Miracle-dz/UniFAR-FTUs huggingface dataset:
Transmission of drug-resistant HIV-1 in Europe remains limited to single classes

Background:The spread of drug-resistant HIV-1 might compromise the future success of current first-line regimens. Objective:To analyse the extent and impact of transmission of drug-resistant HIV-1 variants in Europe. Design and methods:The European prospective programme (SPREAD) collected demographic, clinical and virological data from 1245 HIV-1-infected individuals in 17 countries diagnosed in 2002–2003. The potential impact of transmitted drug resistance mutations (TDRMs) on therapy response was determined by using genotypic interpretation algorithms. Results:The overall prevalence of viruses with drug-resistance mutations was 9.1% [96/1050; 95% confidence interval: 7.5–11.1]. The majority (71%) harboured only a single amino acid substitution with limited effect on predicted drug susceptibility. Mutations associated with resistance to nucleoside reverse transcriptase inhibitors were observed most frequently [57/1050 (5.4%)], followed by mutations related to protease inhibitors [32/1050 (3.0%)] and mutations related to non-nucleoside reverse transcriptase inhibitors (NNRTIs) [27/1050 (2.6%)]. In some cases, however, resistance was quite extensive. Four individuals were infected with viruses with reduced susceptibility to all nucleoside reverse transcriptase inhibitors, 3 to all protease inhibitors and 20 to both NNRTIs. Remarkably, in one individual, the resistance pattern was so extensive that none of the available current antiretroviral drugs was predicted to be fully active. Conclusion:The prevalence of TDRM-HIV is quite prominent (9.1%) but did not increase in comparison with a large retrospective European study. Particularly the presence of single NNRTI mutations may impact the efficacy of the first-line regimens. Continuous prospective monitoring remains indicated to explore the patterns and factors contributing to the transmission of TDRMs as well as the potential clinical consequences.
Should General Circulation Model Radiation Schemes Include Rain

14 Accurate simulation of the Earth’s radiation budget is crucial both for weather forecasting 15 and climate modeling. The effect of rain on radiative fluxes and heating rates is a process 16 that is missing in most general circulation models (GCMs). Yet, to our knowledge, the mag17 nitude of the resulting radiative bias remains unquantified. 18 This study aims to quantify the rain radiative effect (RRE) at a range of temporal and 19 spatial scales, as a step towards determining whether GCM radiation schemes should in20 clude rain. Based on our radiative transfer calculations using input from multi-scale mod21 eling framework (MMF) simulations, we find that rain has a negligible effect on global mean 22 radiative fluxes (less than 0.2 W m-2). Weekly mean RREs at specific locations may be larger 23 (less than 4 W m-2). At the finest temporal and spatial resolutions, the RRE can occasionally 24 be much larger again (greater than 100 W m-2), but values exceeding 10 W m-2 occur in less 25 than 0.1% of cases. Using detailed analysis of case studies we demonstrate that the magni26 tude and direction of the RRE depend on the rain water path, its vertical location with respect 27 to cloud and, for longwave radiation, the temperature at which it occurs. 28 As the RREs are generally small, we conclude that this missing process is unlikely 29 to be important for GCMs. However, the infrequent large RREs suggest that there could be 30 some scenarios where including RREs in GCMs is beneficial. 31
Pattern of cerebral hyperperfusion in Alzheimer’s disease and amnestic mild cognitive impairment using voxel-based analysis of 3D arterial spin-labeling imaging: initial experience

Purpose A three-dimensional (3D) continuous pulse arterial spin labeling (ASL) technique was used to investigate cerebral blood flow (CBF) changes in patients with Alzheimer’s disease (AD), amnestic mild cognitive impairment (aMCI), and age- and sex-matched healthy controls. Materials and methods Three groups were recruited for comparison, 24 AD patients, 17 MCI patients, and 21 age- and sex-matched control subjects. Three-dimensional ASL scans covering the entire brain were acquired with a 3.0 T magnetic resonance scanner. Spatial processing was performed with statistical parametric mapping 8. A second-level one-way analysis of variance analysis (threshold at P<0.05) was performed on the preprocessed ASL data. An average whole-brain CBF for each subject was also included as group-level covariates for the perfusion data, to control for individual CBF variations. Results Significantly increased CBF was detected in bilateral frontal lobes and right temporal subgyral regions in aMCI compared with controls. When comparing AD with aMCI, the major hyperperfusion regions were the right limbic lobe and basal ganglia regions, including the putamen, caudate, lentiform nucleus, and thalamus, and hypoperfusion was found in the left medial frontal lobe, parietal cortex, the right middle temporo-occipital lobe, and particularly, the left anterior cingulate gyrus. We also found decreased CBF in the bilateral temporo-parieto-occipital cortices and left limbic lobe in AD patients, relative to the control group. aMCI subjects showed decreased blood flow in the left occipital lobe, bilateral inferior temporal cortex, and right middle temporal cortex. Conclusion Our results indicated that ASL provided useful perfusion information in AD disease and may be used as an appealing alternative for further pathologic and neuropsychological studies, especially of compensatory mechanisms for cerebral hypoperfusion.
Nuclear Survivin Has Reduced Stability and Is Not Cytoprotective*

Survivin is an essential mitotic protein that is overexpressed in many cancers, and its presence is correlated with increased resistance to radiation and chemotherapy. Here we demonstrate that sending survivin into the nucleus accelerates its degradation in a cdh1-dependent manner, abolishes the radio resistance normally conferred to cells by its overexpression, and prevents survivin from inhibiting apoptosis without affecting its mitotic localization. Our data suggest that targeting survivin to the nucleus provides an efficient means of eliminating it from the cell and may prove a novel strategy in cancer treatment, particularly in combination with radiotherapy.
Cerebellar physiology: links between microcircuitry properties and sensorimotor functions

Existing knowledge of the cerebellar microcircuitry structure and physiology allows a rather detailed description of what it in itself can and cannot do. Combined with a known mapping of different cerebellar regions to afferent systems and motor output target structures, there are several constraints that can be used to describe how specific components of the cerebellar microcircuitry may work during sensorimotor control. In fact, as described in this review, the major factor that hampers further progress in understanding cerebellar function is the limited insights into the circuitry‐level function of the targeted motor output systems and the nature of the information in the mossy fiber afferents. The cerebellar circuitry in itself is here summarized as a gigantic associative memory element, primarily consisting of the parallel fiber synapses, whereas most other circuitry components, including the climbing fiber system, primarily has the role of maintaining activity balance in the intracerebellar and extracerebellar circuitry. The review explores the consistency of this novel interpretational framework with multiple diverse observations at the synaptic and microcircuitry level within the cerebellum.
On a Geometric Structure of Pure Multi-qubit Quantum States and Its Applicability to a Numerical Computation

For one-qubit pure quantum states, it is already proved that the Voronoi diagrams with respect to two distances - Euclidean distance and the quantum divergence - coincide. This fact is a support for a known method to calculate the Holevo capacity. To consider an applicability of this method to quantum states of a higher level system, it is essential to check if the coincidence of the Voronoi diagrams also occurs. In this paper, we show a negative result for that expectation. In other words, we mathematically prove that those diagrams no longer coincide in a higher dimension. That indicates that the method used in one-qubit case to calculate the Holevo capacity might not be effective in a higher dimension.
Program Comprehension through Data Mining

Software development has various stages, that can be conceptually grouped into two phases namely development and production (Figure 1). The development phase includes requirements engineering, architecting, design, implementation and testing. The production phase on the other hand includes the actual deployment of the end product and its maintenance. Software maintenance is the last and most difficult stage in the software lifecycle (Sommerville, 2001), as well as the most costly one. According to Zelkowitz, Shaw and Gannon (1979) the production phase accounts for 67% of the costs of the whole process, whereas according to Van Vliet (2000) the actual cost of software maintenance has been estimated at more than half of the total software development cost. The development phase is critical in order to facilitate efficient and simple software maintenance. The earlier stages should be done by taking into consideration apart from any functional requirements also the later maintenance task. For example the design stage should plan the structure in a way that can be easily altered. Similarly, the implementation stage should create code that can be easily read, understood, and changed, and should also keep the code length to a minimum. According to Van Vliet (2000) the final source code length generated is the determinant factor for the total cost during maintenance, since obviously the less code is written the easier the maintenance becomes. According to Erdil et al. (2003) there are four major problems that can slow down the whole maintenance process: unstructured code, maintenance programmers having insufficient knowledge of the system, documentation being absent, out of date, or at best insufficient, and software maintenance having a bad image. Thus the success of the maintenance phase relies on these problems being fixed earlier in the life cycle. In real life however when programmers decide to perform some maintenance task on a program such as to fix bugs, to make modifications, to create software updates etc. these are usually done in a state of time and commercial pressures and with the logic of cost reduction, thus finally resulting in a problematic system with ever increased complexity. As a consequence the maintainers spend from 50% up to almost 90% of their time trying to comprehend the program (Erdös and Sneed; 1998, Von Mayrhauser and Vans; 1994, Pigoski, 1996). Providing maintainers with tools and techniques to comprehend the programs has become and is receiving a lot of financial and research interest given the widespread of computers and software in all aspects of life. In this work we briefly present some of the most important techniques proposed in the field thus far and focus primarily on the use of data mining techniques in general and especially on association rules. Accordingly we give some possible solutions to problems faced by these methods.
Survival in women exposed to single-dose nevirapine for prevention of mother-to-child transmission of HIV: a stochastic model.

BACKGROUND Single-dose nevirapine (sdNVP)-based regimens reduce mother-to-child transmission (MTCT) of human immunodeficiency virus (HIV) but result in resistance to NVP and may reduce the ability of highly active antiretroviral therapy (HAART) used for prevention of MTCT (PMTCT). The impact that sdNVP has on survival in the era of increasing access to HAART is unknown. METHODS We developed a stochastic simulation model to predict survival and sdNVP-attributable mortality in sub-Saharan African women exposed to different PMTCT regimens. RESULTS Our model predicts that mortality attributable to exposure to sdNVP is low--1.1% (interquartile range [IQR], 0.6%-1.5%) and 3.5% (IQR, 3.1%-3.9%) at 5 and 10 years after PMTCT therapy--when all eligible women receive HAART after PMTCT therapy. Predictions were robust to univariate sensitivity analysis. In the worst-case multivariate sensitivity analysis, the increased mortality attributable to sdNVP was 10.4% (IQR, 10.0%-10.8%) at 10 years after PMTCT therapy. CONCLUSIONS Concern has been expressed that widespread use of sdNVP for PMTCT in resource-poor settings will compromise the effectiveness of HAART in HIV-infected women. Although our model does not address other important outcomes of PMTCT regimens, such as transmission of resistant virus, it provides strong arguments that sdNVP for PMTCT should not be delayed because of fear of compromising the survival of women after PMTCT therapy.
Why Does Geoprivacy Matter? The Scientific Publication of Confidential Data Presented on Maps

We examined published maps containing sensitive data, and the protection methods, if any, that were used. We investigated whether the many published warnings about disclosure risk have been effective in reducing privacy risk. During an 8-year period (2005-2012), 19 journals related to GIScience, geography, spatial crime analysis, and health geography were examined. We identified 41 articles that display actual confidential information and 16 articles where confidential information is protected by the use of a geographical mask. During the investigated time frame, the numbers of articles with unmasked confidential data increased, and in total more than 68,000 home addresses were disclosed. One of the more significant findings of this study is that efforts to instill sensitivity to location privacy and disclosure risk have been relatively unsuccessful.
Sustained low-efficiency dialysis (SLED) with prostacyclin in critically ill patients with acute renal failure.

BACKGROUND Prostacyclin is an easy-to-use and safe antihaemostatic drug for continuous renal replacement therapies (RRTs). No study has been performed so far about its use in critically ill patients with acute renal failure (ARF) treated with sustained low-efficiency dialysis (SLED), a hybrid modality between conventional intermittent and continuous RRTs. METHODS We studied 35 consecutive ICU patients with ARF, in whom data on safety and efficacy were prospectively collected in a single-centre experience over 15 months since August 2001. There were 25 males and 10 females; mean age, 72.1 (SD 11.4); mean APACHE II score at ICU admission, 24 (range 14-43); at RRT start, 27.4 (20-43); 28 patients (80%) were on mechanical ventilation and 17 (48.6%) had sepsis. SLED was performed using a conventional dialysis machine, with blood flow at 200 ml/min, bicarbonate-based ultrapure dialysate running at 100 ml/min, dialysate temperature 35 degrees C and low-flux polysulfone filters. Prostacyclin, under the form of its synthetic analogue epoprostenol, was infused at 6 ng/kg/min before the filter. RESULTS Out of 185 daily sessions performed (8-10 h, median 4 per patient, range 1-19), 19 (in 11 patients) were prematurely interrupted (10.3%; 95% CI: 5.4-18.6), after an average 58.5% of the prescribed treatment time (nine sessions in six patients for circuit clotting). This finding compared favourably with the experience we had at our unit using SLED with saline flushes. With the use of prostacyclin, two episodes of upper gastrointestinal bleeding were observed in 2/35 patients during SLED (5.7%; 95% CI: 0.7-19.2), corresponding to 1.1 episodes per 100 person-day on SLED. Therapeutic intervention for hypotension (fluids and/or vasopressor increase) was required in 45/185 (in 20 patients) of the sessions monitored (24.3%; 95% CI: 17.4-32.9); two sessions had to be interrupted because of refractory hypotension. Urea reduction ratio was 0.50 (SD 0.12); mean prescribed and obtained net ultrafiltration were 1.96 l (range 0.5-5.0) and 1.99 l (0.5-5.0), respectively. In-hospital mortality was 46%; mortality predicted by the APACHE II model at ICU admission was 42%; at SLED start, 51%. CONCLUSIONS Prostacyclin is a safe and effective antihaemostatic agent for SLED.
CASA based speech separation for robust speech recognition

This paper introduces a speech separation system as a front-end processing step for automatic speech recognition (ASR). It employs computational auditory scene analysis (CASA) to separate the target speech from the interference speech. Specifically, the mixed speech is preprocessed based on auditory peripheral model. Then a pitch tracking is conducted and the dominant pitch is used as a main cue to find the target speech. Next, the time frequency (TF) units are merged into many segments. These segments are then combined into streams via CASA initial grouping. A regrouping strategy is employed to refine these streams via amplitude modulate (AM) cues, which are finally organized by the speaker recognition techniques into corresponding speakers. Finally, the output streams are reconstructed to compensate the missing data in the abovementioned processing steps by a cluster based feature reconstruction. Experimental results of ASR show that at low TMR (<-6dB) the proposed method offers significantly higher recognition accuracy. Index term: speech separation, CASA, speaker recognition, pitch tracking, units grouping, reconstruction
Monitoring in the Context of Structured Decision-Making and Adaptive Management

Abstract In a natural resource management setting, monitoring is a crucial component of an informed process for making decisions, and monitoring design should be driven by the decision context and associated uncertainties. Monitoring itself can play ≥3 roles. First, it is important for state-dependent decision-making, as when managers need to know the system state before deciding on the appropriate course of action during the ensuing management cycle. Second, monitoring is critical for evaluating the effectiveness of management actions relative to objectives. Third, in an adaptive management setting, monitoring provides the feedback loop for learning about the system; learning is sought not for its own sake but primarily to better achieve management objectives. In this case, monitoring should be designed to reduce the critical uncertainties in models of the managed system. The United States Geological Survey and United States Fish and Wildlife Service are conducting a large-scale management experiment on 23 National Wildlife Refuges across the Northeast and Midwest Regions. The primary management objective is to provide habitat for migratory waterbirds, particularly during migration, using water-level manipulations in managed wetlands. Key uncertainties are related to the potential trade-offs created by management for a specific waterbird guild (e.g., migratory shorebirds) and the response of waterbirds, plant communities, and invertebrates to specific experimental hydroperiods. We reviewed the monitoring program associated with this study, and the ways that specific observations fill ≥1 of the roles identified above. We used observations from our monitoring to improve state-dependent decisions to control undesired plants, to evaluate management performance relative to shallow-water habitat objectives, and to evaluate potential trade-offs between waterfowl and shorebird habitat management. With limited staff and budgets, management agencies need efficient monitoring programs that are used for decision-making, not comprehensive studies that elucidate all manner of ecological relationships.
Effective Load Balancing Mechanism for Heterogeneous Range Queriable Cloud Storage

The rising popularity of big data processing for semantically rich applications such as social networks and IoT (Internet of Things) has made the range queriable cloud storage increasingly important. To support range queries, the data locality is preserved strictly, which makes the load balancing among nodes a challenging task. Currently, most of the range queriable cloud storage systems adopt the combination of neighbor item exchange and neighbor migration methods, which incurs large overhead, and suffers from slow convergence. In this work, we present a novel virtual node based distributed load balancing method for range queriable cloud systems. In our method, each physical node is partitioned into multiple virtual nodes, and all the virtual nodes are organized with range queriable P2P network. Load balancing is conducted in both overlay level (betweenneighboring virtual nodes) without global knowledge and physical level (among physical nodes) with limited global knowledge. Both theoretical analysis and simulations show that our method can significantly reduce the overhead and shorten the convergence time.
Cerebral vasodilating capacity during forebrain ischemia: effects of chronic estrogen depletion and repletion and the role of neuronal nitric oxide synthase

THE effects of chronic 17β-estradiol (E2) depletion, via ovariectomy (OVX), and its repletion, on cortical cerebral blood flow (CBF) and EEG activities during forebrain ischemia, as well as post-ischemic recovery and neuropathology, were assessed and compared with results obtained in normal female rats. We also examined whether neuronal nitric oxide synthase (nNOS) activity is affected by OVX and E2 replacement and whether NOS-derived NO supports vasodilation during ischemia. OVX females displayed a significantly lower CBF during ischemia (10% of baseline) than did normal females (23% of baseline). In OVX rats, given chronic low-dose E2 treatment (0.1 mg kg−1 day−1), intra-ischemic CBF was similar to normal females (25% of baseline). However, at supraphysiologic E2 doses (≥ 0.5 mg kg−1 day−1), that benefit was diminished or lost. Intra-ischemic EEG power reductions and post-ischemic survival rates, neurological dysfunction, and histopathology displayed similar relative differences among groups as the CBF findings. Intra-ischemic CBF was reduced by nNOS inhibition, with ARL 17477, in normal and low-dose E2-treated OVX rats (4–8% baseline). The repressed intra-ischemic vasodilating function in OVX rats may be due to reductions in nNOS activity, because untreated OVX rats showed a 50% lower cortical nNOS activity than that in normal rats and in rats treated with low or high dose (5 mg kg−1 day−1) E2. However, the inability to restore vasodilating function despite normalization of nNOS activity indicates that another mechanism is responsible for the repression of vasodilatory function in the high-dose group. These findings suggest that E2, at levels within the physiological range, promotes ischemic neuroprotection via improving vasodilating capacity. One possible mechanism may relate to E2 enhancing brain nNOS expression and activity.