LLukas22/scidocs huggingface dataset:
Functional Genomics Analysis of Big Data Identifies Novel Peroxisome Proliferator-Activated Receptor γ Target Single Nucleotide Polymorphisms Showing Association With Cardiometabolic Outcomes.

BACKGROUND
Cardiovascular disease and type 2 diabetes mellitus represent overlapping diseases where a large portion of the variation attributable to genetics remains unexplained. An important player in their pathogenesis is peroxisome proliferator-activated receptor γ (PPARγ) that is involved in lipid and glucose metabolism and maintenance of metabolic homeostasis. We used a functional genomics methodology to interrogate human chromatin immunoprecipitation-sequencing, genome-wide association studies, and expression quantitative trait locus data to inform selection of candidate functional single nucleotide polymorphisms (SNPs) falling in PPARγ motifs.


METHODS AND RESULTS
We derived 27 328 chromatin immunoprecipitation-sequencing peaks for PPARγ in human adipocytes through meta-analysis of 3 data sets. The PPARγ consensus motif showed greatest enrichment and mapped to 8637 peaks. We identified 146 SNPs in these motifs. This number was significantly less than would be expected by chance, and Inference of Natural Selection from Interspersed Genomically coHerent elemenTs analysis indicated that these motifs are under weak negative selection. A screen of these SNPs against genome-wide association studies for cardiometabolic traits revealed significant enrichment with 16 SNPs. A screen against the MuTHER expression quantitative trait locus data revealed 8 of these were significantly associated with altered gene expression in human adipose, more than would be expected by chance. Several SNPs fall close, or are linked by expression quantitative trait locus to lipid-metabolism loci including CYP26A1.


CONCLUSIONS
We demonstrated the use of functional genomics to identify SNPs of potential function. Specifically, that SNPs within PPARγ motifs that bind PPARγ in adipocytes are significantly associated with cardiometabolic disease and with the regulation of transcription in adipose. This method may be used to uncover functional SNPs that do not reach significance thresholds in the agnostic approach of genome-wide association studies.
Callosal Function in Pediatric Traumatic Brain Injury Linked to Disrupted White Matter Integrity.

UNLABELLED
Traumatic brain injury (TBI) often results in traumatic axonal injury and white matter (WM) damage, particularly to the corpus callosum (CC). Damage to the CC can lead to impaired performance on neurocognitive tasks, but there is a high degree of heterogeneity in impairment following TBI. Here we examined the relation between CC microstructure and function in pediatric TBI. We used high angular resolution diffusion-weighted imaging (DWI) to evaluate the structural integrity of the CC in humans following brain injury in a sample of 32 children (23 males and 9 females) with moderate-to-severe TBI (msTBI) at 1-5 months postinjury, compared with well matched healthy control children. We assessed CC function through interhemispheric transfer time (IHTT) as measured using event-related potentials (ERPs), and related this to DWI measures of WM integrity. Finally, the relation between DWI and IHTT results was supported by additional results of neurocognitive performance assessed using a single composite performance scale. Half of the msTBI participants (16 participants) had significantly slower IHTTs than the control group. This slow IHTT group demonstrated lower CC integrity (lower fractional anisotropy and higher mean diffusivity) and poorer neurocognitive functioning than both the control group and the msTBI group with normal IHTTs. Lower fractional anisotropy-a common sign of impaired WM-and slower IHTTs also predicted poor neurocognitive function. This study reveals that there is a subset of pediatric msTBI patients during the post-acute phase of injury who have markedly impaired CC functioning and structural integrity that is associated with poor neurocognitive functioning.


SIGNIFICANCE STATEMENT
Traumatic brain injury (TBI) is the primary cause of death and disability in children and adolescents. There is considerable heterogeneity in postinjury outcome, which is only partially explained by injury severity. Imaging biomarkers may help explain some of this variance, as diffusion weighted imaging is sensitive to the white matter disruption that is common after injury. The corpus callosum (CC) is one of the most commonly reported areas of disruption. In this multimodal study, we discovered a divergence within our pediatric moderate-to-severe TBI sample 1-5 months postinjury. A subset of the TBI sample showed significant impairment in CC function, which is supported by additional results showing deficits in CC structural integrity. This subset also had poorer neurocognitive functioning. Our research sheds light on postinjury heterogeneity.
Mokken Scale Analysis in R

Mokken scale analysis (MSA) is a scaling procedure for both dichotomous and polytomous items. It consists of an item selection algorithm to partition a set of items into Mokken scales and several methods to check the assumptions of two nonparametric item response theory models: the monotone homogeneity model and the double monotonicity model. First, we present an R package mokken for MSA and explain the procedures. Second, we show how to perform MSA in R using test data obtained with the Adjective Checklist.
Bioreduction of Cr (VI) by potent novel chromate resistant alkaliphilic Bacillus sp. strain KSUCr5 isolated from hypersaline Soda lakes

Isolation of Cr (VI) resistant alkaliphilic bacteria from sediment and water samples collected from Wadi Natrun hypersaline Soda lakes (located in northern Egypt), resulted in isolation of several alkaliphilic bacterial strains that can tolerate up to 2.94 g/l of Cr (VI) in alkaline medium. However, with increasing Cr (VI) concentration up to 29.4 g/l, only one strain, KSUCr5, was able to tolerate up to 22 g/l (75 mM) and with MIC value of 23.5 g/l (80 mM) in alkaline medium (pH 10.5) containing 10% NaCl. Based on the 16S rRNA gene analysis, strain KSUCr5 was identified as Bacillus sp. with 99% similarity and was referred to as Bacillus sp. KSUCr5. In addition, Bacillus sp. strain KSUCr5 showed high tolerance to several other heavy metals including Cd 2+ (50 mM), Mo 2+ (75 mM), Mn 2+ (100 mM), Cu 2+ (2 mM), Ni 2+ (100 mM), Pb (75 mM), Co 2+ (5 mM) and Zn 2+ (2 mM). Strain KSUCr5 was shown to be of a high efficiency in detoxifying chromate, as it could rapidly reduce up to 40 mg/l of Cr(VI) to a non detectable level over 24 h. In addition, at initial Cr(VI) concentration of 60 to 80 and 100 mg/l, 100% of the chromate reduction was achieved within 48 and 72 h, respectively. Strain KSUCr5 could reduce Cr(VI) efficiently over a wide range of initial Cr(VI) concentrations (10 to 300 mg/l) in alkaline medium under aerobic conditions without significant effect on the bacterial growth. It was able to reduce Cr(VI) in a wide range of NaCl (0 to 20%) with a maximum reduction yield at concentration of 0 to 1.5%, indicating the halo tolerance nature of the bacterium. It was found that addition of glucose and Na2CO3 to the culture medium caused a dramatic increase in Cr(VI)-reduction by Bacillus sp. strain KSUCr5. The maximum chromate removal was exhibited in alkaline medium (pH 10) containing 1.2% Na2CO3, 1.5% glucose and 1% NaCl and at incubation temperature of 35°C and culture shaking of 150 rpm. Under optimum Cr (VI) reduction conditions, Cr(VI) concentration of 80 mg/l was completely reduced within 24 h, with reduction rate of 3.3 mg h -1 which is one of the highest Cr(VI) reduction rate under high alkaline conditions, compared with other microorganisms that has been reported so far. Furthermore, the presence of other metals such as Ni 2+ , Mo 2+ , Cu 2+ and Mn 2+ at concentration of 100 mg/l together with Cr(VI) in the culture medium slightly increased Cr(VI)-reduction by the strain KSUCr5. Moreover, the isolate, Bacillus sp. strain KSUCr5, exhibited an ability to repeatedly reduce hexavalent chromium without any amendment of nutrients, suggesting its potential application in continuous bioremediation of Cr(VI). The results reveal the possible isolation of potent heavy metals resistant bacteria from extreme environment such as hypersaline Soda lakes and their application in bioremediation of heavy metals.
Cyber Warfare: A Review of Theories, Law, Policies, Actual Incidents - and the Dilemma of Anonymity

In this paper, the authors undertake a study of cyber warfare reviewing theories, law, policies, actual incidents and the dilemma of anonymity. Starting with the United Kingdom perspective on cyber warfare, the authors then consider United States' views including the perspective of its military on the law of war and its general inapplicability to cyber conflict. Consideration is then given to the work of the United Nations' group of cyber security specialists and diplomats who as of July 2010 have agreed upon a set of recommendations to the United Nations Secretary General for negotiations on an international computer security treaty. An examination of the use of a nation's cybercrime law to prosecute violations that occur over the Internet indicates the inherent limits caused by the jurisdictional limits of domestic law to address cross-border cybercrime scenarios. Actual incidents from Estonia (2007), Georgia (2008), Republic of Korea (2009), Japan (2010), ongoing attacks on the United States as well as other incidents and reports on ongoing attacks are considered as well. Despite the increasing sophistication of such cyber attacks, it is evident that these attacks were met with a limited use of law and policy to combat them that can be only be characterised as a response posture defined by restraint. Recommendations are then examined for overcoming the attribution problem. The paper then considers when do cyber attacks rise to the level of an act of war by reference to the work of scholars such as Schmitt and Wingfield. Further evaluation of the special impact that non-state actors may have and some theories on how to deal with the problem of asymmetric players are considered. Discussion and possible solutions are offered. A conclusion is offered drawing some guidance from the writings of the Chinese philosopher Sun Tzu. Finally, an appendix providing a technical overview of the problem of attribution and the dilemma of anonymity in cyberspace is provided. 1. The United Kingdom Perspective "If I went and bombed a power station in France, that would be an act of war. If I went on to the net and took out a power station, is that an act of war? One
Peripheral vascular applications of the Amplatzer vascular plug.

PURPOSE
To present our experience using the Amplatzer vascular plug in various arterial and venous systems, and follow-up results.


MATERIALS AND METHODS
Between May 2005 and October 2006, 20 Amplatzer vascular plugs were used to achieve occlusion in 20 vessels in 12 patients (10 male, 2 female) aged between 24 and 80 years (mean age, 55 years). Localization and indications for embolotherapy were as follows: pulmonary arteriovenous malformations (n = 3; 9 vessels), internal iliac artery embolization before stent-graft repair for aortoiliac aneurysms (n = 4; 4 vessels), preoperative (right hemipelvectomy) embolization of bilateral internal iliac arteries (n = 1), bilateral internal iliac aneurysms (n = 1), large thoracic side branch of the left internal mammary artery coronary by-pass graft causing coronary steal syndrome (n = 1), closure of a transjugular intrahepatic portosystemic shunt (n = 1), and testicular vein embolization for a varicocele (n = 1).


RESULTS
The technical success rate was 100%, with total occlusion of all the targeted vessels. Only one device was used to achieve total occlusion of the targeted vessel in all patients (device size range, 6-16 mm in diameter). No major complications occurred. Target vessel occlusion time after deployment of the Amplatzer vascular plug was 6-10 min in pulmonary arteries (mean, 7.5 min) and 10-35 min (mean, 24.4 min) in systemic arteries. Mean follow-up was 6.7 months (range, 1-18 months).


CONCLUSION
Embolization with the Amplatzer vascular plug is safe, feasible, and technically simple with appropriate patient selection in various vascular territories.
RGB-D mapping: Using Kinect-style depth cameras for dense 3D modeling of indoor environments

RGB-D cameras (such as the Microsoft Kinect) are novel sensing systems that capture RGB images along with per-pixel depth information. In this paper we investigate how such cameras can be used for building dense 3D maps of indoor environments. Such maps have applications in robot navigation, manipulation, semantic mapping, and telepresence. We present RGB-D Mapping, a full 3D mapping system that utilizes a novel joint optimization algorithm combining visual features and shape-based alignment. Visual and depth information are also combined for view-based loop closure detection, followed by pose optimization to achieve globally consistent maps. We evaluate RGB-D Mapping on two large indoor environments, and show that it effectively combines the visual and shape information available from RGB-D cameras.
Frequency and comparative analysis of hapatitis D in petients seeking treatment for hepatitis B.

OBJECTIVE
To find the frequency of hepatitis 'D' in patients of hepatitis 'B' seeking treatment and to compare clinical and biochemical features in patients harboring HDV with those who are not.


DESIGN
Cross-sectional study.


PLACE AND DURATION OF STUDY
Medical Unit-IV, Civil Hospital Karachi, Medical Unit-VI and Surgical Unit-VII, Lyari General Hospital, Dow University of Health Sciences, Karachi; from July 2003 to June 2005.


PATIENTS AND METHODS
HBsAg positive patients seeking treatment were enrolled in the study. Anti-HDV was done in all. Patients were split into two groups according to their anti-HDV status into HDV positive and HDV negative groups. Liver biochemistries and viral profile for HCV, anti-HBc IgM and HBeAg were done and compared between the two groups.


RESULTS
A total of 246 patients were selected. HDV was positive in 66 (26.8%) patients. No significant difference was observed in the frequency and stages of cirrhosis between the two groups while significant differences were observed in the mean SGPT (95% CI: -381.09 to -110.74; P = 0.001) and albumin levels (95% CI: 1.87 to 7.73; P = 0.007) and in the frequency of HBeAg (P = 0.001), anti-HBc IgM (P = 0.02) and HBV DNA (P<0.001).


CONCLUSION
HDV infection was common in patients with HBV in this cohort of patients. All patients of HBV should be screened for HDV before treatment decision for the former is taken.
Circadian pattern of sleep, energy expenditure, and body temperature of young healthy men during the intermittent fasting of Ramadan

We hypothesize that factors other than a sudden shift in eating habits contribute to delay of circadian rhythms during Ramadan. We assessed circadian changes during a baseline period (BL, 1 week before Ramadan), the first week (R1), and the second week (R2), of Ramadan, in six healthy Muslim young adults using portable armband physiological and activity sensor devices. All participants lived in an unconstrained environment and showed delayed sleep phase syndrome, so that they normally slept during the day and ate at night. During Ramadan, there was a further delay in the acrophase of skin temperature during Ramadan, indicating a shift in the circadian pattern of body temperature. Additionally, there was a delay in the peak of energy expenditure during R1 and R2. These results support our hypothesis that in addition to sudden shift in meal times, other factors may affect the sleep pattern and circadian rhythms during Ramadan.
User personality and resistance to mandatory information systems in organizations: a theoretical model and empirical test of dispositional resistance to change

This research is driven by the assumption made in several user resistance studies that employees are generally resistant to change. It investigates the extent to which employees’ resistance to IT-induced change is caused by individuals’ predisposition to resist change. We develop a model of user resistance that assumes the influence of dispositional resistance to change on perceptual resistance to change, perceived ease of use, and usefulness, which in turn influence user resistance behavior. Using an empirical study of 106 HR employees forced to use a new human resources information system, the analysis reveals that 17.0–22.1 percent of the variance in perceived ease of use, usefulness, and perceptual resistance to change can be explained by the dispositional inclination to change initiatives. The four dimensions of dispositional resistance to change – routine seeking, emotional reaction, short-term focus and cognitive rigidity – have an even stronger effect than other common individual variables, such as age, gender, or working experiences. We conclude that dispositional resistance to change is an example of an individual difference that is instrumental in explaining a large proportion of the variance in beliefs about and user resistance to mandatory IS in organizations, which has implications for theory, practice, and future research. Journal of Information Technology advance online publication, 16 June 2015; doi:10.1057/jit.2015.17
The effect of APOE genotype on the delivery of DHA to cerebrospinal fluid in Alzheimer’s disease

Apolipoprotein E (APOE) ɛ4 and low cerebrospinal fluid (CSF) amyloid-β42 (Aβ42) levels are predictors for developing Alzheimer’s disease (AD). The results of several studies indicate an interaction between docosahexaenoic acid (DHA) consumption and cognitive outcomes by APOE genotype. Our objective in the present study was to examine whether APOE ɛ4 genotype and low CSF Aβ42 levels were associated with reduced delivery of DHA to CSF in the Alzheimer’s Disease Cooperative Study-sponsored DHA clinical trial. Phospholipid DHA was assayed in the plasma of 384 participants and CSF of 70 participants at baseline. Forty-four of the 70 participants completed the 18-month follow-up visit after allocation to placebo (n = 15) or DHA (n = 29). Plasma and CSF DHA levels, CSF Aβ42, Tau, and phosphorylated Tau were measured at baseline and after the 18-month intervention. Participants were divided into tertiles based on baseline Aβ42 CSF levels. To assess DHA delivery across the blood-brain barrier, the ratio of CSF to plasma DHA levels was calculated. At baseline, there were no significant differences between CSF or plasma phospholipid DHA levels by CSF Aβ42 tertiles or ɛ4 status. After 18 months of DHA supplementation, participants at the lowest Aβ42 tertile had significantly lower CSF DHA levels (p = 0.01) and lower CSF-to-plasma DHA ratios (p = 0.05) compared to the other tertiles. Baseline CSF Aβ42 levels were significantly lower in ɛ4 carriers than in ɛ4 noncarriers (p = 0.01). Participants carrying the ɛ4 allele (n = 25) demonstrated a less pronounced increase in CSF DHA level compared with noncarriers (n = 4), with a possible interaction effect between treatment and APOE genotype (p = 0.07). APOE ɛ4 allele and lower CSF Aβ42 levels were associated with less transport of DHA to CSF. Brain amyloid pathology may limit the delivery of DHA to the brain in AD. Clinicaltrials.gov identifier: NCT00440050 . Registered on 22 Feb 2007.
Simultaneous treatment of tibial bone and soft-tissue defects with the Ilizarov method.

OBJECTIVES
To evaluate the potential for limb salvage using the Ilizarov method to simultaneously treat bone and soft-tissue defects of the leg without flap coverage.


DESIGN
Retrospective study.


SETTING
Level I trauma centers at 4 academic university medical centers.


PATIENTS/PARTICIPANTS
Twenty-five patients with bone and soft-tissue defects associated with tibial fractures and nonunions. The average soft-tissue and bone defect after debridement was 10.1 (range, 2-25) cm and 6 (range, 2-14) cm respectively. Patients were not candidates for flap coverage and the treatment was a preamputation limb salvage undertaking in all cases.


INTERVENTION
Ilizarov and Taylor Spatial Frames used to gradually close the bone and soft-tissue defects simultaneously by using monofocal shortening or bifocal or trifocal bone transport.


MAIN OUTCOME MEASUREMENTS
Bone union, soft-tissue closure, resolution or prevention of infection, restoration of leg length equality, alignment, limb salvage.


RESULTS
The average time of compression and distraction was 19.7 (range, 5-70) weeks, and time to soft-tissue closure was 14.7 (range, 3-41) weeks. Bony union occurred in 24 patients (96%). The average time in the frame was 43.2 (range, 10-82) weeks. Lengthening at another site was performed in 15 patients. The average amount of bone lengthening was 5.6 (range, 2-11) cm. Final leg length discrepancy (LLD) averaged 1.2 (range, 0-5) cm. Use of the trifocal approach resulted in less time in the frame for treatment of large bone and soft-tissue defects. There were no recurrences of osteomyelitis at the nonunion site. All wounds were closed. There were no amputations. All limbs were salvaged.


CONCLUSIONS
The Ilizarov method can be successfully used to reconstruct the leg with tibial bone loss and an accompanying soft-tissue defect. This limb salvage method can be used in patients who are not believed to be candidates for flap coverage. One also may consider using this technique to avoid the need for a flap. Gradual closure of the defect is accomplished resulting in bony union and soft-tissue closure. Lengthening can be performed at another site. A trifocal approach should be considered for large defects (>6 cm). Advances in technique and frame design should help prevent residual deformity.
How to apply de Bruijn graphs to genome assembly

T development of algorithmic ideas for next-generation sequencing can be traced back 300 years to the Prussian city of Königsberg (present-day Kaliningrad, Russia), where seven bridges joined the four parts of the city located on opposing banks of the Pregel River and two river islands (Fig. 1a). At the time, Königsberg’s residents enjoyed strolling through their city, and they wondered if every part of the city could be visited by walking across each of the seven bridges exactly once and returning to one’s starting location. The solution came in 1735, when the great mathematician Leonhard Euler1 made a conceptual breakthrough that would solve this ‘Bridges of Königsberg problem’. Euler’s first insight was to represent each landmass as a point (called a node) and each bridge as a line segment (called an edge) connecting the appropriate two points. This creates a graph—a network of nodes connected by edges (Fig. 1b). By describing a procedure for determining whether an arbitrary graph contains a path that visits every edge exactly once and returns to where it started, Euler not only resolved the Bridges of Königsberg problem but also effectively launched the entire branch of mathematics known today as graph theory2. Since Euler’s original description, the use of graph theory has turned out to have many additional practical applications, most of which have greater scientific importance than the development of walking itineraries. Specifically, Euler’s ideas were subsequently adapted by Dutch mathematician Nicolaas de Bruijn to find a cyclic sequence of letters taken from a given alphabet for which every possible word of a certain length (k) appears as a string of consecutive characters in the cyclic sequence exactly once (Box 1 and Fig. 2). Application of the de Bruijn graph has also proven invaluable in the field of molecular biology where researchers are faced with the problem of assembling billions of short sequencing reads into a single genome. In the following article, we describe the problems faced when constructing a genome and how the de Bruijn graph approach can be applied to assemble short-read sequences.