Miracle-dz/UniFAR-FTUs huggingface dataset:
A NEW MEMBER OF THE HERPESVIRUS GROUP ISOLATED FROM SOUTH AMERICAN MARMOSETS.

A herpesvirus was isolated from two sick marmoset monkeys (Tamarinus nigricollis), that were believed to be infected with a helminth. The same virus was isolated directly from the kidneys and lungs of two different monkeys. It produced an effect in tissue culture cells resembling that of herpesvirus. The virus produced rapid, fatal infection in marmosets and in suckling mice; and it produced pocks on the chorioallantoic membrane. Antigenically, this virus of new world monkeys was found to be different from classical herpes simplex virus and from B virus of old world monkeys, with no detectable cross reactivity. Its size and structure also show that the virus belongs in the herpes group, which may be briefly characterized as viruses containing DNA cores and possessing icosahedral symmetry with 162 hollow capsomeres. The behavior of the marmoset agent in tissue culture places it in herpesviruses of subgroup A (high titer of free virus) as against those in subgroup B (free virus uncommon). By using primary kidney cell cultures of rabbit and of green and rhesus monkeys, it is possible to distinguish among the primate herpesviruses of subgroup A on the basis of the fact that the rabbit cultures are susceptible to all three, and green monkey cultures to both, of the monkey viruses (old world and new world), but not to the virus of man, whereas rhesus cultures are susceptible only to the old world monkey virus.
Family-based association study of DRD4 gene in methylphenidate-responded Attention Deficit/Hyperactivity Disorder

The 48-basepair (48-bp) variable number tandem repeat (VNTR) polymorphism in exon 3 of the dopamine receptor D4 gene (DRD4) is implicated in the etiology of attention-deficit/ hyperactivity disorder (ADHD). In particular, ADHD in European-ancestry population is associated with an increased prevalence of the 7-repeat (7R) allele of the exon 3 VNTR. However, it is intriguing to note that the 7R allele has been found to be of very low prevalence in the Chinese general population. In a previous case-control study, our research team had found that the 7R allele was similarly absent in Chinese ADHD children in Hong Kong. Instead, there was an increased prevalence of the 2R allele in Chinese ADHD children. Interestingly, in Asian samples, the 2R allele had been found to be an evolutionary derivative of the 7R allele with equivalent biochemical functionality. So, the finding of an association between ADHD and 2R allele in Chinese population does not exactly contradict the original 7R allele finding in European-ancestry population. However, given the potential pitfall of population stratification in the previous case-control design, this current study tested the 2R allele and ADHD association using a methodologically more rigorous family-based approach on 33 Chinese ADHD probands who had favorable clinical responses to stimulant medication (methylphenidate). Haplotype Relative Risk (HRR) analysis and Transmission Disequilibrium Test (TDT) both showed a significant preferential transmission of the 2R allele from the biological parents to ADHD probands (pone-tailed = 0.038, OR = 2.04; pone-tailed = 0.048, OR = 2.29, respectively). A second hypothesis speculates that it is the deviation, including 7R and 2R alleles, from the conserved ancestral 4R allele which confers risk to ADHD. Thus, a preferential transmission of non-4R alleles, against the 4R allele, from biological parents to their ADHD probands is predicted. Both HRR analysis and TDT confirmed such prediction (pone-tailed = 0.029, OR = 2.07; pone-tailed = 0.032, OR = 2.43, respectively). This study re-confirmed the original finding of a previous study that in Chinese population, the 2R allele of the DRD4 exon 3 VNTR was related to ADHD. This endorses the general thesis that DRD4 exon 3 VNTR polymorphism is related to ADHD, despite that the exact length or number of repeats of the associated alleles varies across ethnicity. This in turn supports the dopamine dysregulation theory of ADHD.
A controlled trial for PTSD in mexican victims of criminal violence

One of most important psychological repercussions associated with victims of criminal violence is Posttraumatic Stress Disorder (PTSD). In Mexico, 11 percent of the population over 18 years has experienced a crime. In particular, Ciudad Juarez has been a long-term devastated site because of drug traffic problems and the consequences related, leading the population to a hopeless sense of fear and insecurity. Based on the efficacy of virtual reality (VR) treatments for PTSD, this paper presents preliminary efficacy data in a controlled study of virtual reality treatment for PTSD for criminal violence. Twenty participants, aged between 18 and 65, diagnosed with PTSD were randomly assigned to a virtual reality prolonged exposure treatment group or an imaginal prolonged exposure treatment group. Treatment was delivered in 12, 90-minute individual sessions conducted twice a week. Five VR models were used for PTSD exposure therapy. Data confirm that VR prolonged exposure technique was effective in reducing clinical levels of PTSD, and participants reported a preference and acceptance for this innovative intervention.
Linear Time Construction of Suffix Arrays

We present a linear time algorithm to sort all the suffixes of a string over a large alphabet of integers. The sorted order of suffixes of a string is also called suffix array, a data structure introduced by Manber and Myers that has numerous applications in computational biology. Though the suffix tree of a string can be constructed in linear time and the sorted order of suffixes derived from it, a direct algorithm for suffix sorting is of great interest due to the space requirements of suffix trees. Our result improves upon the best known direct algorithm for suffix sorting, which takes O(n log n) time. We also show how to construct suffix trees in linear time from our suffix sorting result. Apart from being simple and applicable for alphabets not necessarily of fixed size, this method of constructing suffix trees is more space efficient.
Delay Tolerant Networking over the Metropolitan Public Transportation

We discuss MDTN: a delay tolerant application platform built on top of the Public Transportation System (PTS) and able to provide service access while exploiting opportunistic connectivity. Our solution adopts a carrier-based approach where buses act as data collectors for user requests requiring Internet access. Simulations based on real maps and PTS routes with state-of-the-art routing protocols demonstrate that MDTN represents a viable solution for elastic nonreal-time service delivery. Nevertheless, performance indexes of the considered routing policies show that there is no golden rule for optimal performance and a tailored routing strategy is required for each specific case.
Single-molecule DNA detection with an engineered MspA protein nanopore

Nanopores hold great promise as single-molecule analytical devices and biophysical model systems because the ionic current blockades they produce contain information about the identity, concentration, structure, and dynamics of target molecules. The porin MspA of Mycobacterium smegmatis has remarkable stability against environmental stresses and can be rationally modified based on its crystal structure. Further, MspA has a short and narrow channel constriction that is promising for DNA sequencing because it may enable improved characterization of short segments of a ssDNA molecule that is threaded through the pore. By eliminating the negative charge in the channel constriction, we designed and constructed an MspA mutant capable of electronically detecting and characterizing single molecules of ssDNA as they are electrophoretically driven through the pore. A second mutant with additional exchanges of negatively-charged residues for positively-charged residues in the vestibule region exhibited a factor of ≈20 higher interaction rates, required only half as much voltage to observe interaction, and allowed ssDNA to reside in the vestibule ≈100 times longer than the first mutant. Our results introduce MspA as a nanopore for nucleic acid analysis and highlight its potential as an engineerable platform for single-molecule detection and characterization applications.
Implications of LINE1 Methylation for Bladder Cancer Risk in Women

Purpose: Epigenetic alterations including changes to cellular DNA methylation levels contribute to carcinogenesis and may serve as powerful biomarkers of the disease. This investigation sought to determine whether hypomethylation at the long interspersed nuclear elements (LINE1), reflective of the level of global DNA methylation, in peripheral blood–derived DNA is associated with increased risk of bladder cancer. Experimental Design: LINE1 methylation was measured from blood-derived DNA obtained from participants of a population-based incident case-control study of bladder cancer in New Hampshire. Bisulfite-modified DNA was pyrosequenced to determine LINE1 methylation status; a total of 285 cases and 465 controls were evaluated for methylation. Results: Being in the lowest LINE1 methylation decile was associated with a 1.8-fold increased risk of bladder cancer [95% confidence interval (95% CI), 1.12-2.90] in models controlling for gender, age, and smoking, and the association was stronger in women than in men (odds ratio, 2.48; 95% CI, 1.19-5.17 in women; and odds ratio, 1.47; 95% CI, 0.79-2.74 in men). Among controls, women were more likely to have lower LINE1 methylation than men (P = 0.04), and levels of arsenic in the 90th percentile were associated with reduced LINE1 methylation (P = 0.04). Conclusions: LINE1 hypomethylation may be an important biomarker of bladder cancer risk, especially among women. Clin Cancer Res; 16(5); 1682–9
Mild iodine deficiency during pregnancy is associated with reduced educational outcomes in the offspring: 9-year follow-up of the gestational iodine cohort.

CONTEXT Severe iodine deficiency (ID) during gestation is associated with neurocognitive sequelae. The long-term impact of mild ID, however, has not been well characterized. OBJECTIVE The purpose of this study was to determine whether children born to mothers with urinary iodine concentrations (UICs) <150 μg/L during pregnancy have poorer educational outcomes in primary school than peers whose mothers did not have gestational ID (UIC ≥150 μg/L). DESIGN This was a longitudinal follow-up (at 9 years old) of the Gestational Iodine Cohort. Pregnancy occurred during a period of mild ID in the population, with the children subsequently growing up in an iodine-replete environment. SETTING AND PARTICIPANTS Participants were children whose mothers attended The Royal Hobart Hospital (Tasmania) antenatal clinics between 1999 and 2001. MAIN OUTCOME MEASURES Australian national curriculum and Tasmanian state curriculum educational assessment data for children in year 3 were analyzed. RESULTS Children whose mothers had UIC <150 μg/L had reductions of 10.0% in spelling (-41.1 points, 95% confidence interval [CI], -68.0 to -14.3, P = .003), 7.6% in grammar (-30.9 points, 95% CI, -60.2 to -1.7, P = .038), and 5.7% in English-literacy (-0.33 points, 95% CI, -0.63 to -0.03, P = .034) performance compared with children whose mothers' UICs were ≥150 μg/L. These associations remained significant after adjustment for a range of biological factors (maternal age at birth of child, gestational length at time of birth, gestational age at time of urinary iodine collection, birth weight, and sex). Differences in spelling remained significant after further adjustment for socioeconomic factors (maternal occupation and education). CONCLUSIONS This study provides preliminary evidence that even mild iodine deficiency during pregnancy can have long-term adverse impacts on fetal neurocognition that are not ameliorated by iodine sufficiency during childhood.
SLEUTH: Real-time Attack Scenario Reconstruction from COTS Audit Data

We present an approach and system for real-time reconstruction of attack scenarios on an enterprise host. To meet the scalability and real-time needs of the problem, we develop a platform-neutral, main-memory based, dependency graph abstraction of audit-log data. We then present efficient, tag-based techniques for attack detection and reconstruction, including source identification and impact analysis. We also develop methods to reveal the big picture of attacks by construction of compact, visual graphs of attack steps. Our system participated in a red team evaluation organized by DARPA and was able to successfully detect and reconstruct the details of the red team's attacks on hosts running Windows, FreeBSD and Linux.
Characterization and loading estimation of polycyclic aromatic hydrocarbons in road runoff from urban regions of Beijing, China

This paper reports an initial study regarding our quantitative understanding of the characteristics of polycyclic aromatic hydrocarbon (PAH) contamination and loading estimation from road runoff in Beijing (China). The concentrations of 16 PAHs were measured in road runoff and rainwater in a composite commercial and residential catchment of Beijing in 2006. In road runoff samples, geometric mean concentrations of Σ16 PAHs (the sum of 16 PAH concentrations) in the dissolved and particle phases were 548.2 and 3,872.2 ng/L, respectively, and in rainwater samples, the concentrations in the dissolved and particle phases were 172.9 and 274.6 ng/L, respectively. An analysis on spatial variation among the sampling sites showed that PAH concentrations at the branch road (with low traffic volume) were higher than those at the trunk road (with high traffic volume) and that PAH contamination at the bicycle lane was comparable to that at the vehicle lane. Dimensionless cumulative analyses indicated that first flush effect did not occur in all cases, but rather depended on storm event characteristics. According to the annual unit loading rate and the planned road area, the relative magnitude of PAH loading in road runoff was in the following order: Vehicle lane of trunk road > branch road > bicycle lane of trunk road.
S-layer protein of Lactobacillus acidophilus ATCC 4356: purification, expression in Escherichia coli, and nucleotide sequence of the corresponding gene

The cell surfaces of several Lactobacillus species are covered by a regular layer composed of a single species of protein, the S-protein. The 43-kDa S-protein of the neotype strain Lactobacillus acidophilus ATCC 4356, which originated from the pharynx of a human, was purified. Antibodies generated against purified S-protein were used to screen a lambda library containing chromosomal L. acidophilus ATCC 4356 DNA. Several phages showing expression of this S-protein in Escherichia coli were isolated. A 4.0-kb DNA fragment of one of those phages hybridized to a probe derived from an internal tryptic fragment of the S-protein. The slpA gene, coding for the surface layer protein, was located entirely on the 4.0-kb fragment as shown by deletion analysis. The nucleotide sequence of the slpA gene was determined and appeared to encode a protein of 444 amino acids. The first 24 amino acids resembled a putative secretion signal, giving rise to a mature S-protein of 420 amino acids (44.2 kDa). The predicted isoelectric point of 9.4 is remarkably high for an S-protein but is in agreement with the data obtained during purification. The expression of the entire S-protein or of large, C-terminally truncated S-proteins is unstable in E. coli.
The Interpersonal Process in Tissue Donation Requests with “Undecided” Next of Kin

Context Although recent studies have demonstrated that tissue requesters' behavior during conversations about tissue donation affects consent rates, the link between requesters' behavior and consent rates remains unclear. Objective To examine whether positive/collaborative requester behaviors elicit complementary behaviors from next of kin who were initially undecided about their willingness to donate their deceased family member's tissues. Design Audio recordings of requests were coded to assess for interpersonal behavior of each interactant. Setting Audio recordings were gathered from a national sample of tissue banks. Participants One hundred and two requester–next-of-kin dyads, consisting of 102 relatives and 53 requesters. Main Outcome Measures Tissue requester and next-of-kin affiliation and interpersonal control were assessed. Tissue requesters' persuasion, confirmation (eg, approval, empathy, reassurance) and disapproval, as well as next-of-kin approval and disapproval, were examined. Results Tissue requesters and next of kin tended to match one another on affiliation and complement one another on interpersonal control. “Key topics,” which may affect the next of kin's decision, are discussed in only about one-third of requests. Next of kin were less affiliative and more disapproving when requesters were also more disapproving. Interpersonal behavior of the tissue requester, such as affiliation, statements of disapproval, and persuasion, as well as discussion of key topics, was a significant predictor of the interpersonal behavior of the next of kin. Conclusions Positive requester behaviors elicited a positive response from undecided next of kin. Because many next of kin have limited knowledge about tissue donation before the request, the communication process may affect the next of kin's perceptions of donation and thus affect the likelihood of consent. Findings could potentially inform communication skills training for tissue requesters; future research could examine effects of such training on consent rates.
Successful Engraftment After Reduced-Intensity Umbilical Cord Blood Transplantation for Adult Patients with Advanced Hematological Diseases

Purpose: The purpose of this research was to evaluate the feasibility of reduced-intensity unrelated cord-blood transplantation (RI-UCBT) in adult patients with advanced hematological diseases. Experimental Design: Thirty patients (median age, 58.5 years; range, 20–70 years) with advanced hematological diseases underwent RI-UCBT at Toranomon Hospital between September 2002 and August 2003. Preparative regimen composed of fludarabine 25 mg/m2 on days −7 to −3, melphalan 80 mg/m2 on day −2, and 4 Gy total body irradiation on day −1. Graft-versus-host disease prophylaxis was composed of cyclosporin alone. Results: Twenty-six patients achieved primary neutrophil engraftment after a median of 17.5 days. Median infused total cell dose was 3.1 × 107/kg (range, 2.0–4.3 × 107/kg). Two transplant-related mortalities occurred within 28 days of transplant, and another 2 patients displayed primary graft failure. Cumulative incidence of complete donor chimerism at day 60 was 93%. Grade II-IV acute graft-versus-host disease occurred in 27% of patients, with median onset 36 days. Primary disease recurred in 3 patients, and transplant-related mortality within 100 days was 27%. Estimated 1-year overall survival was 32.7%. Excluding 7 patients with documented infection, 19 patients displayed noninfectious fever before engraftment (median onset, day 9). Manifestations included high-grade fever, eruption, and diarrhea. The symptoms responded well to corticosteroid treatments in 7 of 13 treated patients. Conclusion: This study demonstrated the feasibility of RI-UCBT in adults.
Serine Protease Inhibitor Kazal Type 1 Promotes Proliferation of Pancreatic Cancer Cells through the Epidermal Growth Factor Receptor

Serine protease inhibitor, Kazal type 1 (SPINK1) is expressed not only in normal human pancreatic acinar cells but also in a variety of pancreatic ductal neoplasms. There are structural similarities between SPINK1 and epidermal growth factor (EGF). Hence, we hypothesized that SPINK1 binds to EGF receptor (EGFR) to activate its downstream signaling. We first showed that SPINK1 induced proliferation of NIH 3T3 cells and pancreatic cancer cell lines. We showed that SPINK1 coprecipitated with EGFR in an immunoprecipitation experiment and that the binding affinity of SPINK1 to EGFR was about half of that of EGF using quartz-crystal microbalance (QCM) technique. As expected, EGFR and its downstream molecules, signal transducer and activator of transcription 3, v-Akt murine thymoma viral oncogene homologue, and extracellular signal-regulated kinase 1/2, were phosphorylated by SPINK1 as well as EGF. To determine which pathway is the most important for cell growth, we further analyzed the effect of inhibitors. Growth stimulation by EGF or SPINK1 was completely inhibited by EGFR and mitogen-activated protein kinase/extracellular signal-regulated kinase kinase inhibitor but not by Janus-activated kinase and phosphoinositide 3-kinase inhibitors. To further analyze the clinical importance of SPINK1 in the development of pancreatic cancer, we examined the expression of SPINK1 and EGFR in pancreatic tubular adenocarcinomas and pancreatic intraepithelial neoplasm. Both SPNK1 and EGFR were coexpressed not only in the early stage of cancer, PanIN-1A, but also in advanced stages. Taken together, these results suggest that SPINK1 stimulates the proliferation of pancreatic cancer cells through the EGFR/mitogen-activated protein kinase cascade. (Mol Cancer Res 2009;7(9):1572–81)
Normal telomere length and chromosomal end capping in poly(ADP-ribose) polymerase–deficient mice and primary cells despite increased chromosomal instability

Poly(ADP-ribose) polymerase (PARP)-1, a detector of single-strand breaks, plays a key role in the cellular response to DNA damage. PARP-1–deficient mice are hypersensitive to genotoxic agents and display genomic instability due to a DNA repair defect in the base excision repair pathway. A previous report suggested that PARP-1–deficient mice also had a severe telomeric dysfunction consisting of telomere shortening and increased end-to-end fusions (d'Adda di Fagagna, F., M.P. Hande, W.-M. Tong, P.M. Lansdorp, Z.-Q. Wang, and S.P. Jackson. 1999. Nat. Genet. 23:76–80). In contrast to that, and using a panoply of techniques, including quantitative telomeric (Q)-FISH, we did not find significant differences in telomere length between wild-type and PARP-1−/− littermate mice or PARP-1−/− primary cells. Similarly, there were no differences in the length of the G-strand overhang. Q-FISH and spectral karyotyping analyses of primary PARP-1−/− cells showed a frequency of 2 end-to-end fusions per 100 metaphases, much lower than that described previously (d'Adda di Fagagna et al., 1999). This low frequency of end-to-end fusions in PARP-1−/− primary cells is accordant with the absence of severe proliferative defects in PARP-1−/− mice. The results presented here indicate that PARP-1 does not play a major role in regulating telomere length or in telomeric end capping, and the chromosomal instability of PARP-1−/− primary cells can be explained by the repair defect associated to PARP-1 deficiency. Finally, no interaction between PARP-1 and the telomerase reverse transcriptase subunit, Tert, was found using the two-hybrid assay.
Corrections for “Development of an Intelligent Temperature Transducer”

The approximate sensitivity value for the three thermistors under study using the intelligent temperature transducer <xref ref-type="bibr" rid="ref1">[1]</xref> is mistakenly presented as 5 kHz/°C. After intense review of the experimental data of the technique <xref ref-type="bibr" rid="ref1">[1]</xref>, the values of sensitivity are found to be 0.173 kHz/°C for the thermistor-1, 0.273 kHz/°C for the thermistor-2 and 0.0723 kHz/°C for the thermistor-3 respectively in the temperature range 0–100 °C. The revised sensitivity values are presented in <xref rid="table1" ref-type="table">Table 1</xref> in the interest of research fraternity with accurate results. We claim that the values of linearity achieved by the developed technique <xref ref-type="bibr" rid="ref1">[1]</xref> are relatively high in comparison to the other techniques reported in <xref ref-type="bibr" rid="ref1">[1]</xref>.