Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Evidence for the Emergence and Evolution of Pathogenicity and Niche Preferences in the Genus Campylobacter

The genus Campylobacter includes some of the most relevant pathogens for human and animal health; the continuous effort in their characterization has also revealed new species putatively involved in different kind of infections. Nowadays, the available genomic data for the genus comprise a wide variety of species with different pathogenic potential and niche preferences. In this work, we contribute to enlarge this available information presenting the first genome for the species Campylobacter sputorum bv. sputorum and use this and the already sequenced organisms to analyze the emergence and evolution of pathogenicity and niche preferences among Campylobacter species. We found that campylobacters can be unequivocally distinguished in established and putative pathogens depending on their repertory of virulence genes, which have been horizontally acquired from other bacteria because the nonpathogenic Campylobacter ancestor emerged, and posteriorly interchanged between some members of the genus. Additionally, we demonstrated the role of both horizontal gene transfers and diversifying evolution in niche preferences, being able to distinguish genetic features associated to the tropism for oral, genital, and gastrointestinal tissues. In particular, we highlight the role of nonsynonymous evolution of disulphide bond proteins, the invasion antigen B (CiaB), and other secreted proteins in the determination of niche preferences. Our results arise from assessing the previously unmet goal of considering the whole available Campylobacter diversity for genome comparisons, unveiling notorious genetic features that could explain particular phenotypes and set the basis for future research in Campylobacter biology.
BT-Crowds: Crowds-Style Anonymity with Bluetooth and Java

This paper aims to describe a new idea on how privacy in a Crowds-style network could be enhanced by running it over Bluetooth personal area networking. A potential implementation is described using the Java Bluetooth programming interface. The proposal is called BT-Crowds and it describes a store-and-forward Crowds and remailer-style service which uses the Bluetooth protocol stack and provides a system for privacy-enhanced communications that has some significant benefits over Crowds in fixed networks. It leverages the property of a single Bluetooth user being indistinguishable from a group of many, and the property of ad hoc networks being distributed in physical space.
Respiratory syncytial virus (RSV) F, G, M2 (22K), and N proteins each induce resistance to RSV challenge, but resistance induced by M2 and N proteins is relatively short-lived

The ability of recombinant vaccinia viruses that separately encoded 9 of the 10 known respiratory syncytial virus (RSV) proteins to induce resistance to RSV challenge was studied in BALB/c mice. Resistance was examined at two intervals following vaccination to examine early (day 9) as well as late (day 28) immunity. BALB/c mice were inoculated simultaneously by the intranasal and intraperitoneal routes with a recombinant vaccinia virus encoding one of the following RSV proteins: F, G, N, P, SH, M, 1B, 1C, or M2 (22K). A parainfluenza virus type 3 HN protein recombinant (Vac-HN) served as a negative control. One half of the mice were challenged with RSV intranasally on day 9, and the remaining animals were challenged on day 28 postvaccination. Mice previously immunized by infection with RSV, Vac-F, or Vac-G were completely or almost completely resistant to RSV challenge on both days. In contrast, immunization with Vac-HN, -P, -SH, -M, -1B, or -1C did not induce detectable resistance to RSV challenge. Mice previously infected with Vac-M2 or Vac-N exhibited significant but not complete resistance on day 9. However, in both cases resistance had largely waned by day 28 and was detectable only in mice immunized with Vac-M2. These results demonstrate that F and G proteins expressed by recombinant vaccinia viruses are the most effective RSV protective antigens. This study also suggests that RSV vaccines need only contain the F and G glycoproteins, because the immunity conferred by the other proteins is less effective and appears to wane rapidly with time.
Performance modeling for two-hop relay with node selfishness in delay tolerant networks

Delay tolerant networks (DTNs) rely on the mobility of nodes and sequences of their contacts to compensate for lack of continuous connectivity and thus enable messages to be delivered from end to end in a “store-carry-forward” way. Since each node may also need to deliver out its locally generated message, in addition to carrying and forwarding messages for other nodes, the node may become more willing to forward its own message rather than that of others when it encounters some node. This kind of selfish behaviors may become much more significant when the nodes are operating under both QoS requirements (e.g., delivery delay requirements) and energy constraints. In this paper, we analytically explore how this kind of selfish behaviors will influence the delivery performance of the two-hop relay in the challenging DTNs. In particular, a continuous time Markov chain-based theoretical framework is developed to model the complicated message delivery process. With the help of the theoretical framework, closed-form expressions are further derived for both the expected delivery delay and the expected delivery cost, where the important node selfishness issue is carefully incorporated into the analysis.
Performance criteria for testosterone measurements based on biological variation in adult males: recommendations from the Partnership for the Accurate Testing of Hormones.

BACKGROUND Testosterone measurements that are accurate, reliable, and comparable across methodologies are crucial to improving public health. Current US Food and Drug Administration-cleared testosterone assays have important limitations. We sought to develop assay performance requirements on the basis of biological variation that allow physiologic changes to be distinguished from assay analytical errors. METHODS From literature review, the technical advisory subcommittee of the Partnership for the Accurate Testing of Hormones compiled a database of articles regarding analytical and biological variability of testosterone. These data, mostly from direct immunoassay-based methodologies, were used to specify analytical performance goals derived from within- and between-person variability of testosterone. RESULTS The allowable limits of desirable imprecision and bias on the basis of currently available biological variation data were 5.3% and 6.4%, respectively. The total error goal was 16.7%. From recent College of American Pathologists proficiency survey data, most currently available testosterone assays missed these analytical performance goals by wide margins. Data from the recently established CDC Hormone Standardization program showed that although the overall mean bias of selected certified assays was within 6.4%, individual sample measurements could show large variability in terms of precision, bias, and total error. CONCLUSIONS Because accurate measurement of testosterone across a wide range of concentrations [approximately 2-2000 ng/dL (0.069-69.4 nmol/L)] is important, we recommend using available data on biological variation to calculate performance criteria across the full range of expected values. Additional studies should be conducted to obtain biological variation data on testosterone from women and children, and revisions should be made to the analytical goals for these patient populations.
Improving an exact solver for the traveling salesman problem using partition crossover

The best known exact solver for generating provably optimal solutions to the Traveling Salesman Problem (TSP) is the Concorde algorithm. Concorde uses a branch and bound search strategy, as well as cutting planes to reduce the search space. The first step in using Concorde is to obtain a good initial solution. A good solution can be generated using a heuristic solver outside of Concorde, or Concorde can generate its own initial solution using the Chained Lin Kernighan (LK) algorithm. In this paper, we speed up Concorde by improving the initial solutions produced by Chained LK using Partition Crossover. Partition Crossover is a powerful deterministic recombination operator that is able to tunnel between local optima. In every instance we examined, the addition of recombination resulted in an average speed-up of Concorde, and in the majority of cases, the difference in the runtime costs was statistically significant.
Demonstration Paper: A Comparative Study of Surgical Skills Assessment in a Physical Laparoscopy Simulator Using Wireless Inertial Sensors

A novel approach, using wireless inertial sensors (the Orient specks), is presented for the automated assessment of surgical skills in a physical laparoscopic ('keyhole') surgery simulator. Performance metrics are applied to inertial data from subjects categorized by previous laparoscopic experience: novices (less than 2 months); intermediates (less than 2 years) and experts (6 to 10 years of active laparoscopic operating experience). These metrics are shown to distinguish between groups, demonstrating 'construct validity' of the system. The method is evaluated against an optical instrument tracking system and compares favourably, thus demonstrating 'concurrent validity' with an existing method. Our findings suggest that a combination of the proposed metrics can be used to generate a 'technical performance score' for a given laparoscopic simulated task. This has the potential to help guide surgical training and monitoring of surgical performance.
Experimental Studies of Flow Patterns of Different Fluids in a Partially Filled Rotating Cylinder

An attempt has been made to investigate the various parameters affecting the fluid behaviour, partially filled in a rotating cylinder. When the cylinder is rotating at ‘high’ speed, a liquid forms a hollow cylinder. Different patterns are observed in the fluids for the rotatioal speeds below a critical speed. This study should give us some insight into molten metal behaviour during centrifugal casting. An extensive experimental investigation is required to obtain an appropriate functional relationship by knowing and understanding some dimensionless parameters. Here the effect of dimensionless parameters e (which is 2 g/ω 2 d, where g, ω and d denotes gravitational acceleration, container rotation rate and inner diameter of liquid cylinder) and G (number of times the gravity) was studied as variation of rotation speed, viscosity and aspect ratio of the mould.
Isokinetic strength testing does not predict hamstring injury in Australian Rules footballers.

OBJECTIVE: To determine the relation of hamstring and quadriceps muscle strength and imbalance to hamstring injury using a prospective observational cohort study METHOD: A total of 102 senior male Australian Rules footballers aged 22.2 (3.6) years were tested at the start of a football season. Maximum voluntary concentric and eccentric torque of the hamstring and quadriceps muscles of both legs was assessed using a Kin-Com isokinetic dynamometer at angular velocities of 60 and 180 degrees/second. Twelve (11.8%) players sustained clinically diagnosed hamstring strains which caused them to miss one or more matches over the ensuing season. RESULTS: There were no significant differences for any of the isokinetic variables comparing the injured and non-injured legs in players with unilateral hamstring strains (n=9). Neither the injured nor the non-injured leg of injured players differed from the mean of left and right legs in non-injured players for any isokinetic variable. The hamstring to opposite hamstring ratios also did not differ between injured and non-injured players. A hamstring to opposite hamstring ratio of less than 0.90 and a hamstring to quadriceps ratio of less than 0.60 were not associated with an increased risk of hamstring injury. A significantly greater percentage of players who sustained a hamstring strain reported a history of hamstring strain compared with non-injured players (p=0.02). However, this was not related to muscle weakness or imbalance. CONCLUSIONS: Isokinetic muscle strength testing was not able to directly discriminate Australian Rules football players at risk for a hamstring injury.
Efficacy of Homocysteine-Lowering Therapy With Folic Acid in Stroke Prevention: A Meta-Analysis

Background and Purpose— Although a lower serum homocysteine concentration is associated with a reduced risk of stroke in epidemiologic studies, randomized, controlled trials have yielded mixed findings regarding the effect of therapeutic homocysteine lowering on stroke prevention. We performed a meta-analysis of randomized, controlled trials to assess the efficacy of folic acid supplementation in the prevention of stroke. Methods— Salient trials were identified by formal literature search. Relative risk (RR) with 95% CI was used as a measure of the association between folic acid supplementation and risk of stroke, after pooling data across trials in a fixed-effects model. Results— The search identified 13 randomized, controlled trials that had enrolled 39 005 participants for folic acid therapy to reduce homocysteine in which stroke was reported as an outcome measure. Across all trials, folic acid supplementation was associated with a trend toward mild benefit that did not reach statistical significance in reducing the risk of stroke (RR=0.93; 95% CI, 0.85–1.03; P=0.16). The RR for nonsecondary prevention trials was 0.89 (95% CI, 0.79–0.99; P=0.03). In stratified analyses, a greater beneficial effect was seen in the trials testing combination therapy of folic acid plus vitamins B6 and B12 (RR=0.83; 95% CI, 0.71–0.97; P=0.02) and in the trials that disproportionately enrolled male patients (men:women >2; RR=0.84; 95% CI, 0.74–0.94; P=0.003). Conclusions— Folic acid supplementation did not demonstrate a major effect in averting stroke. However, potential mild benefits in primary stroke prevention, especially when folate is combined with B vitamins and in male patients, merit further investigation.
Is routine micropuncture access necessary for percutaneous nephrostomy? A randomized trial.

OBJECTIVE To compare the micropuncture technique and the conventional large-bore needle approach for renal access. METHODS From July 1999 to July 2000, patients referred to interventional radiology for emergent or elective percutaneous nephrostomy with normal coagulation profiles were considered for the study. Nephrostomy procedures were performed using a micropuncture system or large-bore needle for collecting system access; 24 nephrostomy procedures were randomized to each group using permuted blocks and opaque sealed envelopes. Gross hematuria, quantitative urine red blood cell counts, pain scores and procedural success were compared between the 2 groups. RESULTS There was a small difference in the incidence of gross hematuria between the large-bore needle and micropuncture groups (12 [50%] v. 8 [33%] patients), but this difference was not statistically significant. Quantitative urine red blood cell counts obtained immediately after and 24 hours after nephrostomy placement showed no significant differences. Significantly fewer needle passes were required for access in the large-bore needle group than the micropuncture group (1.7 v. 2.8, p = 0.01), and mean procedure duration was 7 minutes longer in the micropuncture group, although this difference was not significant. No differences in pain scores or procedure success were seen. CONCLUSION Percutaneous nephrostomy performed with a micropuncture system in patients with normal coagulation profiles does not significantly decrease organ bleeding or pain. More needle passes and manipulations are required, which may increase procedure duration. The additional costs of routine micropuncture access for percutaneous nephrostomy are not supported by this study.
Bimodal Size Distribution and Shape Anisotropy in Ball-Milled Nano-Sized α-Al2O3

α-Al2O3 prepared by combustion technique was ball-billed in a planetary mill in toluene medium at 300 rpm in ZrO2 pot with a ball to powder ratio 10:1 for 1, 5, 10, 15, and 20 hours. X-ray diffraction pattern from the milled materials showed super-Lorentzian peak shapes for α-Al2O3 peak profiles. The super-Lorentzian peak shape has been attributed to the bimodal size distribution of the α-Al2O3 particles. Rietveld analysis using two different phase fractions of α-Al2O3 with different microstructural features yielded a low goodness-of-fit of the x-ray data indicating the suitability of the assumed model. The phase fraction of α-Al2O3 particles with smaller size increases with the milling time. Further the particles shapes were observed to be cylindrical in this case with the cylinder axis along the crystallographic c-axis. The cylinder diameter and the length were obtained to be 86 Å and 140 Å respectively after 20 hrs of milling. The α-Al2O3 particles of larger size are isotropic. It is, thus, proposed that milling induces bimodal size distribution in the initial hours of milling.
Bringing Semantics in Word Image Retrieval

Performance of the recognition free approaches for document retrieval, heavily depends on the exact or approximate matching of images (in some feature space) to retrieve documents containing the same word. However, the harder problem in information retrieval is to effectively bring semantics into the retrieval pipeline. This is further challenging when the matching is based on visual features. In this work, we investigate this problem, and suggest a solution by directly transferring the semantics from the textual domain. Our retrieval framework uses (i) the language resources like Word Net and (ii) an annotated corpus of document images, to retrieve semantically relevant words from a large word image database. We demonstrate the method on two languages - English and Hindi, and quantitatively evaluate the performance on annotated word image databases of more than a Million images.
Survey of robust and resilient social media tools on Android

We present an overview of robust and resilient social media tools to overcome natural disasters, censorship and Internet kill switches. These social media tools use Android devices to communicate during disasters and aim to overcome attacks on freedom of expression. There is an abundance of projects that aim to provide resilient communication, enhance privacy, and provide anonymity. We focus specifically on the limited set of mature tools with a healthy development community and Internet-deployment.
Operator Patterns for Analysis of Composite Events in Timed Automata

Abstract—Event-triggered real-time systems interact with theenvironment by executing actions in response to monitoredevents. Such systems may be implemented using event conditionaction (ECA) rules, which execute an action if the associatedevent occurs and a specified condition is true. However, the ECArule paradigm is known to be hard to analyze with respect tocorrectness and timeliness, which is not conducive to the highpredictability requirements typically associated with real-timesystems. To still take advantage of the ECA rule paradigm whenevent-triggered real-time systems are developed, we propose anapproach where systems are specified and analyzed in a high-levelformal language (timed automata) and later transformed into theECA rule paradigm. We especially focus on a high-level approachfor specifying and analyzing composite event occurrences in timedautomata
Efficient Runahead Execution: Power-Efficient Memory Latency Tolerance

Today's high-performance processors face main-memory latencies on the order of hundreds of processor clock cycles. As a result, even the most aggressive processors spend a significant portion of their execution time stalling and waiting for main-memory accesses to return data to the execution core. Runahead execution is a promising way to tolerate long main-memory latencies because it has modest hardware cost and doesn't significantly increase processor complexity. Runahead execution improves a processors performance by speculatively pre-executing the application program while the processor services a long-latency (1,2) data cache miss, instead of stalling the processor for the duration of the L2 miss. For runahead execution to be efficiently implemented in current or future high-performance processors which will be energy-constrained, processor designers must develop techniques to reduce these extra instructions. Our solution to this problem includes both hardware and software mechanisms that are simple, implementable, and effective
Phenotypically aberrant astrocytes that promote motoneuron damage in a model of inherited amyotrophic lateral sclerosis

Motoneuron loss and reactive astrocytosis are pathological hallmarks of amyotrophic lateral sclerosis (ALS), a paralytic neurodegenerative disease that can be triggered by mutations in Cu-Zn superoxide dismutase (SOD1). Dysfunctional astrocytes contribute to ALS pathogenesis, inducing motoneuron damage and accelerating disease progression. However, it is unknown whether ALS progression is associated with the appearance of a specific astrocytic phenotype with neurotoxic potential. Here, we report the isolation of astrocytes with aberrant phenotype (referred as “AbA cells”) from primary spinal cord cultures of symptomatic rats expressing the SOD1G93A mutation. Isolation was based on AbA cells’ marked proliferative capacity and lack of replicative senescence, which allowed oligoclonal cell expansion for 1 y. AbA cells displayed astrocytic markers including glial fibrillary acidic protein, S100β protein, glutamine synthase, and connexin 43 but lacked glutamate transporter 1 and the glial progenitor marker NG2 glycoprotein. Notably, AbA cells secreted soluble factors that induced motoneuron death with a 10-fold higher potency than neonatal SOD1G93A astrocytes. AbA-like aberrant astrocytes expressing S100β and connexin 43 but lacking NG2 were identified in nearby motoneurons, and their number increased sharply after disease onset. Thus, AbA cells appear to be an as-yet unknown astrocyte population arising during ALS progression with unprecedented proliferative and neurotoxic capacity and may be potential cellular targets for slowing ALS progression.
Initial design and physical characterization of a polymeric device for osmosis‐driven delayed burst delivery of vaccines

Achieving the combination of delayed and immediate release of a vaccine from a delivery device without applying external triggers remains elusive in implementing single administration vaccination strategies. Here a means of vaccine delivery is presented, which exploits osmosis to trigger delayed burst release of an active compound. Poly(ε‐caprolactone) capsules of 2 mm diameter were prepared by dip‐coating, and their burst pressure and release characteristics were evaluated. Burst pressures (in bar) increased with wall thickness (t in mm) following Pburst = 131.t + 3.4 (R2 = 0.93). Upon immersion in PBS, glucose solution‐filled capsules burst after 8.7 ± 2.9 days. Copolymers of hydrophobic ε ‐caprolactone and hydrophilic polyethylene glycol were synthesized and their physico–chemical properties were assessed. With increasing hydrophilic content, the copolymer capsules showed increased water uptake rates and maximum weight increase, while the burst release was earlier: 5.6 ± 2.0 days and 1.9 ± 0.2 days for 5 and 10 wt% polyethylene glycol, respectively. The presented approach enables the reproducible preparation of capsules with high versatility in materials and properties, while these vaccine delivery vehicles can be prepared separately from, and independently of the active compound. Biotechnol. Bioeng. 2015;112: 1927–1935. © 2015 Wiley Periodicals, Inc.