded very promising results, where rule intents extraction produced an average precision of 78% and recall of 80%.
Effects of intracerebral hemorrhage on 5-hydroxymethylcytosine modification in mouse brains

The past decade has resulted in an increase in the knowledge of molecular mechanisms underlying brain injury induced by intracerebral hemorrhage (ICH). Recent advances have provided a link between epigenetic modification and the regulation of gene expression. 5-hydroxymethylcytosine (5hmC) converted from 5-methylcytosine by the ten-eleven translocation (TET) family of proteins has emerged as a new epigenetic modification. While the dynamics of 5hmC during cerebral ischemia have recently been reported, whether 5hmC is involved in ICH remains unexplored. In this study, we investigated the effects of ICH on DNA hydroxymethylation. We showed that the global level of 5hmC rapidly decreased as early as 24 hours after ICH and persisted until 72 hours. Furthermore, the level of 5hmC in the CpG-rich regions of Akt2, Pdpk1 and Vegf genes was significantly decreased with a minimum level observed at 48 hours or 72 hours. Decreased 5hmC was observed in parallel with an increase in 5-methylcytosine over this time course, and mRNA levels of Akt2, Pdpk1 and Vegf were downregulated upon ICH injury. Finally, Tet1, Tet2 and Tet3 mRNA levels were dramatically decreased in the ICH brain. Our study for the first time established the correlation between DNA hydroxymethylation and ICH injury. Further investigations should examine whether 5hmC modification could be a therapeutic target for the treatment of ICH injury.
Chylomicrons Promote Intestinal Absorption and Systemic Dissemination of Dietary Antigen (Ovalbumin) in Mice

Background A small fraction of dietary protein survives enzymatic degradation and is absorbed in potentially antigenic form. This can trigger inflammatory responses in patients with celiac disease or food allergies, but typically induces systemic immunological tolerance (oral tolerance). At present it is not clear how dietary antigens are absorbed. Most food staples, including those with common antigens such as peanuts, eggs, and milk, contain long-chain triglycerides (LCT), which stimulate mesenteric lymph flux and postprandial transport of chylomicrons through mesenteric lymph nodes (MLN) and blood. Most dietary antigens, like ovalbumin (OVA), are emulsifiers, predicting affinity for chylomicrons. We hypothesized that chylomicron formation promotes intestinal absorption and systemic dissemination of dietary antigens. Methodology/Principal Findings Absorption of OVA into MLN and blood was significantly enhanced when OVA was gavaged into fasted mice together with LCT compared with medium-chain triglycerides (MCT), which do not stimulate chylomicron formation. The effect of LCT was blocked by the addition of an inhibitor of chylomicron secretion, Pluronic L-81. Adoptively transferred OVA-specific DO11.10 T-cells proliferated more extensively in peripheral lymph nodes when OVA was gavaged with LCT than with MCT or LCT plus Pluronic L-81, suggesting that dietary OVA is systemically disseminated. Most dietary OVA in plasma was associated with chylomicrons, suggesting that these particles mediate systemic antigen dissemination. Intestinal-epithelial CaCo-2 cells secreted more cell-associated, exogenous OVA when stimulated with oleic-acid than with butyric acid, and the secreted OVA appeared to be associated with chylomicrons. Conclusions/Significance Postprandial chylomicron formation profoundly affects absorption and systemic dissemination of dietary antigens. The fat content of a meal may affect immune responses to dietary antigens by modulating antigen absorption and transport.
Talent identification and early development of elite water-polo players: a 2-year follow-up study

The processes of talent detection and early development are critical in any sport programme. However, not much is known about the appropriate strategies to be implemented during these processes, and little scientific inquiry has been conducted in this area. The aim of this study was to identify variables of swimming, ball handling and physical ability, as well as game intelligence, which could assist in the selection process of young water-polo players. Twenty-four players aged 14–15 years underwent a battery of tests three times during a 2-year period, before selection to the junior national team. The tests included: freestyle swim for 50, 100, 200 and 400 m, 100-m breast-stroke, 100-m ‘butterfly’ (with breast-stroke leg motion), 50-m dribbling, throwing at the goal, throw for distance in the water, vertical ‘jump’ from the water, and evaluation of game intelligence by two coaches. A comparison of those players eventually selected to the team and those not selected demonstrated that, 2 years before selection, selected players were already superior on most of the swim tasks (with the exception of breast-stroke and 50-m freestyle), as well as dribbling and game intelligence. This superiority was maintained throughout the 2 years. Two-way tabulation revealed that, based on baseline scores, the prediction for 67% of the players was in agreement with the final selection to the junior national team. We recommend that fewer swim events be used in the process of selecting young water-polo players, and that greater emphasis should be placed on evaluation of game intelligence.
Minirhizotron imaging reveals that nodulation of field-grown soybean is enhanced by free-air CO2 enrichment only when combined with drought stress.

The rate of N2 fixation by a leguminous plant is a product of the activity of individual nodules and the number of nodules. Initiation of new nodules and N2 fixation per nodule are highly sensitive to environmental conditions. However, the effects of global environmental change on nodulation in the field are largely unknown. It is also unclear whether legumes regulate nodulation in response to environment solely by varying root production or also by varying nodule density per unit of root length. This study utilised minirhizotron imaging as a novel in situ method for assessing the number, size and distribution of nodules in field-grown soybean (Glycine max (L.) Merr. ) exposed to elevated atmospheric CO2 ([CO2]) and reduced precipitation. We found that nodule numbers were 134-229% greater in soybeans grown at elevated [CO2] in combination with reduced precipitation, and this response was driven by greater nodule density per unit of root length. The benefits of additional nodules were probably offset by an unfavourable distribution of nodules in shallow, dry soil in reduced precipitation treatment under elevated [CO2] but not ambient [CO2]. In fact, significant decreases in seed and leaf nitrogen concentration also occurred only in elevated [CO2] with reduced precipitation. This study demonstrates the potential of minirhizotron imaging to reveal previously uncharacterised changes in nodule production and distribution in response to global environmental change.
Vision in 3D Environments: Representing, perceiving, and remembering the shape of visual space

Humans constantly engage in automatic and rapid analysis of spatial scene structure when navigating an environment or searching for objects. This chapter draws on current research from computational, behavioral and neuroscience perspectives aimed at understanding how the human brain perceives, represents, and remembers the shape of space. Space can be described with both structural descriptions, which reflect layout of surfaces in the physical world, and semantic descriptions, which incorporate an observers understanding of the environment. We first review two formal approaches which can quantify the structural properties of scene layout: the isovist representation and the spatial envelope representation. Next we explore how space is experienced by observers, by reviewing behavioral results in which different factors distort the perceived space away from a veridical representation. Finally, we examine how representations of specific views of space are maintained in memory, and discuss potential neural mechanisms involved in integrating views into larger environments. Gaining a formal understanding of how geometric aspects of space map onto human perceptual, cognitive, and neural systems will help to create efficient functional spaces for our daily interactions with the world.
Azurophilic granules of human neutrophilic leukocytes are deficient in lysosome-associated membrane proteins but retain the mannose 6-phosphate recognition marker.

During granulocyte differentiation in the bone marrow (BM), neutrophilic leukocyte precursors synthesize large amounts of lysosomal enzymes. These enzymes are sequestered into azurophilic storage granules until used days later for digestion of phagocytized microorganisms after leukocyte emigration to inflamed tissues. This azurophil granule population has previously been defined as a primary lysosome, i.e., a membrane-bound organelle containing acid hydrolases that have not entered into a digestive event. In this study, azurophil granules were purified and shown to contain large amounts of mannose 6-phosphate-containing glycoproteins (Man 6-P GP) but little lysosome-associated membrane proteins (LAMP). In addition, the fine structural localization of Man 6-P GP and LAMP was investigated at various stages of maturation in human BM and blood. Man 6-P GP were present within the azurophilic granules at all stages of maturation and in typical multivesicular bodies (MVB) as well as in multilaminar compartments (MLC), identified by their content of concentric arrays of internal membranes. LAMP was absent in all identified granule populations, but was consistently found in the membranes of vesicles, MVB, and MLC. The latter compartment has not been previously described in this cell type. In conclusion, the azurophilic granules, which contain an abundance of lysosomal enzymes and Man 6-P GP, lack the LAMP glycoproteins. By current criteria, they therefore cannot be classified as lysosomes, but rather may have the functional characteristics of a regulated secretory granule. Rather, the true lysosomes of the resting neutrophil are probably the MVB and MLC. Finally, the typical "dense bodies" or mature lysosomes described in other cells are not present in resting neutrophils.
Cellular dimensions affecting the nucleocytoplasmic volume ratio

Although it has long been appreciated that larger eukaryotic cells have larger nuclei, little is known about how this size relationship is maintained. Here we describe a method for measuring the aqueous volume ratio of nucleus to cytoplasm, two compartments which are interconnected via the pores in the nuclear envelope. We then use that method to identify proportional cellular dimensions in variously treated cells and in different cell types. Cells were scrape loaded with a mixture of fluorescent dextrans: Texas red dextran, average mol wt = 10,000 (TRDx10), and fluorescein isothiocyanate dextran, average mol wt = 70,000 (FDx70). After introduction into the cytoplasmic space, the TRDx10 distributed into both the nucleus and cytoplasm, whereas the FDx70 was restricted to cytoplasm, due to size exclusion by the nuclear pores. The aqueous nucleocytoplasmic volume ratio (RN/C) was determined by measuring, from fluorescence images of spread cells, total cellular fluorescence of each of the two probes and the fluorescence ratio of those probes in the cytoplasm. RN/C was unaffected by the measurement procedure or by varying temperatures between 23 degrees and 37 degrees C. Loading excess unlabeled dextrans had little effect on RN/C, with the single exception that high concentrations of large dextrans could lower RN/C in endothelial cells. Expanding intracellular membranous compartments of macrophages by phagocytosis of latex beads decreased RN/C. Expanding the same compartment by pinocytosis of sucrose, which nearly doubled total cell volume, had little effect on RN/C, indicating that nuclear volume was more closely linked to the cytoplasmic volume, exclusive of vesicular organelles, than to total cell volume. RN/C was the same in mononucleate and binucleate endothelial cells. Finally, measurements of RN/C in murine bone marrow-derived macrophages, bovine aortic endothelial cells, Swiss 3T3 fibroblasts, PtK2 cells, and CV-1 cells revealed that nuclear volume scaled allometrically with cell volume. The allometric relationship indicated that cell volume was proportional to nuclear surface area.