Miracle-dz/UniFAR-FTUs huggingface dataset:
Characteristics of hepatitis B virus in Ghana: Full length Genome sequences indicate the endemicity of genotype E in West Africa

Hepatitis B virus (HBV) genotypes from A to H have distinct geographical distributions and have been shown to affect the clinical features as well as the course of the HBV infection. HBV genotype E has been found only in Africa. However, the complete genomes of this genotype, which were isolated mainly from West Africa, were available only for a few samples. In this study, five full‐length genomes and seven other small S genes of HBV strains from Ghanaian blood donors were sequenced and investigated. Following phylogenetic analysis, all of the Ghanaian HBV strains were clustered closely in genotype E. All of the 12 small S genes showed the same characteristic of subtype ayw4. The complete genomes of the five Ghanaian strains showed marked similarity with each other and with the reported genotype E strains (96.7%–99.1%). Genotype E strains showed low intra‐genotypic diversity (1.8%) and carried the conserved signature pattern in pre‐S1 as well as in the full genome sequence. Of note, the finding of the G145R escape mutant in an unvaccinated Ghanaian blood donor might raise concern as to the ongoing nation‐wide hepatitis B vaccination program in Ghana. J. Med. Virol. 78:178–184, 2006. © 2005 Wiley‐Liss, Inc.
DIAGNOSTIC AND THERAPEUTIC ADVANCES IN HEPATOLOGY Drug Therapy: Telaprevir

A 52-year-old asymptomatic man is evaluated for chronic hepatitis C (CHC). The aspartate aminotransferase is 138 U/L and the alanine aminotransferase is 164 U/L, with normal bilirubin, alkaline phosphatase, albumin, and complete blood counts. The international normalized ratio is 1.1 and the serum creatinine is 0.9 mg/dL. Hepatitis C virus (HCV) RNA is 1.6 million IU/mL, and genotype is 1b. The patient has read about telaprevir and wants to know whether he is a candidate for treatment with this drug. He also wants to know whether he really requires a liver biopsy prior to initiation of treatment. Would you use telaprevir with interferon and ribavirin in this patient? How will you determine whether he is responding to the drug regimen, how long will you give the medications, and how will you monitor for side effects? How do you determine whether treatment-related anemia is related to telaprevir and not ribavirin or interferon? Which of the side effects of telaprevir would warrant discontinuation of treatment? Would your approach be different if the patient had genotype 2, genotype 3, or genotype 4 disease? Would your approach be different if he had the CC genotype for the interleukin-28 (IL-28) polymorphism?
Relationship between tumor-infiltrating T lymphocytes and clinical response after reduced-intensity allogeneic hematopoietic stem cell transplantation for advanced renal cell carcinoma: a single center prospective study.

OBJECTIVE Renal cell carcinoma (RCC) is refractory to conventional therapy, including chemotherapy and radiation. However, because RCC is sensitive to cytokine therapy, an immunotherapeutic approach such as hematopoietic stem cell transplantation (HSCT) might lead to a cure. We performed an institutional clinical study of HSCT for refractory RCC patients. METHODS RCC patients aged 50 years or over, refractory to therapy, were eligible for the study. HSCT was performed after reduced-intensity conditioning. Primary endpoint was defined as the survival at day 100 after HSCT with complete donor chimerism, and secondary endpoint was the effectiveness of HSCT. RESULTS Seven patients, provided with written informed consent, were enrolled in the study. Six of the seven patients achieved complete donor chimera at day 30 after HSCT, but one patient received second HSCT because of graft rejection. Four patients achieved a partial response (PR) and stable disease was observed in another patient, but these responses were temporary. The disease of the other two patients became progressive. Autopsy findings revealed an accumulation of CD8(+) lymphocytes and degenerative changes in the local RCC lesion in three of six patients who responded clinically. An autopsy of a patient who had obtained a PR revealed lymphocyte involvement with a cytotoxic T cell (CTL) phenotype in the metastasis of RCC. CONCLUSIONS Our results demonstrate the efficacy of HSCT for RCC and suggest that the graft-versus-tumor effect elicited by CTLs is induced in vivo. HSCT should be further explored as a potential curative treatment for RCC.
Quantifying the effort individuals with aphasia invest in working memory tasks through heart rate variability.

PURPOSE The objective of this study was to quantify cognitive effort that individuals with aphasia and neurologically intact participants dedicate to verbal compared with spatial working memory tasks by using a physiological measure of effort: heart rate variability (HRV). METHOD Participants included 8 individuals with aphasia and 19 neurologically intact adults. Participants completed 3 verbal and 3 spatial working memory tasks that varied in difficulty. Performance accuracy and effort allocated to tasks was recorded. Effort was quantified as the change in the 0.07-0.14 Hz band of HRV from baseline to task conditions. RESULTS Results indicated that individuals with aphasia and control participants allocated effort to verbal and spatial working memory tasks. Unlike the control participants, participants with aphasia did not differentially invest effort based on task difficulty. Neither group allocated effort differentially based on task type. CONCLUSIONS Results of the physiological data provide preliminary support for accounts indicating that individuals with aphasia do not properly allocate effort to cognitive-linguistic tasks. Analysis of the Group × Difficulty interaction indicated that the aphasia group did not allocate extra effort when it was required. The lack of a difference in HRV for spatial and verbal tasks suggests that this difference is not specific to verbal stimuli.
Agrammatic primary progressive aphasia in two dextral patients with right hemispheric involvement

Agrammatic primary progressive aphasia (PPA-G) has been known to be associated with focal brain atrophy involving the left posterior frontal and anterior insular regions. However, aphasia can also rarely result from right hemispheric lesions in right-handed patients, so-called crossed aphasia in dextrals (CAD). We report two right-handed patients with PPA-G whose 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET) showed hypometabolism predominantly in the right hemisphere, implicating “crossed PPA-G. ”
Analog Building Blocks for Organic Smart Sensor Systems in Organic Thin-Film Transistor Technology on Flexible Plastic Foil

In this work, we present the implementation and measurement results of all analog building blocks of an organic smart sensor system on foil. The presented building blocks are a 1D and a 2D 4 × 4 pixel flexible capacitive touch sensor with a sample rate of 1.5 kS/s, a DC-connected two-stage opamp with a 20 dB DC gain, a Dickson DC-DC up-converter with output bias voltages up to 60 V and down to - 40 V which are used as a bias voltage in the other building blocks, and a ΔΣ ADC with a 26.5 dB precision and a band width of 15.6 Hz. The sensors, the opamp, the DC-DC converter and the ADC respectively consume 6 μA, 15 μA, 1 μA and 100 μA from a 15 V power supply.
Relativistic mean field model for entrainment in general relativistic superfluid neutron stars

General relativistic superfluid neutron stars have a significantly more intricate dynamics than their ordinary fluid counterparts. Superfluidity allows different superfluid (and superconducting) species of particles to have independent fluid flows, a consequence of which is that the fluid equations of motion contain as many fluid element velocities as superfluid species. Whenever the particles of one superfluid interact with those of another, the momentum of each superfluid will be a linear combination of both superfluid velocities. This leads to the so-called entrainment effect whereby the motion of one superfluid will induce a momentum in the other superfluid. We have constructed a fully relativistic model for entrainment between superfluid neutrons and superconducting protons using a relativistic $\sigma - \omega$ mean field model for the nucleons and their interactions. In this context there are two notions of ``relativistic'': relativistic motion of the individual nucleons with respect to a local region of the star (i.e. a fluid element containing, say, an Avogadro's number of particles), and the motion of fluid elements with respect to the rest of the star. While it is the case that the fluid elements will typically maintain average speeds at a fraction of that of light, the supranuclear densities in the core of a neutron star can make the nucleons themselves have quite high average speeds within each fluid element. The formalism is applied to the problem of slowly-rotating superfluid neutron star configurations, a distinguishing characteristic being that the neutrons can rotate at a rate different from that of the protons.
Cellular mechanisms of orexin actions on paraventricular nucleus neurones in rat hypothalamus

Using whole‐cell patch clamp techniques we have examined the cellular mechanisms underlying the effects of orexin A (OX‐A) on electrophysiologically identified magnocellular and parvocellular neurones in the rat hypothalamic paraventricular nucleus (PVN). The majority of magnocellular neurones (67 %) showed concentration‐dependent, reversible depolarizations in response to OX‐A. These effects were abolished in tetrodotoxin (TTX), suggesting them to be indirect effects on this population of neurones. OX‐A also caused increases in excitatory postsynaptic current (EPSC) frequency and amplitude in magnocellular neurones. The former effects were again blocked in TTX while increases in mini‐EPSC amplitude remained. Depolarizing effects of OX‐A on magnocellular neurones were also found to be abolished by kynurenic acid, supporting the conclusion that these effects were the result of activation of a glutamate interneurone. Parvocellular neurones (73 % of those tested) also showed concentration‐dependent, reversible depolarizations in response to OX‐A. In contrast to magnocellular neurones, these effects were maintained in TTX, indicating direct effects of OX‐A on this population of neurones. Voltage clamp analysis using slow voltage ramps demonstrated that OX‐A enhanced a non‐selective cationic conductance with a reversal potential of ‐40 mV in parvocellular neurones, effects which probably explain the depolarizing effects of this peptide in this subpopulation of PVN neurones. These studies have identified separate cellular mechanisms through which OX‐A influences the excitability of magnocellular and parvocellular PVN neurones.
A comparison of transmission schemes for scalable video over MIMO relay networks

This paper investigates a comparison of transmission schemes for the scalable video over multiple-input multiple-output relay networks. We consider three time-division multiple-access cooperative schemes by using embedded space time codes with various degrees of broadcasting and receiving collision. In this paper, we assume that base station and relay station are equipped two antennas and mobile stations have only one antenna. The relay station operates decode-and-forward mode for cooperative transmission. The base station broadcasts scalable video bit stream by encoding embedded space time codes with the assistance of relay. Upon the amount of received information of each cooperative scheme, Mobile stations get the corresponding efficient decoding. With the help of relayed information, base layer retrieves better protection for ensuring the basic quality of scalable video. Visual quality is refined by enhancement layers carried in transmitted signal. We investigate the diversity performance of various schemes in term of bit error rate. Scalable video performance is also provided for comparing and evaluating the effectiveness of scalable video transmission schemes. Based on the need of users, it's possible to select the suitable scheme for trading off between the protection of base and enhancement layers.
Metallo beta lactamases in Pseudomonas aeruginosa and Acinetobacter species

The multi drug resistant gram negative bacteria especially Pseudomonas aeruginosa and Acinetobacter species are on the rise. The major defense in these bacteria against beta-lactam antibiotics is production of metallo beta lactamases (MBLs) which degrade this group of antibiotics including carbapenems. Till now five main types of MBLs have been described throughout the World – IMP, VIM, SPM, GIM and SIM. A new MBL has been recently reported in P. aeruginosa from Australia – bla AIM-1. There are no standard guidelines by CLSI for detection of these enzymes in various bacteria. A number of phenotypic tests based on different beta lactam-inhibitor combinations are being evaluated and used for routine testing. Regarding the treatment options – colistin, various antibiotic combinations and a few novel antibiotics are being tried and evaluated. Prevention is based on age old practices of strict infection control and judicious use of antibiotics.
Asymmetric leaf development and blade expansion in Arabidopsis are mediated by KANADI and YABBY activities

Asymmetric development of plant lateral organs is initiated by a partitioning of organ primordia into distinct domains along their adaxial/abaxial axis. Two primary determinants of abaxial cell fate are members of the KANADI and YABBY gene families. Progressive loss of KANADI activity in loss-of-function mutants results in progressive transformation of abaxial cell types into adaxial ones and a correlated loss of lamina formation. Novel, localized planes of blade expansion occur in some kanadi loss-of-function genotypes and these ectopic lamina outgrowths are YABBY dependent. We propose that the initial asymmetric leaf development is regulated primarily by mutual antagonism between KANADI and PHB-like genes, which is translated into polar YABBY expression. Subsequently, polar YABBY expression contributes both to abaxial cell fate and to abaxial/adaxial juxtaposition-mediated lamina expansion.
Voltage margins identification on commercial x86-64 multicore microprocessors

In this paper, we explore the pessimistic voltage guardbands of two multicore x86-64 microprocessor chips that belong to different microarchitectures (one ultra-low power and one high-performance microprocessor), when programs are executed on individual cores of the CPU chips. We also examine the energy and temperature gains as positive effects of lowering the voltage in both chips while preserving the functional correctness of programs. The behavior of the cores was examined executing 8 different workloads from the SPEC CPU2006 suite. Our differential experimental study is performed on two state-of-the-art x86-64 microprocessors: an ultra-low power Intel Core i5-4200U and a high-performance Intel Core i7-3970X. Based on the results, the cores on each microprocessor chip behave differently for different workloads when undervolted, and the voltage guardbands are more than 15% below the nominal voltage levels. We show that the energy efficiency can be increased by a maximum of 20% and the reduction of temperature can be up to 25%.
Masking of speech in young and elderly listeners with hearing loss.

This study examined the contributions of various properties of background noise to the speech recognition difficulties experienced by young and elderly listeners with hearing loss. Three groups of subjects participated: young listeners with normal hearing, young listeners with sensorineural hearing loss, and elderly listeners with sensorineural hearing loss. Sensitivity thresholds up to 4000 Hz of the young and elderly groups of listeners with hearing loss were closely matched, and a high-pass masking noise was added to minimize the contributions of high-frequency (above 4000 Hz) thresholds, which were not closely matched. Speech recognition scores for monosyllables were obtained in the high-pass noise alone and in three noise backgrounds. The latter consisted of high-pass noise plus one of three maskers: speech-spectrum noise, speech-spectrum noise temporally modulated by the envelope of multi-talker babble, and multi-talker babble. For all conditions, the groups with hearing impairment consistently scored lower than the group with normal hearing. Although there was a trend toward poorer speech-recognition scores as the masker condition more closely resembled the speech babble, the effect of masker condition was not statistically significant. There was no interaction between group and condition, implying that listeners with normal hearing and listeners with hearing loss are affected similarly by the type of background noise when the long-term spectrum of the masker is held constant. A significant effect of age was not observed. In addition, masked thresholds for pure tones in the presence of the speech-spectrum masker were not different for the young and elderly listeners with hearing loss. (ABSTRACT TRUNCATED AT 250 WORDS)
The Effect of Individualized Professional Support on Duration of Breastfeeding: A Randomized Controlled Trial

Atrialwas conducted with 51women randomly assigned either to a conventional nursing care group or to an individualized professional support group; to examine the effect of professional support on breastfeeding status at 4 weeks postpartum. All participants identified themselves as having no prior support. At 4 weeks postpartum, 17 out of 25 (68%) and 26 out of 26 (100%) women in the control and intervention groups, respectively, continued to breastfeed (P=.005). Results indicate that postpartum care augmented with individualized professional support commenced in the hospital and continued in the community significantly increases the duration of breastfeeding among women who identify themselves as being without support for the first month postpartum.
Harvesting the Genomic Promise: Recombineering Sequences for Phenotypes

Abstract The past decade has witnessed the construction of linkage and physical maps defining quantitative trait loci (QTL) in various domesticated species. Targeted chromosomal regions are being further characterized through the construction of bacterial artificial chromosome (BAC) contigs in order to isolate and characterize genes contributing towards phenotypic variation. Whole‐genome BAC contigs are also being constructed that will serve as the tiling path for genomic sequencing. Harvesting this genetic information for biological gain requires either genetic selection or the production of genetically modified animals. This later approach when coupled with nuclear transfer technology (NT) provides “clones” of genetically modified animals. However, to date, the production of genetically modified animals has been limited to either microinjection of small gene constructs into embryos with random insertion or complex gene constructs designed to knock‐out targeted gene expression. Neither of these approaches provides for introducing directed genetic manipulation allowing for allelic substitution [knock‐in], subsequent analyses of gene expression, and cloning. An alternative approach utilizing genomic sequence information and recombineering to direct gene targeting of specific porcine BACs is presented here.
Anti‐atherogenic effect of berberine on LXRα‐ABCA1‐dependent cholesterol efflux in macrophages

Berberine, a botanical alkaloid purified from Cortidis rhizoma, has effects in cardiovascular diseases, yet the mechanism is not fully understood. Foam cells play a critical role in the progression of atherosclerosis. This study aimed to investigate the effect of berberine on the formation of foam cells by macrophages and the underlying mechanism. Treatment with berberine markedly suppressed oxidized low‐density lipoprotein (oxLDL)‐mediated lipid accumulation, which was due to an increase in cholesterol efflux. Berberine enhanced the mRNA and protein expression of ATP‐binding membrane cassette transport protein A1 (ABCA1) but did not alter the protein level of ABCG1 or other scavenger receptors. Additionally, functional inhibition of ABCA1 with a pharmacological inhibitor or neutralizing antibody abrogated the effects of berberine on cholesterol efflux and lipid accumulation. Moreover, berberine induced the nuclear translocation and activation of liver X receptor α (LXRα) but not its protein expression. Knockdown of LXRα mRNA expression by small interfering RNA abolished the berberine‐mediated protective effects on ABCA1 protein expression and oxLDL‐induced lipid accumulation in macrophages. These data suggest that berberine abrogates the formation of foam cells by macrophages by enhancing LXRα‐ABCA1‐dependent cholesterol efflux. J. Cell. Biochem. 111: 104–110, 2010. © 2010 Wiley‐Liss, Inc.
Joint Optimization of Denoising Autoencoder and DNN Acoustic Model Based on Multi-Target Learning for Noisy Speech Recognition

Denoising autoencoders (DAEs) have been investigated for enhancing noisy speech before feeding it to the back-end deep neural network (DNN) acoustic model, but there may be a mismatch between the DAE output and the expected input of the back-end DNN, and also inconsistency between the training objective functions of the two networks. In this paper, a joint optimization method of the front-end DAE and the back-end DNN is proposed based on a multi-target learning scheme. In the first step, the front-end DAE is trained with an additional target of minimizing the errors propagated by the back-end DNN. Then, the unified network of DAE and DNN is fine-tuned for the phone state classification target, with an extra target of input speech enhancement imposed to the DAE part. The proposed method has been evaluated with the CHiME3 ASR task, and demonstrated to improve the baseline DNN as well as the simple coupling of DAE with DNN. The method is also effective as a post-filter of a beamformer.
Assessment of wildland fire impacts on watershed annual water yield: Analytical framework and case studies in the United States

More than 50% of water supplies in the conterminous United States originate on forestland or rangeland and are potentially under increasing stress as a result of larger and more severe wildfires. Little is known, however, about the long‐term impacts of fire on annual water yield and the role of climate variability within this context. We here propose a framework for evaluating wildland fire impacts on streamflow that combines double‐mass analysis with new methods (change point analysis, climate elasticity modeling, and process‐based modeling) to distinguish between multiyear fire and climate impacts. The framework captures a wide range of fire types, watersheds characteristics, and climate conditions using streamflow data, as opposed to other approaches requiring paired watersheds. The process is illustrated with three case studies. A watershed in Arizona experienced a +266% increase in annual water yield in the 5 years after a wildfire, where +219% was attributed to wildfire and +24% to precipitation trends. In contrast, a California watershed had a lower (−64%) post‐fire net water yield, comprised of enhanced flow (+38%) attributed to wildfire offset (−102%) by lower precipitation in the post‐fire period. Changes in streamflow within a watershed in South Carolina had no apparent link to periods of prescribed burning but matched a very wet winter and reports of storm damage. The presented framework is unique in its ability to detect and quantify fire or other disturbances, even if the date or nature of the disturbance event is uncertain, and regardless of precipitation trends.