Miracle-dz/UniFAR-FTUs huggingface dataset:
15-712 Project Proposal

For this class project, we plan to work on the system integration and evaluate the performance in term of system scalability. Specifically, our system is the behavior-based email filtering system. We already have the prospective design of the system and the detection algorithm. Briefly, we use the behavioral patterns that we have learnt from the malware in the past to detect new and unknown malware. We are going to improve the scalability on Xen by applying the flash cloning [2] and copy-on-write [3] techniques.
Application of fluorescence lifetime imaging of enhanced green fluorescent protein to intracellular pH measurements

We have shown that the intracellular pH of a single HeLa cell expressing the enhanced green fluorescent protein (EGFP) can be imaged using the fluorescence lifetime of EGFP, which can be interpreted in terms of the pH-dependent ionic equilibrium of the p -hydroxybenzylidene-imidazolidinone structure of the chromophore of EGFP.
Health Related Quality of Life in Adolescents with Idiopathic Scoliosis

The present study is organized into four parts: at the beginning, the authors explore the historical origin of the HRQOL construct and its definition correlating it to the concepts of body image, stress and family function. The second part is about the impact of the scoliosis diagnosis and conservative treatment on the patient. The third part is a brief description of the measuring instruments and the last one discusses authors’ contribution to the field.
Challenges in testing TSV-based 3D stacked ICs: Test flows, test contents, and test access

Three-dimensional stacked ICs (3D-SICs) based on Through-Silicon Vias (TSVs) have many attractive benefits and hence are quickly gaining ground. Testing such products for manufacturing defects is still fraught with many challenges. This paper provides an overview of those challenges and their emerging solutions, categorized in the areas of (1) test flows, (2) test contents, and (3) test access.
Substance misuse trends in South Africa

This paper, the first in a series related to the Joint European South African Research Network in Anxiety Disorders programme, examines substance use trends in South Africa. Alcohol remains the substance with the greatest burden of harm. Yet, trends vary by region, with for example methamphetamine being a major driver of psychiatric and substance abuse treatment demand in the Western Cape province. Heroin use is increasing in several provinces, where rapid intervention is required to avoid an epidemic. In particular, the state (the main funder of drug services) urgently needs to provide opioid substitution treatment. Apart from an inadequate number of treatment services, barriers to treatment are high. Barriers are predominantly cost, transport and resource related. Services are also impacted by a small and inadequately trained workforce and poor integration with mental health services. To adequately intervene with substance use disorders, South Africa needs an evidence‐based policy and service planning framework that forges linkages with the mental health service system. Copyright © 2012 John Wiley & Sons, Ltd.
Rapid Molecular Microbiologic Diagnosis of Prosthetic Joint Infection

ABSTRACT We previously showed that culture of samples obtained by prosthesis vortexing and sonication was more sensitive than tissue culture for prosthetic joint infection (PJI) diagnosis. Despite improved sensitivity, culture-negative cases remained; furthermore, culture has a long turnaround time. We designed a genus-/group-specific rapid PCR assay panel targeting PJI bacteria and applied it to samples obtained by vortexing and sonicating explanted hip and knee prostheses, and we compared the results to those with sonicate fluid and periprosthetic tissue culture obtained at revision or resection arthroplasty. We studied 434 subjects with knee (n = 272) or hip (n = 162) prostheses; using a standardized definition, 144 had PJI. Sensitivities of tissue culture, of sonicate fluid culture, and of PCR were 70.1, 72.9, and 77.1%, respectively. Specificities were 97.9, 98.3, and 97.9%, respectively. Sonicate fluid PCR was more sensitive than tissue culture (P = 0.04). PCR of prosthesis sonication samples is more sensitive than tissue culture for the microbiologic diagnosis of prosthetic hip and knee infection and provides same-day PJI diagnosis with definition of microbiology. The high assay specificity suggests that typical PJI bacteria may not cause aseptic implant failure.
Motivations and Usage Patterns of Social Networking Sites: Exploring Cultural Differences Between United States & Sri Lanka

Cybernetics has experienced a major breakthrough and led to the utilization of computers at nearly all parts of daily life including social networking. Even though Social Networking Sites (SNS) is a global phenomenon, it is constrained by local conditions such as culture. Thus, the purpose of the study is to incorporate cultural dimensions to the motivations and usage patterns of the SNS considering SNS as a collection of features. Present study replicates a study made in the United States in Sri Lanka, and identified differences, trace them to cultural reasons. Findings revealed that while patterns of SNS usage do not differ across cultures, some of the motivations behind them do differ. Theoretical and practical implications of these findings, possible cultural reasons for differences and directions for further research are discussed.
Effectiveness of peri-abortion counselling in preventing subsequent unplanned pregnancy: a systematic review of randomised controlled trials

Objective This systematic review and meta-analysis assessed whether enhanced peri-abortion contraceptive counselling had an effect on subsequent unplanned pregnancies and the uptake and continuation of contraceptive methods. Methods and materials A systematic review of English-language articles published prior to May 2014 was conducted, using MEDLINE, EMBASE and the Cochrane Library. Only randomised controlled trials (RCTs) involving enhanced pre- and post-abortion contraceptive counselling were included. The authors independently applied the inclusion and exclusion criteria to the identified records, and extracted data from each included paper using a predefined extraction form. Risk of bias was assessed using the Cochrane Collaboration's tool. Meta-analyses were undertaken where appropriate and based on random effects models. Results Six RCTs met the inclusion criteria. Three RCTs investigated the effect of enhanced counselling on subsequent unplanned pregnancy. The results of the meta-analysis were non-significant [pooled odds ratio (OR) 0.47; 95% confidence interval (95% CI) 0.12–1.90]. Four RCTs reported results relating to the uptake of long-acting reversible contraception (LARC) and continuation of chosen method of contraception at 3 months. Findings were non-significant (pooled OR 1.07; 95% CI 0.20–5.69 and pooled OR 3.22; 95% CI 0.85–12.22, respectively). Conclusions This review found no evidence of effect resulting from enhanced peri-abortion contraceptive counselling on subsequent unplanned pregnancy rate or the uptake of LARC. However, these findings are limited by the small number of relevant studies available and the marked heterogeneity between published studies. Further, larger-scale RCTs should be undertaken to ensure that there is sufficient power to detect an effect.
Molecular Signaling Mechanisms Underlying Epileptogenesis

Epilepsy, a disorder of recurrent seizures, is a common and frequently devastating neurological condition. Available therapy is only symptomatic and often ineffective. Understanding epileptogenesis, the process by which a normal brain becomes epileptic, may help identify molecular targets for drugs that could prevent epilepsy. A number of acquired and genetic causes of this disorder have been identified, and various in vivo and in vitro models of epileptogenesis have been established. Here, we review current insights into the molecular signaling mechanisms underlying epileptogenesis, focusing on limbic epileptogenesis. Study of different models reveals that activation of various receptors on the surface of neurons can promote epileptogenesis; these receptors include ionotropic and metabotropic glutamate receptors as well as the TrkB neurotrophin receptor. These receptors are all found in the membrane of a discrete signaling domain within a particular type of cortical neuron—the dendritic spine of principal neurons. Activation of any of these receptors results in an increase Ca2+concentration within the spine. Various Ca2+-regulated enzymes found in spines have been implicated in epileptogenesis; these include the nonreceptor protein tyrosine kinases Src and Fyn and a serine-threonine kinase [Ca2+-calmodulin–dependent protein kinase II (CaMKII)] and phosphatase (calcineurin). Cross-talk between astrocytes and neurons promotes increased dendritic Ca2+ and synchronous firing of neurons, a hallmark of epileptiform activity. The hypothesis is proposed that limbic epilepsy is a maladaptive consequence of homeostatic responses to increases of Ca2+concentration within dendritic spines induced by abnormal neuronal activity. The epilepsies, disorders of recurrent seizures, affect about 1% of the population worldwide. Available therapy is symptomatic in that drugs inhibit seizures but are not disease-modifying; that is, no effective pharmacological prevention or cure has been identified. The term "epileptogenesis" refers to the process by which a normal brain becomes epileptic. Understanding the cellular mechanisms of epileptogenesis in molecular terms may help identify molecular targets for which small-molecule therapeutics can be developed to prevent epileptogenesis in individuals at high risk. A number of acquired and genetic causes of this disorder have been identified, and various in vivo and in vitro models of epileptogenesis have been established. The objective of this STKE Review, with 5 figures, 2 tables, and 199 references, is to review current insights into the molecular signaling mechanisms underlying epileptogenesis, focusing on limbic epileptogenesis in particular.
Multiple sclerosis.

Multiple sclerosis is the prototype inflammatory autoimmune disorder of the central nervous system and, with a lifetime risk of one in 400, potentially the most common cause of neurological disability in young adults. As with all complex traits, the disorder results from an interplay between as yet unidentified environmental factors and susceptibility genes. Together, these factors trigger a cascade of events, involving engagement of the immune system, acute inflammatory injury of axons and glia, recovery of function and structural repair, post-inflammatory gliosis, and neurodegeneration. The sequential involvement of these processes underlies the clinical course characterised by episodes with recovery, episodes leaving persistent deficits, and secondary progression. The aim of treatment is to reduce the frequency, and limit the lasting effects, of relapses, relieve symptoms, prevent disability arising from disease progression, and promote tissue repair. Despite limited success in each of these categories, everyone touched by multiple sclerosis looks for a better dividend from applying an improved understanding of the pathogenesis to clinical management.
Model-free Contact Localization for Manipulated Objects using Biomimetic Tactile Sensors

Manipulation tasks often require robots to make contact between a grasped tool and another object in the robot’s environment. The ability to detect and estimate the positions and directions of these contact points is crucial for monitoring the progress of the task, and detecting failures. In this paper, we present a data-driven approach for detecting and localizing contacts between a grasped object and the environment using tactile sensing. We explore framing the contact localization as both a regression and a classification problem and train neural networks accordingly to estimate the contact parameters. We also compare the neural networks with Gaussian process regression and support vector machine classification with spatiotemporal hierarchical matching pursuit feature learning. We evaluate the presented approach using hundreds of contact events on eighteen objects with different shapes, sizes and material properties. The experiments show that the neural network approach can learn to localize contact events for individual objects with a mean absolute error of less than 2.5 cm for the positions and less than 10◦ for the directions.
FANCD2-Controlled Chromatin Access of the Fanconi-Associated Nuclease FAN1 Is Crucial for the Recovery of Stalled Replication Forks

ABSTRACT Fanconi anemia (FA) is a cancer predisposition syndrome characterized by cellular hypersensitivity to DNA interstrand cross-links (ICLs). Within the FA pathway, an upstream core complex monoubiquitinates and recruits the FANCD2 protein to ICLs on chromatin. Ensuing DNA repair involves the Fanconi-associated nuclease 1 (FAN1), which interacts selectively with monoubiquitinated FANCD2 (FANCD2Ub) at ICLs. Importantly, FANCD2 has additional independent functions: it binds chromatin and coordinates the restart of aphidicolin (APH)-stalled replication forks in concert with the BLM helicase, while protecting forks from nucleolytic degradation by MRE11. We identified FAN1 as a new crucial replication fork recovery factor. FAN1 joins the BLM-FANCD2 complex following APH-mediated fork stalling in a manner dependent on MRE11 and FANCD2, followed by FAN1 nuclease-mediated fork restart. Surprisingly, APH-induced activation and chromatin recruitment of FAN1 occur independently of the FA core complex or the FAN1 UBZ domain, indicating that the FANCD2Ub isoform is dispensable for functional FANCD2-FAN1 cross talk during stalled fork recovery. In the absence of FANCD2, MRE11 exonuclease-promoted access of FAN1 to stalled forks results in severe FAN1-mediated nucleolytic degradation of nascent DNA strands. Thus, FAN1 nuclease activity at stalled replication forks requires tight regulation: too little inhibits fork restart, whereas too much causes fork degradation.
Infliximab in Pediatric Crohn Disease Patients With Enterovesicular Fistulas

Pediatric Gastroenterology and Nutrition, The Children’s Hospital at Monmouth Medical Center, Long Branch, NJ, {Division of Pediatric Gastroenterology and Nutrition Sciences, University of Alabama at Birmingham, Journal of Pediatric Gastroenterology and Nutrition 44:279–282 # 2007 by European Society for Pediatric Gastroenterology, Hepatology, and Nutrition and North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition
Gastric emptying rate and chyme characteristics for cooked brown and white rice meals in vivo.

BACKGROUND Rice structure is important to rice grain and starch breakdown during digestion. The objective of this study was to determine the gastric emptying and rice composition during gastric digestion of cooked brown and white medium-grain (Calrose variety) rice using the growing pig as a model for the adult human. RESULTS Brown and white rice did not show significantly different gastric emptying rates of dry matter or starch, but brown rice had slower protein emptying (P < 0.05). Moisture content was greater and pH was lower in the distal stomach compared to the proximal stomach (P < 0.0001), and varied with time (P < 0.0001). The mechanism of physical breakdown for brown and white rice varied. Brown rice exhibited an accumulation of bran layer fragments in the distal stomach, quantified by lower starch and higher protein content. CONCLUSION The quantity of gastric secretions observed after a brown or white rice meal may be related to the meal buffering capacity, and are accumulated in the distal stomach. The delayed rate of protein emptying in brown rice compared to white rice was most likely due to the accumulation of bran layers in the stomach.
How important are role models in making good doctors?

The use of teaching staff as role models for professional behaviour has long been an informal part of medical training. The authors consider whether role models can still be an effective means of imparting professional values, attitudes, and behaviours in a health service that is increasingly sensitive to society's expectations Role models—people we can identify with, who have qualities we would like to have, and are in positions we would like to reach—have been shown as a way to inculcate professional values, attitudes, and behaviours in students and young doctors. 1 2 Because good role models are seen as important in the making of a good doctor, we need to know more about them. What are the attributes young people look for in role models? Are these the attributes they really emulate? How do they react when they find that seniors lack these attributes? We consider these questions and whether we should rely on role models as a mechanism for developing doctors who are more patient centred and ethically sensitive. #### Summary points The attributes of medical role models have been the subject of several interesting studies. Wright and colleagues looked at physicians who had been identified as excellent role models by students and residents.3– …
Experimental Results of Rician K-Factor and Co-Polarization Ratio of 60 GHz Wireless Channel in an Underground Mine Gallery

In this work, experimental results of the Rician K-factor and the co-polarization ratio (CPR) are obtained and discussed from measurements conducted at 40 m CANMET underground mine gallery with Horn and Omnidirectional antennas with Horizontal (H) and Vertical (V) polarizations. These results suggest that the VV polarization offers a larger number of multipath components than the HH polarization, a correlation coefficient of about 0.86 between them, and an average CPR of about 6 dB. Furthermore, the average value of the Rician K-factor shows little or no difference between the HH and VV polarizations. The average CPR value remains around 6 dB. A correlation coefficient of multipath total power between HH and VV polarization is also found to be 0.8649.
Studies of immune and normal opsonins during experimental staphylococcal infection in rabbits.

Antibacterial antibody response was studied in rabbits that were experimentally infected with staphylococci so as to simulate human endocarditis and osteomyelitis. Sera from rabbits inoculated intravenously twice weekly for 4 weeks contained high titers of opsonic, agglutinating, and complement-fixing antibodies. In a second group of rabbits, single intramedullary inoculations of staphylococci successfully produced osteomyelitis. These animals also developed high titers of opsonic and agglutinating antibodies. The titers of complement-fixing antibodies were generally lower in rabbits with experimental osteomyelitis than they were in animals with recurrent bacteremia. Opsonic antibodies were specifically and completely absorbed by the infecting strain of Staphylococcus aureus. No evidence was obtained for “leukophilic” γ globulin with phagocytosis-promoting activity. Sucrose gradient fractionation of immune rabbit sera indicated that the primary heat-stable opsonin was 7 S γG.
Increasing the confidence of nursing staff to address the sexual health needs of people living with HIV: the use of motivational interviewing

The need to promote safer sexual behaviour has taken on new urgency in the UK because of large increases in the number of sexually transmitted infections (STIs). The sexual health needs of people living with HIV and AIDS (PLHA) also require attention as part of health promotion efforts. Many sexual health clinics are however struggling with high demand and limited resources. Within this context, this paper describes an innovate attempt at STI prevention with PLHA. Specifically, nursing staff were trained in the use of motivational interviewing to address sexual health issues and safer sexual behaviour in PLHA. We describe the training package and the impact upon participants. We conclude that by providing a positive training experience, front-line health staff that see the highest volume of PLHA with repeat STIs, can be assisted in developing their skills and confidence in prevention work with clients.
Remote control of tumour‐targeted Salmonella enterica serovar Typhimurium by the use of l‐arabinose as inducer of bacterial gene expression in vivo

We have used Salmonella enterica serovar Typhimurium (S. typhimurium) which are able to colonize tumours besides spleen and liver. Bacteria were equipped with constructs encoding green fluorescent protein or luciferase as reporters under control of the promoter PBAD that is inducible with l‐arabinose. Reporter genes could be induced in culture but also when the bacteria resided within the mouse macrophages J774A.1. More important, strong expression of reporters by the bacteria could be detected in mice after administration of l‐arabinose. This was especially pronounced in bacteria colonizing tumours. Histology demonstrated that the bacteria had accumulated in and close to necrotic areas of tumours. Bacterial gene induction was observed in both regions. PBAD is tightly controlled also in vivo because gene E of bacteriophage ΦX174 could be introduced as inducible suicide gene. The possibility to deliberately induce genes in bacterial carriers within the host should render them extremely powerful tools for tumour therapy.
Agonist‐selective signaling of G protein‐coupled receptor: Mechanisms and implications

Agonist‐selective signaling or ligand‐biased signaling of G protein‐coupled receptor (GPCR) has become the focus of an increasing number of laboratories. The principle of this concept is that agonist possesses different abilities to activate different signaling pathways. Current review summarizes the observations of agonist‐selective signaling of various GPCRs, indicating the significance of agonist‐selective signaling in biological processes. In addition, current review also provides an overview on how agonist‐selective signaling is initiated. Especially, the relationship between GPCR‐G protein interaction and GPCR‐β‐arrestin interaction is discussed in depth. © 2010 IUBMB IUBMB Life, 62(2): 112–119, 2010