Miracle-dz/UniFAR-FTUs huggingface dataset:
Venue-Based Networks May Underpin HCV Transmissions amongst HIV-Infected Gay and Bisexual Men

Background This study aimed to investigate the potential influence of venue-based networks on HCV transmission in HIV-positive gay and bisexual men (GBM). Methods This was a prospectively recruited cohort of HIV-infected GBM with recently-acquired HCV infection resident in Melbourne and Sydney. Clinical and demographic data were collected together with blood samples for HCV sequencing. Phylogenies were inferred and clusters of individuals infected with HCV with genetic sequence homology were identified. Venues used for sourcing sexual partners were identified; sourcing partners from the same venue was considered a potential social link. Using the Jaccard similarity coefficient, associations were identified between the network of sites where men sourced sex partners and transmission relationships as defined by phylogenetic clustering. Results Forty individuals were recruited, of whom 62.5% were considered to have sexually- and 37.5% IDU-acquired HCV. Venue use was consistent with men being members of a more sexually adventurous gay community subculture. Six phylogenetically-determined pairs or clusters were identified, comprising fifteen (15/28, 53.6%) individuals. Participants belonging to phylogenetic clusters were observed within the same networks. There was a significant correlation between the network and phylogenetic clustering when both cities were considered simultaneously (p = 0.005), raising the possibility that social connections may be important for HCV transmissions. Conclusions Venue-based network elicitation is a promising approach for elucidating HCV transmissions amongst HIV-infected GBM. Public health approaches targeting individuals and venues prominent within networks may reduce onward HCV transmission.
Photodeoxygenation of dinaphthothiophene, benzophenanthrothiophene, and benzonaphthothiophene S-oxides

Photoinduced deoxygenation of dibenzothiophene S -oxide (DBTO) has been suggested to release atomic oxygen [O(^3P)]. To expand the conditions and applications where O(^3P) could be used, generation of O(^3P) at longer wavelengths was desirable. The sulfoxides benzo[ b ]naphtho-[1,2, d ]thiophene S -oxide, benzo[ b ]naphtho[2,1, d ]thiophene S -oxide, benzo[ b ]phenanthro[9,10- d ]thiophene S -oxide, dinaphtho[2,1- b :1′,2′- d ]thiophene S -oxide, and dinaphtho[1,2- b :2′,1′- d ]thiophene S -oxide all absorb light at longer wavelengths than DBTO. To determine if these sulfoxides could be used to generate O(^3P), quantum yield studies, product studies, and computational analysis were performed. Quantum yields for the deoxygenation were up to 3 times larger for these sulfoxides compared to DBTO. However, oxidation of the solvent by these sulfoxides resulted in different ratios of oxidized products compared to DBTO, which suggested a change in deoxygenation mechanism. Density functional calculations revealed a much larger singlet–triplet gap for the larger sulfoxides compared to DBTO. This led to the conclusion that the examined sulfoxides could undergo deoxygenation by two different mechanisms.
Evaluation of peripheral matrix metalloproteinase-1 in Parkinson's disease: a case-control study

Background: Several types of proteinases are implicated in extracellular matrix (ECM) degradation, but the major enzymes are considered to be matrix metalloproteinases (MMPs). Matrix metalloproteinase-1 (MMP-1) is a major proteinase of the MMP family. MMP-1 is critical for modeling and remodeling of the extracellular matrix. In the present study, we evaluated circulating level of MMP-1 in Parkinson's disease (PD) patients and controls. Method: Enzyme linked immunosorbent assay (ELISA) was used to determine the serum level of MMP-1 in Parkinson's patients and matched healthy controls. Results: The mean age of Parkinson's patients (65%) and controls (62.5%) were 55.80 ± 9.69 and 54.05 ± 8.71 years respectively, with similar male/female ratio between patients and controls. The MMP-1 level was (p = 0.005) significantly lower in Parkinson's patients (2380.32 ± 2245.27 pg/ml) as compared to controls (4453.07 ± 3321.01 pg/ml). Poor correlation was found between MMP-1 level and disease duration (r = 0.36, p = 0.02), however it was statistically significant. Conclusion: Significantly lower level of serum MMP-1 was found in PD patients in comparison to controls. This difference in MMP-1 level was more prominent in females.
In Contact: Pinching, Squeezing and Twisting for Mediated Social Touch

Mediated social touch has the potential to enhance our interactions with machines and with each other. We present three wearable tactile devices that generate affective haptic sensations via three localised skin stretching modalities; pinching, squeezing, and twisting. The Pinch device is adhered to the skin of the forearm, generating pinching sensations in three locations. The Squeeze and Twist devices are wristbands that elicit squeezing and twisting sensations on the skin of the wrist. All of these devices are powered by shape memory alloy actuators, enabling them to be quiet, lightweight and discreet wearable interfaces, unlike their vibrotactile or servo-motor driven counterparts. We investigate the potential for these devices to be used in mediated social touch interactions by conducting preliminary psychometric tests measuring affective response. The Pinch device and Squeeze wristband were found to simulate positive affective touch sensations, particularly in comparison to vibrotactile stimuli.
Demographics, socio‐behavioral factors, and drug use patterns: What matters in spontaneous HCV clearance?

Hepatitis C virus (HCV), an emerging bloodborne pathogen, causes chronic liver disease frequently except in about 10–20% of infections which undergo spontaneous resolution. Investigating factors that influence viral clearance is essential to understand the natural history of this infection and establishing novel strategies for prevention and treatment. HCV clearance was estimated in a unique cohort of 1,260 HIV and HBV negative current drug users enrolled for a hepatitis B vaccination study. It was defined as the inability to detect viral RNA using a PCR method in presence of serum anti‐HCV antibody EIA. Associated demographic and socio‐behavioral factors including drug use patterns were identified from the enrolled subjects using multivariate regression analysis. 33.3% (420/1260) of drug users were found positive for anti‐HCV antibodies and 14.8% (62/420) of these individuals achieved viral clearance (negative PCR test). Race or ethnicity of the participants was the only significant factor associated with HCV clearance. Hispanics (OR = 3.4, 95% CI: 1.3–8.5, P = 0.01) and Caucasians (OR = 3.1, 95% CI: 1.5–6.6, P = 0.003) had significantly higher odds of clearing the virus compared to African Americans when adjusted for age and gender. None of the socio‐behavioral factors including alcohol intake and drug use patterns were significant determinants of HCV clearance. Racial or ethnic differences in HCV clearance were observed in this study suggesting an important role of host genetic susceptibility factors in determining the clinical course of this disease. Further research is needed to examine these genetic associations of host–virus relationships. J. Med. Virol. 84:235–241, 2012. © 2011 Wiley Periodicals, Inc.
Modification of ovine opsin with the photosensitive hydrophobic probe 1-azido-4-[125I]iodobenzene. Labelling of the chromophore-attachment domain.

The hydrophobic photosensitive probe 1-azido-4-[125I]iodobenzene (AIB) partitioned preferentially into photoreceptor disc membranes and, upon u.v. irradiation, became covalently bound to opsin and phospholipid. The labelling of both protein and phospholipid was linearly related to AIB concentration. The amount of probe incorporated into protein was not significantly different when membranes were irradiated at -100 degrees, 4 degrees or 25 degrees C, but irreversible aggregation of monomeric opsin was dramatically reduced by performing the photolysis at -100 degrees C. Labelling of opsin after irradiation at -100 degrees or 4 degrees was not significantly reduced by the presence of lysine in the aqueous buffer, indicating that significant amounts of reactive species did not enter the aqueous phase. The incorporation into phospholipid, unlike that into opsin, decreased as the temperature of irradiation increased. Some labelling of opsin occurred on incubation with pre-photoactivated AIB, indicating that reaction may also occur with reactive species of longer lifetimes than the nitrene. Proteolysis of labelled opsin with Staphylococcus aureus V8 proteinase yielded two radiolabelled membrane-bound fragments. The location of the modified sites (cysteine, tryptophan, tyrosine, lysine and histidine residues: all nucleophiles) in the smaller fragment was entirely consistent with putative models for the protein derived from other studies.
A Role for Inducible Costimulator Protein in the CD28- Independent Mechanism of Resistance to Toxoplasma gondii1

Long-term resistance to Toxoplasma gondii is dependent on the development of parasite-specific T cells that produce IFN-γ. CD28 is a costimulatory molecule important for optimal activation of T cells, but CD28−/− mice are resistant to T. gondii, demonstrating that CD28-independent mechanisms regulate T cell responses during toxoplasmosis. The identification of the B7-related protein 1/inducible costimulator protein (ICOS) pathway and its ability to regulate the production of IFN-γ suggested that this pathway may be involved in the CD28-independent activation of T cells required for resistance to T. gondii. In support of this hypothesis, infection of wild-type or CD28−/− mice with T. gondii resulted in the increased expression of ICOS by activated CD4+ and CD8+ T cells. In addition, both costimulatory pathways contributed to the in vitro production of IFN-γ by parasite-specific T cells and when both pathways were blocked, there was an additive effect that resulted in almost complete inhibition of IFN-γ production. Although in vivo blockade of the ICOS costimulatory pathway did not result in the early mortality of wild-type mice infected with T. gondii, it did lead to increased susceptibility of CD28−/− mice to T. gondi associated with reduced serum levels of IFN-γ, increased parasite burden, and increased mortality compared with the control group. Together, these results identify a critical role for ICOS in the protective Th1-type response required for resistance to T. gondii and suggest that ICOS and CD28 are parallel costimulatory pathways, either of which is sufficient to mediate resistance to this intracellular pathogen.
Decision making by parents and healthcare professionals when considering continued care for pediatric patients with cancer.

PURPOSE/OBJECTIVES To better define the treatment-related decisions considered most difficult by parents of pediatric patients with cancer and the factors that influenced their final decisions. DESIGN Retrospective-descriptive design. SETTING Pediatric oncology institution in the mid-southern region on the United States. SAMPLE 39 parents representing 37 of 83 eligible families, 16 attending physicians, three nurses, and two chaplains. METHODS Parent participants responded by telephone to six open-ended interview questions and a 15-item questionnaire about factors that were important when making the decision to continue care. Healthcare professionals were interviewed face-to-face. MAIN RESEARCH VARIABLES Most difficult treatment-related decisions; factors influencing decision making. FINDINGS Parents reported 15 types of difficult decisions, the majority of which were made late in the course of treatment. Deciding between a phase I drug study or no further treatment (n = 14), maintaining or withdrawing life support (n = 11), and giving more chemotherapy or giving no further treatment (n = 8) were the most frequently reported difficult decisions. Parents rated "recommendations received from healthcare professionals" as the questionnaire factor most important in their decision making, and healthcare professionals rated "discussion with the family of the patient" as the most important factor. CONCLUSION Parents of children or adolescents with cancer and their healthcare providers face difficult treatment-related decisions, many of which occur late in the course of treatment. Parents and healthcare professionals cite similar factors in their decision making but differ in their ratings of the factors' importance. For parents, the information and recommendations they receive from healthcare professionals figure most frequently and most importantly in their decision making. For healthcare professionals, the certainty that the patient will not get better and discussions with the patient's family figure most importantly in their decision making. Once parents conclude that their child can not get better, they are more likely to choose noncurative options such as choosing no further treatment or withdrawing life support. IMPLICATIONS FOR NURSING PRACTICE Nurses can help determine what information parents need in their decision making. Particular attention must be given to ways to communicate the likelihood of the their child's survival.
Selecting type of response for chat-like spoken dialogue systems based on acoustic features of user utterances

This paper describes a method of automatically selecting types of responses in conversational dialog systems, such as back-channel responses, changing the topic, or expanding the topic, using acoustic features extracted from user utterances. These features include spectral information described by MFCCs and LSPs, pitch information expressed by F0, loudness, etc. A corpus of dialogues between elderly people and an interviewer was constructed, and the results of evaluation experiments showed that our method achieved an F-measure of 49.3% in a speech segment identification task. Moreover, further improvement was achieved by utilizing the delta coefficients of each feature.
Mouse SmI cortex: qualitative and quantitative classification of golgi-impregnated barrel neurons.

The neurons in layer IV of the mouse somatosensory cortex are arranged in a remarkably consistent pattern of multicellular cytoarchitectonic units called "barrels. " Each barrel is known to be related, in a one to one manner, to a contralateral whisker or vibrissa on the animal's face. In this study we have examined Golgi-impregnated neurons that comprise the "barrels. " Several criteria, some being quantitative measures of dendritic arbors and somal sizes which were obtained with a computer-microscope system, suggest that all barrel neurons can be placed in two classes, the members of which are present in approximately equal numbers. The cells in the two classes can be further subdivided on the basis of the relationship of their processes to the barrels: 85% of them have processes restricted to a single barrel; 15% of them distribute their processes to two or more barrels. From these observations it is possible to suggest that a majority of neurons comprising the barrels would respond initially to movements of only one whisker while the remainder would respond to movements of two or more whiskers. In addition it has been shown that the quantitation of neuronal structure can provide a numerical basis for the classification of neurons in the central nervous system.
Analyzing the expression of annoyance during phone calls to complaint services

The identification of emotional hints from speech shows a large number of applications. Machine learning researchers have analyzed sets of acoustic parameters as potential cues for the identification of discrete emotional categories or, alternatively, of the dimensions of emotions. Experiments have been carried out over records including simulated or induced emotions, even if recently more research has been carried out on spontaneous emotions. However, it is well known that emotion expression depends not only on cultural factors but also on the individual and also on the specific situation. In this work we deal with the tracking of annoyance shifts during real phone-calls to complaint services. The audio files analyzed show different ways to express annoyance, as, for example, disappointment, impotence or anger. However variations of parameters derived from intensity combined with some spectral information and suprasegmental features have shown to be very robust for each speaker and annoyance rate. The work also discussed the annotation problem and proposed an extended rating scale in order to include annotators disagreements. Our frame classification results validated the annotation procedure. Experimental results also showed that shifts in customer annoyance rates could be potentially tracked during phone calls.
A prospective study of asymptomatic bacteriuria in sexually active young women.

BACKGROUND Asymptomatic bacteriuria is common in young women, but little is known about its pathogenesis, natural history, risk factors, and temporal association with symptomatic urinary tract infection. METHODS We prospectively evaluated 796 sexually active, nonpregnant women from 18 through 40 years of age over a period of six months for the occurrence of asymptomatic bacteriuria (defined as at least 10(5) colony-forming units of urinary tract pathogens per milliliter). The women were patients at either a university student health center or a health maintenance organization. Periodic urine cultures were taken, daily diaries were kept, and regularly scheduled interviews were performed. Escherichia coli strains were tested for hemolysin, the papG genotype, and the ribosomal RNA type. RESULTS The prevalence of asymptomatic bacteriuria (the proportion of urine cultures with bacteriuria in asymptomatic women) was 5 percent (95 percent confidence interval, 4 percent to 6 percent) among women in the university group and 6 percent (95 percent confidence interval, 5 percent to 8 percent) among women in the health-maintenance-organization group. Persistent asymptomatic bacteriuria with the same E. coli strain was rare. Symptomatic urinary tract infection developed within one week after 8 percent of occasions on which a culture showed asymptomatic bacteriuria, as compared with 1 percent of occasions when asymptomatic bacteriuria was not found (P<0.001). Asymptomatic bacteriuria was associated with the same risk factors as for symptomatic urinary tract infection, particularly the use of a diaphragm plus spermicide and sexual intercourse. CONCLUSIONS Asymptomatic bacteriuria in young women is common but rarely persists. It is a strong predictor of subsequent symptomatic urinary tract infection.
Segmentation the speech of hard of hearing children

One service provided by our application ‘Speech Assistant System’ assisting the teaching of the hearing impaired to speak is the automatic assessment of words and sentences in the course of practice and feedback to the person. Individual speech sounds can only be correctly evaluated if they are compared with the appropriate reference speech sounds. This requires segmenting the speech to be examined. The methods currently known do not give sufficiently accurate results for the speech of the hearing impaired, which is often so distorted and halting so that it prevents understanding. The paper presents a reference generation method suitable for segmenting distorted speech, a modification of dynamic time warping and its comparison with traditional methods. The procedure presented has been successfully used for the automatic assessment of the pronunciation of the hearing impaired.
Cytokine gene signatures in neural tissue of horses with equine protozoal myeloencephalitis or equine herpes type 1 myeloencephalopathy

This study was designed to determine the relative levels of gene transcription of selected pathogens and cytokines in the brain and spinal cord of 12 horses with equine protozoal myeloencephalitis (epm), 11 with equine herpesvirus type 1 (ehv-1) myeloencephalopathy, and 12 healthy control horses by applying a real time pcr to the formalin-fixed and paraffin-embedded tissues. Total rna was extracted from each tissue, transcribed to complementary dna (cdna) and assayed for Sarcocystis neurona, Neospora hughesi, ehv-1, equine gapdh (housekeeping gene), tumour necrosis factor (tnf)-α, interferon (ifn)-γ, interleukin (il)-1β, il-2, il-4, il-6, il-8, il-10 and il-12 p40. S neurona cdna was detected in the neural tissue from all 12 horses with epm, and two of them also had amplifiable cdna of N hughesi. The relative levels of transcription of protozoal cdna ranged from 1 to 461 times baseline (mean 123). All the horses with ehv-1 myeloencephalopathy had positive viral signals by pcr with relative levels of transcription ranging from 1 to 1618 times baseline (mean 275). All the control horses tested negative for S neurona, N hughesi and ehv-1 cdna. The cytokine profiles of each disease indicated a balance between pro- and anti-inflammatory markers. In the horses with epm the pro-inflammatory Th1 cytokines (il-8, tnf-α and ifn-γ) were commonly expressed but the anti-inflammatory Th2 cytokines (il-4, il-6 and il-10) were absent or rare. In the horses with ehv-1 the proinflammatory cytokine il-8 was commonly expressed, but il-10 and ifn-γ were not, and tnf-α was rare. Tissue from the control horses expressed only the gene gapdh.
Schwann cells of the myelin-forming phenotype express neurofilament protein NF-M

Immature Schwann cells of the rat sciatic nerve can differentiate into myelin-forming or non-myelin-forming cells. The factors that influence this divergent development are unknown but certain markers such as galactocerebroside distinguish the two cell populations at an early stage of Schwann cell differentiation. Because myelination requires extensive changes in cell morphology, we have investigated the composition and structure of the Schwann cell cytoskeleton at a time when these cells become committed to myelination. Here we show that Schwann cells express a cytoskeletal protein of M(r) 145 before diverging into the myelin-forming path, i.e., before they acquire cell- surface galactocerobroside. The p145 protein has the characteristics of an intermediate filament (IF) protein and immunoelectron microscopy shows that it colocalizes with vimentin, which suggests that these two proteins can coassemble into IFs. Elevated intracellular cAMP levels, which can mimic some of the early effects of axons on Schwann cell differentiation, induced p145 synthesis, therefore, we conclude that myelin-forming Schwann cells express this protein at a very early stage in their development. Immunological comparisons with other IF proteins revealed a close similarity between p145 and the neurofilament protein NF-M; the identification of p145 as NF-M was confirmed by isolating and sequencing a full-length clone from a Schwann cell cDNA library. These data demonstrate that Schwann cells remodel their IFs by expressing NF- M before acquiring the myelin-forming phenotype and that IF proteins of the neurofilament-type are not restricted to neurons in the vertebrate nervous system.