Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural basis for the specificity of the initiation of HIV‐1 reverse transcription

Initiation of human immunodeficiency virus type 1 (HIV‐1) reverse transcription requires specific recognition of the viral genome, tRNA3Lys, which acts as primer, and reverse transcriptase (RT). The specificity of this ternary complex is mediated by intricate interactions between HIV‐1 RNA and tRNA3Lys, but remains poorly understood at the three‐dimensional level. We used chemical probing to gain insight into the three‐dimensional structure of the viral RNA–tRNA3Lys complex, and enzymatic footprinting to delineate regions interacting with RT. These and previous experimental data were used to derive a three‐dimensional model of the initiation complex. The viral RNA and tRNA3Lys form a compact structure in which the two RNAs fold into distinct structural domains. The extended interactions between these molecules are not directly recognized by RT. Rather, they favor RT binding by preventing steric clashes between the nucleic acids and the polymerase and inducing a viral RNA–tRNA3Lys conformation which fits perfectly into the nucleic acid binding cleft of RT. Recognition of the 3′ end of tRNA3Lys and of the first template nucleotides by RT is favored by a kink in the template strand promoted by the short junctions present in the previously established secondary structure.
Comparison of PCR‐ELISA and galactomannan detection for the diagnosis of invasive aspergillosis

Aim: To compare PCR with galactomannan antigen detection for the diagnosis of invasive aspergillosis (IA). Methods: We prospectively collected serial blood samples from haematological patients at risk of IA, and analysed their samples retrospectively for galactomannan (GM) antigen using the Platelia test and for aspergillus DNA using an in‐house PCR‐ELISA assay. Matched GM and PCR analyses were performed on 263 samples from 25 patients. Patients were classified for potential IA according to international consensus criteria, with five patients classified as positive (four proven, one probable) and 20 classified as negative (seven possible, 13 no evidence IA). Results: All five patients with IA were positive by PCR with positive results in 24 of 82 samples, whereas three of five patients were positive by GM with four of 82 samples being positive. Three of 20 patients without IA were positive by PCR in 18 of 181 samples, whereas corresponding results for GM detection were one of 20 and one of 181, respectively. Adjustment of ELISA cut‐off values and/or the requirement for two consecutive samples to be positive generated different results; however, lowering the positivity index (PI) for GM detection to 0.5 did not improve the sensitivity of the assay. Optimal results for PCR detection and GM were: 100% and 60% sensitivity, 85% and 95% specificity, 0.625 and 0.75 positive predictive value, and 1.0 and 0.8 negative predictive value, with a false‐positive sample rate of 8 and 0.4%, positive likelihood ratio of 6.66 and 11.99 and negative likelihood ratio of 0 and 0.42, respectively. Conclusions: This PCR method is very sensitive for the diagnosis of IA but is associated with a moderate rate of false positives; the GM assay exhibited poor sensitivity but high specificity. Further evaluation of PCR assays for the diagnosis of IA and other invasive fungal infections is warranted.
A season of aseptic meningitis in Germany: epidemiologic, clinical and diagnostic aspects

Objective. We assessed epidemiologic, clinical and laboratory features of aseptic meningitis during one season of multiserotype enteroviral meningitis in East Germany in 70 consecutive patients with aseptic meningitis admitted to the Children’s University Hospital Leipzig. Results. Patients, age 1 to 16 years, typically presented with headache, emesis and fever, whereas signs of meningeal irritation were only moderately expressed in one-half of the patients. The median number of leukocytes in the CSF was 151 cells/mm3 (range, 2 to 1820) with a high percentage of polymorphonuclear cells (PMNs). Initial blood counts showed mild leukocytosis and pronounced PMN predominance (78.9 ± 1.3%). The percentage of PMNs in the peripheral blood decreased in favor of mononuclear cells after 3 days to a pattern more compatible with viral infection as opposed to that suggestive for bacteria in the beginning. Mean cerebrospinal fluid values of protein, glucose and lactate and the C-reactive protein were mildly elevated or normal. Nonpolio enteroviruses were detected in 30 of 70 patients. Subsequent serotyping revealed echovirus type 13 (13 patients), type 6 (2), type 30 (1) and coxsackie B virus type 5 (2). There were no differences in demographic or clinical data between enterovirus positive and negative patients. Conclusions. Even though individual laboratory values do not solely allow discrimination between viral and bacterial meningitis, the combined epidemiologic, clinical and laboratory data facilitate the diagnosis of aseptic meningitis in most cases. Viral diagnostics, identifying echovirus type 13 that thus far has not been associated with epidemics of meningitis, adds important epidemiologic information.
Correlations of thalamic reductions with verbal fluency impairment in those born prematurely

Prematurity is associated with reduced brain volume, and the thalamus is among the structures most affected. We used a voxel-based morphometry analysis of gray matter to map regional atrophy in the thalamus in a sample of 30 adolescents with antecedents of very preterm birth. The preterm sample was compared with 30 controls matched by age, sex, handedness and sociocultural status. Individuals with very preterm birth differed from controls in several thalamic nuclei, and semantic and phonetic fluency showed different correlation patterns with brain volume. Semantic fluency achieved significant correlations with more thalamic nuclei than phonetic fluency. These results agree with functional magnetic resonance imaging studies showing that semantic fluency involves more cerebral regions than phonetic fluency.
Childhood Infections and the Risk of Asthma: A Longitudinal Study Over 37 Years

JA Byrnes, M Abramson, LC Gurrin. Chest. 2012;142(3):649–660 To determine if past common childhood illnesses and infectious diseases including pneumonia, pertussis, measles, mumps, rubella, chickenpox, and diphtheria are associated with an increased risk of asthma persisting at various ages In the Tasmanian Longitudinal Health Study, 8583 Tasmanian schoolchildren were surveyed in 1968 at age 7 years and again at age 13 years. In 2004, a detailed respiratory questionnaire was completed by 5729 of the original participants. Each child’s history was cross-referenced for a history of measles, …
Carpal Tunnel Syndrome Symptoms and Associated Risk Factors for Assembly Line workers Engaged in Shocker Manufacturing industries: A Study

The Carpal Tunnel Syndrome (CTS) and associated risk factors for shocker manufacturing industries in Haryana were carried out. A comparison of CTS and other upper hand extremities amongst traditional and semi-ergonomic shocker manufacturing workers in actual industrial environment has been analysed through questionnaire and physical tests. Fisher’s exact test and ‘t’ test are used for statistical data analysis. From Fisher’s exact test, it is observed that due to wrist/hand problems 80 % of traditional and 20 % of semi-ergonomic shocker manufacturing workers (p < 0.05), have been unable to perform the usual activities. The results reflect that the traditional shocker manufacturing workers are more CTS symptoms occurrence than the semi-ergonomic shocker manufacturing workers.
Strategies for research about design: a multidisciplinary graduate workshop

We are developing a graduate curriculum and summer workshop on design research intended to prepare graduate students to do research about the nature of design or research about a class of designs, including concepts, models, and methods for that class. We expect our workshop to advance the science of design of software-intensive systems by creating a open community of design researchers, both in software design and in related disciplines, who are knowledgeable about design and design research methods and who are interested in advancing the field. The curriculum will create a common basis for discussion and identify core material to master, while the flexible format of the workshop will encourage the introduction of new ideas and new methods. The goals of our course and workshop are to (1) develop an open community of graduate students, faculty, and industry researchers who are actively engaged in the advancement of software design research and (2) to associate this community with the larger community of researchers from related areas of design research who can contribute to the software design community and who can take ideas from software design back to their own research communities. We will offer a week-long summer workshop in May 2007, in which PhD students who are just beginning to develop their research proposals will have the opportunity to work closely with faculty and researchers who are on the forefront of software design research and related design fields.
Accuracy of Self-reported Prescribed Analgesic Medication Use: Linkage Between the Quebec Pain Registry and the Quebec Administrative Prescription Claims Databases

Objectives:The validity of studies conducted with patient registries depends on the accuracy of the self-reported clinical data. As of now, studies about the validity of self-reported use of analgesics among chronic pain (CP) populations are scarce. The objective of this study was to assess the accuracy of self-reported prescribed analgesic medication use. This was attained by comparing the data collected in the Quebec Pain Registry (QPR) database to those contained in the Quebec administrative prescription claims database (Régie de l’assurance maladie du Québec [RAMQ]). Methods:To achieve the linkage between the QPR and the RAMQ databases, the first 1285 patients who were consecutively enrolled in the QPR between October 31, 2008 and January 27, 2010 were contacted by mail and invited to participate in a study in which they had to provide their unique RAMQ health insurance number. Using RAMQ prescription claims as the reference standard, &kgr; coefficients, sensitivity, specificity, and their respective 95% confidence intervals were calculated for each therapeutic class of prescribed analgesic drugs that the participants reported taking currently and in the past 12 months. Results:A total of 569 QPR patients responded to the postal mailing, provided their unique health insurance number, and gave informed consent for the linkage (response proportion=44%). Complete RAMQ prescription claims over the 12 months before patient enrollment into the QPR were available for 272 patients, who constituted our validated study population. Regarding current self-reported prescribed analgesic use, &kgr; coefficients measuring agreement between the 2 sources of information ranged from 0.66 to 0.78 for COX-2-selective nonsteroidal anti-inflammatory drugs, anticonvulsants, antidepressants, skeletal muscle relaxants, synthetic cannabinoids, opiate agonists/partial agonists/antagonists, and antimigraine agents therapeutic classes. For the past 12-month self-reported prescribed analgesic use, QPR patients were less accurate regarding anticonvulsants (&kgr;=0.59), opiate agonists/partial agonists/antagonists (&kgr;=0.57), and antimigraine agents use (&kgr;=0.39). Discussion:Information about current prescribed analgesic medication use as reported by CP patients was accurate for the main therapeutic drug classes used in CP management. Accuracy of the past year self-reported prescribed analgesic use was somewhat lower but only for certain classes of medication, the concordance being good on all the others.
Data upload from a static Underwater network to an AUV: Polling or random access?

In this paper, we consider data uploading from a network of fixed sensors to a mobile Autonomous Underwater Vehicle (AUV). We approach the problem using both random and controlled access: in particular, we propose UW-Polling, a data retrieval protocol based on controlled access, and evaluate it against channel access protocols based on random access. We compare the performance of these protocols in terms of throughput, Packet Delivery Ratio and energy consumption, discussing the impact of the source power level on these metrics. Our results show that our polling-based protocol outperforms the other protocols in several cases, and thereby confirm that polling is an effective approach to enable AUVs to retrieve data from a network of fixed sensors.
Endoscopic ultrasound duplex scanning for measurement of portal venous flow. Validation against transit time ultrasound flowmetry in pigs.

BACKGROUND Endoscopic ultrasound (EUS) is a new technique that makes it possible to measure portal venous flow when transabdominal ultrasound fails. As the technique has not been evaluated previously, we compared simultaneous measurements of portal venous flow using EUS Doppler with that of transit time ultrasound (TTU) in healthy pigs. The ability of EUS to detect changes in the portal venous flow after pharmacologic intervention was also investigated. METHODS Six anaesthetized pigs were studied. Portal venous flow was measured simultaneously by EUS duplex scanning, using a Pentax FG-32UA echoendoscope connected to a Hitachi EUB 515-A ultrasound scanner, and by TTU with a Cardiomed CM 4000 flowmeter probe placed on the portal vein. Terlipressin, 1 mg, and placebo were administered in a blind, randomized, crossover design. Measurements were taken at base line and 30 min after each drug administration. RESULTS Portal venous flow measured by EUS flowmetry and TTU flowmetry correlated significantly (R = 0.92, P < 0.001, n = 18). The limits of agreement in a Bland-Altman plot were from -0.262 l/min to +0.164 l/min. The change in portal venous flow after terlipressin measured by EUS and TTU correlated significantly (R = 0.88, P < 0.05, n = 6). All values used for analyses were the means of five repeated measurements. CONCLUSIONS EUS measures portal venous flow with an acceptable correlation and agreement with TTU in anaesthetized pigs. The method is capable of monitoring the effects of pharmacologic intervention on the portal system.
Others’ opinions count, but not all of them: anchoring to ingroup versus outgroup members’ behavior in charitable giving

Because of the large amount of information and the difficulty in selecting an appropriate recipient in the context of charitable giving, people tend to make extensive use of heuristics, which sometimes leads them to wrong decisions. In the present work, we focused on exploring how individuals are influenced by anchoring heuristics and how group membership interacts with this heuristic. In Experiment 1, two different groups of participants were informed about low versus high average donations of other people, and a third control group did not receive any information about the others’ donations. The results showed that participants were willing to donate significantly more in the high-anchor condition compared to the low-anchor condition, as well as about the same amount of money in the low-anchor condition and no-anchor condition. Experiment 2 and 3 showed that high anchors are more effective when the information about others’ donations reflects members of the ingroup rather than the outgroup. Other variables related to these results are further discussed.
MICROSEISMIC EVENT ANALYSIS IN CONJUNCTION WITH STIMULATION TREATMENTS AT THE GEOTHERMAL RESEARCH WELL GTGRSK 4 / 05 IN GROß

The technical feasibility of geothermal power production will be demonstrated in the geothermal research wells Groß Schönebeck using a borehole doublet. This task includes safeguarding the thermal fluid cycle and the optimisation of energy conversion technology at the surface. In order to complete the Enhanced Geothermal System, three massive hydraulic stimulations were performed injecting a total of 13000 m3 of water into the well Gt GrSk 4/05. To monitor injection-induced seismicity during the main injection a combined surface and downhole seismic network was deployed including a downhole seismic sensor at 3800 m depth at only 500 m distance to the injection point. During the injection period of six days with injection rates of up to 150 l/s and maximum injection pressures of nearly 600 bar a total of 70 events were detected and located. Spectral parameters were calculated and magnitudes were found to cover the range -1.9<M<-1.1. The events show a strong spatial and temporal clustering with a maximum number of 22 events per day. The majority of events occurred towards the end of major stimulation phases indicating a similar behavior as observed at similar treatments in crystalline environments but at smaller level of seismic activity and at lowers magnitudes.
Cytoplasmic cytology of primary and secondary Brown-Pearce tumors.

1. In malignant cells of primary tumor the predominant form of mitochondria is the filamentous one, while in cells of different metastases mitochondria exist in the form of granules.2. In cells of primary tumor, besides the dictyosome-like form of Golgi apparatus which is found also in different metastatic cells, a second type of Golgi apparatus exists in the form of osmiophilic granules.3. The degree of development of Golgi elements and the amount of mitochondrial granules vary with the organ localisation of metastases.4. In cells of different metastases the elements of Golgi apparatus are well developed with an increase in the number of mitochondrial granules when compared with that found in cells of primary tumor.5. In malignant cells of old primary and secondary tumors the Golgi elements are well developed along with an increase in the number of mitochondrial granules in comparison with that observed in cells of the homologous young tumors.
Differential Activation of p70 and p85 S6 Kinase Isoforms during Cardiac Hypertrophy in the Adult Mammal*

An adult feline right ventricular pressure overload (RVPO) model was used to examine the two S6 kinase (S6K) isoforms, p70S6K and p85S6K, that are involved in translational and transcriptional activation. Biochemical and confocal microscopy analyses at the level of the cardiocyte revealed that p70S6K is present predominantly in the cytosol, substantially activated in 1-h RVPO (>12 fold), and phosphorylated in the pseudosubstrate domain at the Ser-411, Thr-421, and Ser-424 sites. p85S6K, which was localized exclusively in the nucleus, showed activation subsequent to p70S6K, with a sustained increase in phosphorylation for up to 48 h of RVPO at equivalent sites of p70S6K, Thr-421 and Ser-424, but not at Ser-411. Neither isoform translocated between the cytosol and the nucleus. Further studies to determine potential upstream elements of S6K activation revealed: (i) similar time course of activation for protein kinase C isoforms (α, γ, and ε) and c-Raf, (ii) absence of accompanying phosphatidylinositol 3-kinase activation, (iii) activation of c-Src subsequent to p70S6K, and (iv) similar changes in adult cardiocytes after treatment with 12-O-tetradecanoylphorbol-13-acetate. Thus, these studies suggest that a protein kinase C-mediated pathway couples pressure overload to growth induction via differential activation of S6K isoforms in cardiac hypertrophy.
Time‐course and risk factors of hypothyroidism following allogeneic hematopoietic stem cell transplantation (HSCT) in children conditioned with fractionated total body irradiation

Hypothyroidism is a complication of hematopoietic stem cell transplantation (HSCT) 1 that has been studied primarily in children after matched sibling bone marrow transplantation. Unrelated donors and umbilical cord blood (CB) are now used in transplantation, and hypothyroidism in these populations is undocumented. Children who underwent fractionated total body irradiation (fTBI) and received bone marrow or umbilical cord blood transplantation from siblings or unrelated donors were examined for hypothyroidism over time.
A deletion mutant of L-A double-stranded RNA replicates like M1 double-stranded RNA

X double-stranded RNA (dsRNA) is a 0.52-kilobase dsRNA molecule that arose spontaneously in a nonkiller strain of Saccharomyces cerevisiae originally containing L-A and L-BC dsRNAs (L-BC is the same size as L-A but shares no homology with it). X hybridized with L-A, and direct RNA sequencing of X showed that the first 5' 25 base pairs (of the X positive strand) and at least the last 110 base pairs of the 3' end were identical to the ends of L-A dsRNA. X showed cytoplasmic inheritance and, like M1, was dependent on L-A for its maintenance. X was encapsidated in viruslike particles whose major coat protein was provided by L-A (as is true for M1), and X was found in viruslike particles with one to eight X molecules per particle. This finding confirms our "head-full replication" model originally proposed for M1 and M2. Like M1 or M2, X lowers the copy number of L-A, especially in a ski host. Surprisingly, X requires many chromosomal MAK genes that are necessary for M1 but not for L-A.
Fear Itself: The Effects of Distressing Economic News on Birth Outcomes

I use new administrative data on mass layoffs and plant closings to study the effects of distressing economic news. Exposure to stressful events during pregnancy can impair fetal development. I find that announcement of impending job losses leads to a transient decrease in the mean birth weight within the firm's county one to four months before the job losses. A loss of 500 jobs corresponds roughly to a decrease of 15-20g and 16 percent greater risk of low birth weight. Layoffs announced late in pregnancy are most strongly linked to decreased birth outcomes.
Domain Inverted Acousto- and Electrooptic Devices and Their Application to Optical Communication, Sensing, Laser Sources, and Quantum Key Distribution

The current status of domain inverted lithium niobate acousto- and electrooptic devices is reviewed. We introduce the main domain microengineering techniques and their impact on modulators' performance in terms of reduced power consumption and enablers for a new class of integrated devices. We will then review potential applications of the devices in increasingly important areas, such as advanced optical communication modulation formats, reconfigurable networks, sensors and quantum key distribution.