Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of the endomembrane systems of trypanosomatids – conservation and specialisation

ABSTRACT Parasite surfaces support multiple functions required for survival within their hosts, and maintenance and functionality of the surface depends on membrane trafficking. To understand the evolutionary history of trypanosomatid trafficking, where multiple lifestyles and mechanisms of host interactions are known, we examined protein families central to defining intracellular compartments and mediating transport, namely Rabs, SNAREs and RabGAPs, across all available Euglenozoa genomes. Bodonids possess a large trafficking repertoire, which is mainly retained by the Trypanosoma cruzi group, with extensive losses in other lineages, particularly African trypanosomes and phytomonads. There are no large-scale expansions or contractions from an inferred ancestor, excluding direct associations between parasitism or host range. However, we observe stepwise secondary losses within Rab and SNARE cohorts (but not RabGAPs). Major changes are associated with endosomal and late exocytic pathways, consistent with the diversity in surface proteomes between trypanosomatids and mechanisms of interaction with the host. Along with the conserved core family proteins, several lineage-specific members of the Rab (but not SNARE) family were found. Significantly, testing predictions of SNARE complex composition by proteomics confirms generalised retention of function across eukaryotes. Summary: The trafficking systems of trypanosomes are shown to vary considerably, with much minimisation in systems with antigenic variation and more complexity in cell invasive forms.
Outcome following onset of juvenile idiopathic inflammatory arthritis: II. predictors of outcome in juvenile arthritis.

OBJECTIVE To assess the relative contributions of demographic, clinical and laboratory variables in predicting outcome in juvenile idiopathic inflammatory arthritis (JIA), based on a review of the existing literature. METHODS Electronic reference database searches for the previous 10 yr were conducted and studies examining the role of major potential predictors of main outcomes were identified. Where possible, subjects were grouped by JIA disease subtype. In addition to demographic variables, the following disease-related predictors were assessed: nature of joint involvement, acute-phase response, and presence of autoantibodies. These were then analysed for three main outcomes of interest: remission as assessed by disease activity; functional impairment; and structural damage as assessed by radiological joint erosions. RESULTS In general, female gender, polyarticular and symmetrical joint involvement, elevated inflammatory markers and rheumatoid factor positivity were the most consistent predictors of a poor outcome, although the studies were frequently inconsistent in both the direction and the magnitude of the effects. CONCLUSIONS These data are too variable to accurately identify those predictors associated with poor outcome following the onset of JIA. Although some of this variation may be the result of true differences between study populations, the vast majority of inconsistencies are explainable by the absence of standardized classification systems, outcome definitions, therapeutic approach and research tools. More comprehensive prospective evaluation is required before robust prediction models can be generated.
Persuasive technology for health and wellness: State-of-the-art and emerging trends

The evolving field of persuasive and behavior change technology is increasingly targeted at influencing behavior in the area of health and wellness. This paper provides an empirical review of 16 years (85 papers) of literature on persuasive technology for health and wellness to: (1.) answer important questions regarding the effectiveness of persuasive technology for health and wellness, (2.) summarize and highlight trends in the technology design, research methods, motivational strategies, theories, and health behaviors targeted by research to date, (3.) uncover pitfalls of existing persuasive technological interventions for health and wellness, and (4.) suggest directions for future research.
A walk on the client side: Monitoring enterprise Wifi networks using smartphone channel scans

During the one minute it takes to read this abstract, two billion smartphones worldwide will perform billions of Wifi channel scans recording the signal strength of nearby Wifi Access Points (APs). Yet despite this ongoing planetary-scale wireless network measurement, few systematic efforts are made today to recover this potentially valuable data. In this paper we ask the question: “Are the smartphone channel scans useful in monitoring enterprise Wifi networks? ” More specifically, can these client-side measurements provide new insights compared to the AP-side measurements that enterprise Wifi networks already perform? Beginning with two Wifi scan datasets collected on two large scale smartphone testbeds, we conduct case studies that show how smartphone channel scans can be used to (1) improve AP spectrum management, and (2) predict the impact of AP failure or overload. In each case, a walk on the client side yields valuable insights for network operators that are otherwise impossible to gain from AP-side measurements, and together our results demonstrate the value of smartphone channel scans.
Plasmacytoid dendritic cells initiate a complex chemokine and cytokine network and are a viable drug target in chronic HCV patients

Plasmacytoid dendritic cells (pDCs) are the professional type I interferon (IFN)-producing cells, and upon activation they traffic to lymph organs, where they bridge innate and adaptive immunity. Using multianalyte profiling (MAP), we have mapped the key chemokines and cytokines produced in response to pDC activation, taking into consideration the role of autocrine IFN, as well as paracrine effects on other innate cells (e.g., monocytes and conventional DCs). Interestingly, we identify four distinct cytokine/chemokine loops initiated by Toll-like receptor engagement. Finally, we applied this analytic approach to the study of pDC activity in chronic hepatitis C patients. Based on the activation state of pDCs in fresh blood, the lack of agonistic activity of infectious virions, the production of a broad array of cytokines/chemokines once stimulated, and the direct effects of pDCs on other PBMCs, we conclude that the pDCs from hepatitis C virus (HCV)-infected individuals are fully functional and are, indeed, a viable drug target. In sum, this study provides insight into the use of MAP technology for characterizing cytokine networks, and highlights how a rare cell type integrates the activation of other inflammatory cells. Furthermore, this work will help evaluate the therapeutic application of pDC agonists in diseases such as chronic HCV infection.
PCR Detection of Fusarium oxysporum f. sp. basilici on Basil.

Sixty-nine amplified DNA fragments, generated from different isolates of Fusarium oxysporum f. sp. basilici, were tested for F. oxysporum f. sp. basilici-specificity in a dot blot assay. One 1,038-bp fragment hybridized to DNA from all F. oxysporum f. sp. basilici isolates but not to DNA obtained from F. oxysporum isolates nonpathogenic to basil or representatives of other formae speciales of F. oxysporum, or from isolates of F. redolens, F. tabacinum, Rhizoctonia solani, Sclerotinia sclerotiorum, S. minor, and Pythium ultimum obtained from diseased basil. This fragment was cloned and sequenced, and three pairs of F. oxysporum f. sp. basilici-specific primers were designed, giving rise to amplification products of 943, 382, and 330 bp. A nested PCR assay allowed detection of F. oxysporum f. sp. basilici in diseased seedlings and in artificially and naturally contaminated seeds. The theoretical detection limit of this system was 102 fungal propagules per 100 seeds on artificially contaminated samples, while on naturally contaminated commercial seed lots, 32 propagules per 100 seeds were detected.
Exploring the memory-bandwidth tradeoff in an information-centric network

An information-centric network should realize significant economies by exploiting a favourable memory-bandwidth tradeoff: it is cheaper to store copies of popular content close to users than to fetch them repeatedly over the Internet. We evaluate this tradeoff for some simple cache network structures under realistic assumptions concerning the size of the content catalogue and its popularity distribution. Derived cost formulas reveal the relative impact of various cost, traffic and capacity parameters, allowing an appraisal of possible future network architectures. Our results suggest it probably makes more sense to envisage the future Internet as a loosely interconnected set of local data centers than a network like today's with routers augmented by limited capacity content stores.
Generalized stacking fault energies in the basal plane of triclinic molecular crystal 1,3,5-triamino-2,4,6-trinitrobenzene (TATB)

Molecular dynamics and molecular statics simulations were used to investigate dislocation glide in the basal plane (i.e. the – plane, where , and define the edge vectors of the unit cell) of -triamino--trinitrobenzene (TATB) using generalized stacking fault energy surfaces (-surfaces). Triclinic symmetry and molecular packing arrangement result in two glide plane types for the same glide plane normal. The unstable stacking fault energies () are less than at K and atm, indicating easy dislocation glide. Glide in the and – directions is preferred compared to the direction at atm. A stable stacking fault is predicted in the – direction at atm and 5 GPa. A compound twin with energy is predicted to be stable in the basal plane. Unequal values of about the stable stacking fault in the and – traces indicate an asymmetric barrier to dislocation glide. High pressure ( GPa) results in an increase in the values. The extremely small barriers to twinning and dislocation glide might be sources for observed second-harmonic generation in the nominally centrosymmetric crystal.
New physical insight and modeling of second breakdown (It/sub 2/) phenomenon in advanced esd protection devices

Second breakdown phenomenon in advanced NMOS ESD protection devices has remained an enigma due to the complex electrical and thermal effects that are responsible for its triggering. For the first time, we present a critical study of the high current phenomenon in ultra short-time scale to understand the physics of instability in protection devices around the second breakdown region. It is demonstrated that for advanced protection devices, carrier heating in the high field drain region causes a fall in the saturation drift velocity, which increases the transit time of carriers through the depletion region. This in turn, causes greater impact ionization due to higher accumulation of avalanche-generated carriers; leading to the formation of a propagating ionizing wave front, which culminates in a regenerative avalanche injection induced second breakdown failure
Efficacy of intravenous tramadol and low-dose ketamine in the prevention of post-spinal anesthesia shivering following cesarean section: a double-blinded, randomized control trial

Background Shivering is a frequent and undesirable complication of spinal anesthesia. It is a physiologic response to increase the body core temperature in an attempt to raise metabolic heat production. However, shivering may trigger myocardial ischemia; increase intraocular and intracranial pressures, increase wound pain, delay wound healing and interfere with pulse rate, blood pressure and electrocardiogram monitoring. We aimed to compare the efficacy of intravenous (IV) ketamine with IV tramadol for the prevention of shivering in patients who underwent cesarean delivery under spinal anesthesia. Patients and methods A prospective, randomized, double-blind study was conducted. One hundred and twenty-three American Society of Anesthesiologist I and II patients, aged between 18 and 39 years, who underwent cesarean section were included in the study. Patients were randomly allocated to one of three groups: group S (n=41; control group) received saline, group K (n=41) received ketamine 0.2 mg/kg and group T (n=41) received tramadol 0.5 mg/kg. Incidence and grade of shivering and side effects between the treatment groups were recorded. Results The incidence of shivering was significantly reduced in the ketamine and tramadol groups (41.5% and 53.7%, respectively) compared to the saline group (70.7%; p=0.028). Grade 3 shivering occurred in 16 (39%) patients in the saline group, compared to 9 (22%) in the tramadol group and 8 (19.5%) in the ketamine group (p=0.011). Only two cases in the saline group developed grade 4 shivering (p<0.01). Neonatal outcome and perioperative complications were comparable among the three groups. Conclusion The prophylactic administration of low-dose IV ketamine or IV tramadol is effective for reducing the incidence and intensity of shivering. We recommend low-dose IV ketamine or tramadol prophylaxis for parturients undergoing cesarean section under spinal anesthesia.
A second Epstein-Barr virus early antigen gene in BamHI fragment M encodes a 48- to 50-kilodalton nuclear protein

We used antiserum raised against the bacterially synthesized product of one of the open reading frames in Epstein-Barr virus (EBV) BamHI fragment M to demonstrate that this reading frame (BMRF1) codes for a nuclear protein of the diffuse early antigen (EA) class. In indirect immunofluorescence assays, the rabbit anti-BMRF1 antiserum gave nuclear staining in approximately 5% of Raji cells which had been treated with sodium butyrate, and positive fluorescence was observed in both acetone- and methanol-fixed cells. Uninduced Raji cultures contained less than 0.1% positive cells regardless of whether indirect immunofluorescence or anti-complement immunofluorescence was used. In immunoblot analyses, the rabbit serum identified a family of polypeptides of 46 to 55 kilodaltons (kDa) in total protein extracts from B95-8 cells or from butyrate-induced Raji cells. In both cell types, the dominant polypeptides were the 48- and 50-kDa species. This same family of polypeptides was identified when the immunoblots were reacted with the R3 monoclonal antibody, and we concluded that this antibody also recognized the product of the BMRF1 open reading frame. Fibroblast cell lines containing EBV BamHI fragment M were established by cotransfection of baby hamster kidney cells with BamHI-M and the gene for neomycin resistance. Aminoglycoside G418-resistant colonies which showed evidence for EBV antigen expression in immunofluorescence assays were selected, and clonal cell lines were established. After 3 to 4 months of passaging, constitutive synthesis of EA was no longer detectable in these cell lines either by immunofluorescence or by immunoblot analysis. However, in the one cell line examined, synthesis of the 48- to 50-kDa EA was induced by treatment of the culture with sodium butyrate. Thus, the regulation of expression of this EA in transfected fibroblasts is analogous to that seen in Raji lymphoblasts. We showed previously that BamHI fragment M also contains the coding sequences for a 60-kDa nuclear EA, and hence BamHI-M encodes two separate components of the diffuse EA complex.
Enabling One-Sided Communication Semantics on ARM

In this paper, we present our work to enable optimized one-sided communication operations on the ARM v8 architecture using a high-performance InfiniBand network interconnect, as well as an evaluation of our implementation. For this study, we started with an OpenSHMEM implementation based on Open MPI/SHMEM, and combined it with the UCX framework and the XPMEM kernel extension for shared memory communication. UCX is a unified communication abstraction that provides high-performance communication services over a variety of network interconnects and shared memory technologies. The UCX, XPMEM, and OpenSHMEM components were specially ported for this work in order to enable efficient access to shared memory and RDMA network capabilities on ARM. To the best of our knowledge, this is the first investigation of one-sided communication semantics and OpenSHMEM on the ARM architecture combined with a high-performance InfiniBand network and XPMEM shared memory transport.
Selective and enduring deficits in spatial learning after limited neonatal binge alcohol exposure in male rats.

BACKGROUND In rats, heavy bingelike alcohol exposure during the neonatal brain growth spurt [postnatal days (PD) 4-9] can impair development of spatial learning. This study tested whether binge exposure limited to the latter half of this period (PD 7-9) produced selective spatial learning deficits that endured into adulthood. METHODS On PD 7 to 9, Long-Evans rats were given intubations of alcohol (5.25 g/kg/day), sham intubations, or no intubations. Rats were tested as adults (>or=PD 70) in the Morris water maze under one of three different conditions: place (submerged escape platform in the same location each trial), random (submerged platform in a different, random location each trial), or redundant (visible platform that protruded above the water, in the same location for each trial). A 60-sec probe trial (with no platform present) followed the last acquisition trial. RESULTS The mean peak blood alcohol concentration was 401 mg/dl on PD 7. Neonatal alcohol treatment significantly impaired acquisition and reduced place biases on the probe trial in place-trained males, but not females. Neonatal alcohol treatment had no significant effects on acquisition performance of the random or redundant groups. Redundant training yielded rapid acquisition for all groups. The visible cue overshadowed place cues for all treatment groups, but small place biases were evident in controls. After random training, no group showed place biases. CONCLUSIONS Heavy alcohol exposure in rats limited to the last half of the neonatal brain growth spurt caused enduring deficits in spatial learning, but only in males. The deficits were specific to place learning in the Morris water maze and emerged only when learning and performance depended on the use of distal place cues.
Imaging the Intentional Stance in a Competitive Game

The "intentional stance" is the disposition to treat an entity as a rational agent, possessing particular beliefs, desires, and intentions, in order to interpret and predict it's behavior. The intentional stance is a component of a broader social cognitive function, mentalizing. Here we report a study that investigates the neural substrates of "on-line" mentalizing, using PET, by asking volunteers to second-guess an opponent. In order to identify brain activity specifically associated with adoption of an intentional stance, we used a paradigm that allowed tight control of other cognitive demands. Volunteers played a computerised version of the children's game "stone, paper, scissors. " In the mentalizing condition volunteers believed they were playing against the experimenter. In the comparison condition, volunteers believed they were playing against a computer. In fact, during the actual scanning, the "opponent" produced a random sequence in both conditions. The only difference was the attitude, or stance, adopted by the volunteer. Only one region was more active when volunteers adopted the intentional stance. This was in anterior paracingulate cortex (bilaterally). This region has been activated in a number of previous studies involving mentalizing. However, this is the first study suggesting a specific link between activity in this brain region and the adoption of an intentional stance.
Integrating EBL and ILP to Acquire Control Rules for Planning

Most approaches to learning control information in pla~nlng systems use explanation-based learning to generate control rules. Unfortunately, EBL alone often produces overly complex rules that actually decrease planning efficiency. This paper presents a novel learning approach for control knowledge acquisition that integrates explanation-based learning with techniques from inductive logic programming. EBL is used to constrain an inductive search for selection heuristics that help a planner choose between competing plan refinements. ScoPE is one of the few systems to address learning control information i the newer partial-order p]annFxs. Specifically, SCOPE learns domain-specific control rules for a version of the UCPOP p)anning algorithm. The resulting system is shown to produce significant speedup in two different p~annlng domalnA.
Bone Surface Mapping Method

Bone shape is an important factor to determine the bone's structural function. For the asymmetrically shaped and anisotropically distributed bone in vivo, a surface mapping method is proposed on the bases of its geometric transformation invariance and its uniqueness of the principal axes of inertia. Using spiral CT scanning, we can make precise measurements to bone in vivo. The coordinate transformations lead to the principal axes of inertia, with which the prime meridian and the contour can be set. Methods such as tomographic reconstruction and boundary development are employed so that the surface of bone in vivo can be mapped. Experimental results show that the surface mapping method can reflect the shape features and help study the surface changes of bone in vivo. This method can be applied to research into the surface characteristics and changes of organ, tissue or cell whenever its digitalized surface is obtained.
Single Nucleotide Polymorphisms of Toll-Like Receptor 7 and Toll-Like Receptor 9 in Hepatitis C Virus Infection Patients from Central China

Purpose To analyze the correlation of polymorphisms of toll-like receptor 7 (TLR7) (rs179009) and toll-like receptor 9 (TLR9) (rs187084) in hepatitis C virus (HCV) infections in the Han population. Materials and Methods The genotypes of TLR7IVS2-151 in HCV infection were detected by Sanger sequencing using polymerase chain reaction-restriction fragment length polymorphism to determine the TLR9 T-1486C single nucleotide polymorphisms (SNP) for all enrolled patients. Results We found no significant difference between males with spontaneous clearance of HCV versus those chronically infected [χ2=2.71, p=0.10, odd ratios (OR)=0.58, 95% confidence interval (CI) 0.31-1.11]. However, significant differences were found for the distribution of TLR7 (rs179009) in females (χ2=9.46, p=0.01). In females, a significant difference was also found between chronic hepatitis C and those with spontaneous clearance of HCV in terms of TLR7 IVS2-151G/A allele frequencies (χ2=9.50, p=0.00, OR=0.46, 95% CI 0.28-0.75). In HCV-infected patients, no significant association was found between the frequency of TLR9 genotypes and alleles. Conclusion The site of TLR7 IVS2-151 (rs179009) G/A may be a factor for susceptibility of chronic HCV in the female Han population. TLR9T-1486C (rs18084) SNP may not play a major role in HCV infection. However, individual risk profiles for HCV infection did vary by sex and this relationship should be further investigated.