Miracle-dz/UniFAR-FTUs huggingface dataset:
Recovery of Replication-Competent Residual HIV-1 from Plasma of a Patient Receiving Prolonged, Suppressive Highly Active Antiretroviral Therapy

ABSTRACT The clinical significance of persistent residual viremia in patients on prolonged highly active antiretroviral therapy (HAART) is not clear. Moreover, it remains to be demonstrated whether residual viremia consists of viruses capable of spreading infection in vivo upon termination of therapy. Using residual viral RNAs (vRNAs) isolated from a HAART-treated patient's plasma, we cloned full-length viral genomes and found that most of them could produce infectious, replication-competent HIVs when transfected into TZM-bl cells, suggesting that residual viruses produced in the absence of therapy can initiate fresh cycles of infection and spread in host cells. The data further indicate that residual viremia may pose a major concern with regard to the emergence of drug-resistant HIVs during periods of low adherence to therapy.
Effects of short-term lifestyle activity modification on adiponectin mRNA expression and plasma concentrations

Abstract Adiponectin mRNA and plasma concentrations were reduced in obesity. Exercise training may reduce the adipose tissue (AT), although it is not well known, whether exercise – induced change in AT, increases adiponectin mRNA expression and plasma concentrations or not. Therefore, the purpose of this study was to examine the effects of short-term lifestyle activity modification (LAM) on adiponectin mRNA and plasma concentrations. Sixteen obese and overweight middle-aged men (age, 35–50 years) with type 2 diabetes participated in this study. The subjects were randomly assigned to LAM group (n=8) or control group (n=8). The subjects in LAM group walked two miles in 30 min on a treadmill on 4 days per week for 12 weeks according to the guidelines of the Centers for Disease Control and Prevention and American College of Sports Medicine. The results showed that body mass, body mass index, central visceral adipose tissue and subcutaneous adipose tissue volume and hip and thigh subcutaneous adipose tissue (hip and thigh SAT) volume were decreased in the LAM group compared to the control group (P<0.05). Adiponectin mRNA in abdominal and gluteal subcutaneous AT were increased significantly in the LAM group compared to the control group (P<0.05), while plasma adiponectin concentrations, hs-CRP and insulin resistance did not change significantly. In conclusion, adiponectin mRNA levels increase after 12 weeks of LAM; however, plasma adiponectin levels were not affected by this protocol in obese and overweight middle-aged men with type 2 diabetes.
TOWARDS THE ESSENCE OF THE REFLECTION ABOUT EVERYTHING

Phenomenology is one of the major strands to existential philosophy and existential therapy, but its history and successive definitions are not well known. Its waters came into contact with the influence of the existential writers: Kierkegaard, Dostoevsky and Nietzsche, on the one hand and met with the more ontological philosophers on the other, such as Kant and Hegel. Phenomenology is also a critique of the rationalists, eg Galileo, Descartes, Spinoza and Leibniz. I believe that if current users of existential-phenomenological theory were more aware of the successive definitions of phenomenology, they would be better informed in making decisions when they apply it. I provide some historical information and ask readers to make sense of it in the context of making existential-phenomenological therapy. As phenomenology precedes the creation of Heidegger's hermeneutic phenomenology of existence, the basis for existential therapy, the (re)creation of a phenomenology for psychotherapeutic healing is an aim. First of all, some brief definitions of the word phenomenology prior to its major usage by Edmund Husserl. Next, Franz Brentano's position must be described so the link between the movement's instigator and its developers can be understood. The next sections define the major senses of phenomenology as given by Husserl, followed by some of its inconsistencies and problems. Finally, the practical consequences are noted for therapists. The work of Spiegelberg, briefly a student of Husserl, is a source for applying this approach to therapy (Spiegelberg, 1972, 1982).
Comparison of reactions to human and armadillo lepromins in leprosy.

To assess the usefulness of Mycobacterium leprae-infected armadillo tissue as a substitute for human lepromas for the manufacture of lepromin, we compared skin reactions to preparations from these two sources in 115 leprosy patients. The patient sample represented all the primary clinical forms of leprosy. Lepromin derived from the armadillo (lepromin-A) provoked the same pattern of responses as human derived lepromin (lepromin-H), i.e., lepromatous patients gave the weakest reactions. Lepromin-A reactions were consistently more intense than those to lepromin-H. We conclude that lepromin-A is a promising alternative to lepromin-H and may make the worldwide distribution of a standardized skin testing reagent feasible.
Biological Control of Hog Waste Odor through Stimulated Microbial Fe(III) Reduction

ABSTRACT Odor control and disposal of swine waste have inhibited expansion of swine production facilities throughout the United States. Swine waste odor is associated primarily with high concentrations of volatile fatty acids (VFAs). Here, we demonstrate that stimulated Fe(III) reduction in hog manure can rapidly remove the malodorous compounds and enhance methane production by 200%. As part of these studies, we enumerated the indigenous Fe(III)-reducing population in swine waste and identified members of the family Geobacteraceae as the dominant species. These organisms were present at concentrations as high as 2 × 105 cells g−1. Several pure cultures of Fe(III) reducers, including Geobacter metallireducens, Geobacter humireducens, Geobacter sulfurreducens, Geobacter grbiciae, Geothrix fermentans, and Geovibrio ferrireducens, readily degraded some or all of the malodorous VFAs found in swine manure. In contrast, Shewanella algae did not degrade any of these compounds. We isolated an Fe(III) reducer, Geobacter strain NU, from materials collected from primary swine waste lagoons. This organism degraded all of the malodorous VFAs tested and readily grew in swine waste amended with Fe(III). When raw waste amended with Fe(III) was inoculated with strain NU, the VFA content rapidly decreased, corresponding with an almost complete removal of the odor. In contrast, the raw waste without Fe(III) or strain NU showed a marked increase in VFA content and a rapid pH drop. This study showed that Fe(III) supplementation combined with appropriate bioaugmentation provides a simple, cost-effective approach to deodorize and treat swine waste, removing a significant impediment to the expansion of pork production facilities.
Natural history of fetal simple renal cysts detected in early pregnancy.

PURPOSE In this 12-year prospective, longitudinal study we investigated the natural history of fetal simple renal cysts identified by ultrasonography in early pregnancy. MATERIALS AND METHOD A detailed sonographic examination of the fetus was performed between January 1987 and June 1998 in 29,984 consecutive pregnancies at 14 to 16 weeks of gestation. Amniocenteses and chromosomal investigations were done in all cases in which a simple renal cyst was detected in the fetus. Followup sonography was done in all cases of renal cyst during pregnancy, infancy and, when indicated, childhood. RESULTS Simple renal cysts were diagnosed at 14 to 16 weeks of gestation in 28 fetuses (1/1,100 pregnancies, 0.09%). In 25 fetuses the cysts resolved during pregnancy. In 2 fetuses the cysts remained benign but persisted postnatally and in 1 a renal cyst that was initially defined as simple was the first sign of unilateral multicystic dysplastic kidney. Except for nonseptated cystic hygroma in 1 fetus, none of the others had associated anomalies of the urinary or other organ systems and no chromosomal anomalies. Postnatal followup in all cases revealed healthy children. CONCLUSIONS A fetal simple renal cyst can be identified by ultrasonography in early pregnancy. In the absence of associated anatomical or chromosomal abnormalities, the majority of cysts will resolve during pregnancy without any sequelae. Given the transient nature of most fetal simple renal cysts detected in early pregnancy, it is possible that these cysts represent a distinct entity within the spectrum of cystic kidney diseases.
Assessing Privacy in Social Media Aggregators

Social Media Aggregator (SMA) applications present a platform enabling users to manage multiple Social Networking Sites (SNS) in one convenient application, which results in a unique concentration of data from several SNS accounts in addition to the user’s mobile phone data available to them. We describe a three-step methodology to assess how privacy is considered in these applications: 1) We inspect the mobile data and social media data; 2) we study any privacy policies and their compliance with respect to distributor’s vetting policies; and 3) we perform a qualitative assessment of traceability between privacy policies and the actual transparency and control mechanisms offered to users by the apps’ interfaces. We then present the results we obtained for 13 popular SMAs from 3 app stores, showing a variation in data accessed by the individual applications, an absence of privacy policies for 5 of the SMAs evaluated, and a lack of traceability between privacy policies and transparency and control of interface operations. After this, we report our experiences using the methodology and the lessons learned, together with potential future work to improve the methodology and its potential to also assess privacy in other mobile applications that also connect with social media.
Combinations of 2'-C-Methylcytidine Analogues with Interferon-α2b and Triple Combination with Ribavirin in the Hepatitis C Virus Replicon System

Background: Hepatitis C virus (HCV) polymerase is an essential enzyme for HCV replication and has multiple inhibitor binding sites making it a major target for antiviral intervention. It is apparent that no single drug can inhibit HCV replication in humans. Hence, combinations of nucleoside analogues β-D-2'-C-methylcytidine (2'-C-MeC; NM-107) or β-D-2'-deoxy-2'-fluoro-2'-C-methylcytidine (2'-F-C-MeC; PSI-6130) with interferon-α2b (IFN-α2b) or triple combination with ribavirin (RBV) were evaluated. Methods: Huh-7 cells containing the self-replicating subgenomic HCV replicon (Clone B) were used for drug combination studies. After drug treatment for 5 days, total cellular RNA was then extracted and both ribosomal RNA and HCV replicon RNA were amplified in a single-step multiplex real-time PCR assay. Drug interaction analyses were performed using the CalcuSyn program. Results: Double combinations of 2'-C-MeC or 2'-F-C-MeC with IFN-α2b at all ratios tested had weighted average combination index (CIwt) values <1 indicating synergistic inhibition of HCV replication in the replicon system. For the triple combinations of IFN-α2b plus RBV with either 2'-C-MeC or 2'-F-C-MeC, the CIwt values at 1:1:1 ratio tested were 0.5 and 0.8, respectively, indicating synergistic antiviral effects. No apparent cytotoxicity effects were observed with any of the combinations tested. Conclusion: These promising in vitro data warrant clinical investigation of the nucleosides analogues such as 2'-C-MeC or 2'-F-C-MeC in their prodrug forms, together with IFN-α2b and RBV, for successful treatment of HCV infections.
Measuring the mustard seed: first exercise in modelling the real world

Constructing, reading and understanding graphs is an interdisciplinary and important skill in today’s world. Though being such an important skill students are not taught explicitly to develop this important skill. Also there has been an urge in the literature for the students to use real world data to make sense of the concepts that they learn. In general students are not provided with opportunities to make the skill explicit, and link it up with their life experiences the concepts and subjects that they learn. We present here a simple task which provides the students a context in which real world data is collected, and used to construct a simple linear mathematical model. This task connects different skills like measurement, graphicacy, mathematical modelling and at the same time also helps a two way transition between the abstract mathematical world and the concrete physical world.
Scaling and Its Impact on Burn-in

This article describes how CMOS IC technology scaling impacts on semiconductor burn-in and burn-in procedures. Burn-in is a quality improvement procedure challenged by the high leakage currents that are rapidly increasing with IC technology scaling. These currents are expected to increase even more under the new burn-in environments leading to higher junction temperatures, possible thermal runaway, and yield loss of good parts during burn-in. The paper discusses the effect of junction temperature on device reliability, aging, and burn-in procedure optimization. The effect of device thermal runaway and the requirements it forces on commercial burn-in ovens, device package and device cooling are also described.
Patients' satisfaction with the NHS is growing, survey shows

Residents of a block of flats in Zurich who are fed up with the assisted suicide group Dignitas taking dead bodies out of the building in body bags are asking the local council to act. The controversial clinic that has helped more than 450 people, including more than 30 British people, to end their lives since it opened in 1998 administers its lethal injections in rooms in a residential apartment block on Gloria Street in Zurich's Wiedikon district. But people living in the block say they have had enough of the stream of bodies being …
Molecular analysis of Escherichia coli O157 strains isolated from cattle and pigs by the use of PCR and pulsed-field gel electrophoresis methods

Fourteen Escherichia coli O157 strains isolated from cattle and pigs in Poland and in Germany were investigated, using PCR, for the genetic markers associated with Shiga toxin-producing E. coli (STEC). Only two strains, both of cattle origin, were positive for the fliC (H7) gene and could be classified as O157 : H7. Nine isolates had stx shiga toxin genes, either stx1 (1 strain), stx2 (4 isolates) or both (4 strains). e stx2-carrying samples were further subtyped by PCR for the stx2c, stx2d, and stx2e toxin variants. It was shown that all but one stx2-positive bacteria possessed the stx2c Shiga toxin gene type and one stx2 STEC isolate had the stx2d virulence factor sub- type. e eaeA (intimin) gene was found in 9 strains (8 isolates from cattle and one strain from pigs); all of them harboured the genetic marker characteristic of the gamma intimin variant. e translocated intimin receptor (tir) gene was detected in 7 isolates tested and among them only one tir-positive strain was recovered from pigs. e ehly E. coli enterohemolysin gene was amplified in all but one strains obtained from cattle and only in one isolate of porcine origin. e genetic relatedness of the analysed E. coli O157 strains was examined by restriction fragment length polymorphism (RFLP) of chromosomal DNA digested with XbaI. Two distinct but related RFLP pattern clusters were observed: one with 9 strains (8 isolates of bovine origin and one strain obtained from pigs) and the other one comprises the remaining 5 E. coli isolates (4 of porcine origin and one strain recovered from cattle). e results suggest that pigs, besides cattle, may be a reservoir of E. coli O157 strains potentially pathogenic to humans. Moreover, epidemiologically unrelated isolates of the O157 serogroup, recovered from different animal species, showed a clonal relationship as demonstrated by the RFLP analysis.
Thinning of large mammalian cells for cryo‐TEM characterization by cryo‐FIB milling

Focused ion beam milling at cryogenic temperatures (cryo‐FIB) is a valuable tool that can be used to thin vitreous biological specimens for subsequent imaging and analysis by cryo‐transmission electron microscopy (cryo‐TEM) in a frozen‐hydrated state. This technique offers the potential benefit of eliminating the mechanical artefacts that are typically found with cryo‐ultramicrotomy. However, due to the additional complexity in transferring samples in and out of the FIB, contamination and devitrification of the amorphous ice is commonly encountered. To address these problems, we have designed a sample cryo‐shuttle that directly and specifically accepts Polara TEM cartridges to simplify the transfer process between FIB and TEM. We optimized several parameters in the cryo‐FIB and cryo‐TEM processes using the quality of the samples’ ice as an indicator and demonstrated high‐quality milling with large mammalian cells. By comparing the results from HeLa cells to those from Escherichia coli cells, we discuss some of the artefacts and challenges we have encountered using this technique.
Power and resource aware scheduling with multiple voltages

In this paper, we address the problem of timing-constrained scheduling with resources operating at multiple voltages. Without the resource concern, a dual piecewise-linear programming formulation is proposed which can be transformed into a min-cost flow problem on a simplified flow graph. We present a two-stage method to minimize power and resource usage. In the first stage, an optimal dual piecewise-linear network simplex method (DPLNSM) is proposed to minimize the power consumption. The method is efficient, especially when the given maximum control step is large. In the second stage, a tabu-search based scheduling method is proposed to decrease the resource usage on the basis of power optimization, where tree transformation and list scheduling are done in each iteration. Experimental results show that our proposed method generates optimal solutions on the given benchmarks in a short time.
Rapid language adaptation tools and technologies for multilingual speech processing systems

The performance of speech and language processing technologies has improved dramatically over the past decade, with an increasing number of systems being deployed in a large variety of applications, such as spoken dialog systems, speech summarization and information retrieval systems, and speech translation systems. Most efforts to date were focused on a very small number of languages with large number of speakers, economic potential, and information technology needs of the population. However, speech technology has a lot to contribute even to those languages that do not fall into this category. Languages with a small number of speakers and few linguistic resources may suddenly become of interest for humanitarian and military reasons. Furthermore, a large number of languages are in danger of becoming extinct, and ongoing projects for preserving them could benefit from speech technology.
The two week referral for colorectal cancer: a retrospective analysis

Objective The two‐week referral (TWR) system was introduced in July 2000 to address the delays in referral, diagnosis and treatment of colorectal cancer (CRC) and lessen the associated psychological morbidity of prolonged waiting. General practitioners complete a proforma outlining ‘high‐risk’ criteria for CRC to ensure an urgent referral within 14 days. The aim of the study was to analyse the TWR process and the proforma criteria.
Fault detection for dissipative nonlinear systems: An energy balance method

This paper addresses the problem of fault detection for dissipative nonlinear systems. A new method based on energy balance is proposed for dissipative nonlinear systems. The nonlinear system is described by the T-S fuzzy model. Based on the dissipation of the T-S fuzzy model, the energy balance is constructed. Then faults can be detected by judging whether the energy balance of system construction is established. The effectiveness of the proposed scheme is illustrated by a numerical example.
Highly Ordered Vertical Structure ofSynechococcus Populations within the One-Millimeter-Thick Photic Zone of a Hot Spring Cyanobacterial Mat

ABSTRACT A variety of contemporary techniques were used to investigate the vertical distribution of thermophilic unicellular cyanobacteria,Synechococcus spp. , and their activity within the upper 1-mm-thick photic zone of the mat community found in an alkaline siliceous hot spring in Yellowstone National Park in Wyoming. Detailed measurements were made over a diel cycle at a 61°C site. Net oxygenic photosynthesis measured with oxygen microelectrodes was highest within the uppermost 100- to 200-μm-thick layer until midmorning, but as the day progressed, the peak of net activity shifted to deeper layers, stabilizing at a depth of 300 μm from midday throughout the afternoon. Examination of vertical thin sections by bright-field and autofluorescence microscopy revealed the existence of different populations of Synechococcus which form discrete bands at different vertical positions. Denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene segments from horizontal cryosections obtained at 100-μm-thick vertical intervals also suggested vertical stratification of cyanobacterial, green sulfur bacterium-like, and green nonsulfur bacterium-like populations. There was no evidence of diel migration. However, image analysis of vertical thin sections revealed the presence of a narrow band of rod-shapedSynechococcus cells in which the cells assumed an upright position. These upright cells, located 400 to 800 μm below the surface, were observed only in mat samples obtained around noon. In mat samples obtained at other time points, the cells were randomly oriented throughout the mat. These combined observations reveal the existence of a highly ordered structure within the very thin photic zone of this hot spring microbial mat, consisting of morphologically similarSynechococcus populations that are likely to be differentially adapted, some co-occurring with green sulfur bacterium-like populations, and all overlying green nonsulfur bacterium-like populations.
Detecting similar components between android applications with obfuscation

Many Android researches which focus on clone Android applications (or apps) and third-party libraries are both related to detect similar components between apps or between app and third-party library. We conclude a set of stable features of a class which will not change during obfuscation through studying the app's bytecode and ProGuard, the most popular obfuscator used in Android development. Based on the stable features, we proposed a program analysis approach to detect similar packages, classes or methods between apps. We generate app's fingerprints based on the stable features, and compare the fingerprints later. So our approach can work well with obfuscated apps. We evaluate our approach through manually written apps and evaluate the functionality through two groups of app. And the result shows that our approach can analyze a pair of apps within 2min, which is feasible to detect similar components between apps.
Picolinamidium squarate and di-p-toluidinium squarate dihydrate.

The crystal structure determinations of picolinamidium squarate, C 6 H 7 N 2 O + . C 4 O 4 - , (I), and di-p-toluidinium squarate dihydrate, 2C 7 H 10 N + . C 4 O 4 2 - . 2H 2 O, (II), are reported. While salt formation occurs by donation of one H atom from squaric acid to the picolinamide molecule in (I), in compound (II), each squaric acid molecule donates one H atom to the p-toluidine N atom of two trans p-toluidine molecules. In (I), the pyridine ring is coplanar with the squarate monoanion through imposed crystallographic mirror symmetry; in (II), the dihedral angle between the p-toluidine moiety and the squarate dianion is 70.71(1)°. In (I), a three-dimensional structure is formed via van der Waals interactions between parallel planes of molecules, with hydrogen-bond interactions (N-H.O and O-H.O) acting within the planes; hydrogen bonds form a three-dimensional network in (II).