bluuebunny/crossref_metadata_2025_split huggingface dataset:
Point-of-Care Cepheid Xpert HIV-1 Viral Load Test in Rural African Communities Is Feasible and Reliable
Authors: Moyo Sikhulile , Mohammed Terence , Wirth Kathleen E. , Prague Melanie , Bennett Kara , Holme Molly Pretorius , Mupfumi Lucy , Sebogodi Philemon , Moraka Natasha O. , Boleo Corretah , Maphorisa Comfort N. , Seraise Boitumelo , Gaseitsiwe Simani , Musonda Rosemary M. , van Widenfelt Erik , Powis Kathleen M. , Gaolathe Tendani , Tchetgen Tchetgen Eric J. , Makhema Joseph M. , Essex Max , Lockman Shahin , Novitsky Vladimir 
Published: October 2016

ABSTRACT

Routine monitoring of HIV-1 RNA or viral load (VL) in patients on antiretroviral therapy (ART) is important, but there are multiple impediments to VL testing in resource-constrained settings. An accurate point-of-care (POC) HIV-1 VL test could alleviate many of these challenges. We compared the performance of the Cepheid Xpert HIV-1 VL assay against the laboratory-based Abbott
m
2000sp/
m
2000rt assay (Abbott assay). ART-naive individuals participating in the Botswana Combination Prevention Project in 20 communities provided EDTA-blood specimens during household surveys. Both the POC Xpert HIV-1 VL and Abbott assays were performed on specimens sampled from 277 individuals. We found a high correlation between the Xpert HIV-1 VL and Abbott assay results (
r
2
= 0.92;
P
< 0.001). The overall mean difference in the HIV-1 RNA values obtained by Xpert HIV-1 VL assay and Abbott assay was 0.34 log
10
copies/ml (95% confidence interval [CI], 0.26 to 0.40 log
10
copies/ml) (
P
< 0.001). Using a clinically relevant level of 1,000 copies/ml as a threshold, agreement was 90.6% (95% CI, 87.9 to 93.1%), with a sensitivity of 98.6% (95% CI, 97.2 to 100%). The two methods agreed on their detectability of HIV-1 RNA (>40 copies/ml) at 97.1% (95% CI, 95.5 to 98.7%), with a sensitivity of 99.6% (95% CI, 97.2 to 100%). The POC Cepheid Xpert HIV-1 VL assay showed high agreement and accuracy with a laboratory-based method of HIV-1 RNA testing. The POC Xpert HIV-1 VL assay tended to overestimate HIV-1 VL, although the difference was below a clinically relevant threshold of 0.5 log
10
copies/ml. The POC Cepheid Xpert HIV-1 VL assay is a promising tool for monitoring patients on ART in southern Africa.
A Rapid Immunoassay for Detection of Shiga Toxin-Producing Escherichia coli Directly from Human Fecal Samples and Its Performance in Detection of Toxin Subtypes
Authors: Boone Jeremy T. , Campbell Davina E. , Dandro Amy S. , Chen Li , Herbein Joel F. 
Published: October 2016

ABSTRACT

Fecal samples (
n
= 531) submitted to a regional clinical laboratory during a 6-month period were tested for the presence of Shiga toxin using both a Vero cell cytotoxicity assay and the Shiga Toxin Quik Chek test (STQC), a rapid membrane immunoassay. Testing the samples directly (without culture), 9 positives were identified by the Vero cell assay, all of which were also detected by the STQC. The correlation between the two assays was 100%. Not all of the identified positive samples were detected when fecal broth cultures were tested. By testing broth cultures of characterized isolates representing all described Shiga toxin subtypes, the STQC detected all subtypes. Levels of induction of toxin production by ciprofloxacin differed among the strains tested, with more toxin induction seen in strains harboring Stx2 phages than in those harboring Stx1 phages.
Clinical Isolates of Human Coronavirus 229E Bypass the Endosome for Cell Entry
Authors: Shirato Kazuya , Kanou Kazuhiko , Kawase Miyuki , Matsuyama Shutoku 
Published: October 2016

ABSTRACTHuman coronavirus 229E (HCoV-229E), a causative agent of the common cold, enters host cells via two distinct pathways: one is mediated by cell surface proteases, particularly transmembrane protease serine 2 (TMPRSS2), and the other by endosomal cathepsin L. Thus, specific inhibitors of these proteases block virus infection. However, it is unclear which of these pathways is actually utilized by HCoV-229E in the human respiratory tract. Here, we examined the mechanism of cell entry used by a pseudotyped virus bearing the HCoV-229E spike (S) protein in the presence or absence of protease inhibitors. We found that, compared with a laboratory strain isolated in 1966 and passaged for a half century, clinical isolates of HCoV-229E were less likely to utilize cathepsin L; rather, they showed a preference for TMPRSS2. Two amino acid substitutions (R642M and N714K) in the S protein of HCoV-229E clinical isolates altered their sensitivity to a cathepsin L inhibitor, suggesting that these amino acids were responsible for cathepsin L use. After 20 passages in HeLa cells, the ability of the isolate to use cathepsin increased so that it was equal to that of the laboratory strain; this increase was caused by an amino acid substitution (I577S) in the S protein. The passaged virus showed a reduced ability to replicate in differentiated airway epithelial cells cultured at an air-liquid interface. These results suggest that the endosomal pathway is disadvantageous for HCoV-229E infection of human airway epithelial cells; therefore, clinical isolates are less able to use cathepsin.IMPORTANCEMany enveloped viruses enter cells through endocytosis. Viral spike proteins drive the fusion of viral and endosomal membranes to facilitate insertion of the viral genome into the cytoplasm. Human coronavirus 229E (HCoV-229E) utilizes endosomal cathepsin L to activate the spike protein after receptor binding. Here, we found that clinical isolates of HCoV-229E preferentially utilize the cell surface protease TMPRSS2 rather than endosomal cathepsin L. The endosome is a main site of Toll-like receptor recognition, which then triggers an innate immune response; therefore, HCoV-229E presumably evolved to bypass the endosome by entering the cell via TMPRSS2. Thus, the virus uses a simple mechanism to evade the host innate immune system. Therefore, therapeutic agents for coronavirus-mediated diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), should target cell surface TMPRSS2 rather than endosomal cathepsin.
Connecting the backwater hydraulics of coastal rivers to fluvio-deltaic sedimentology and stratigraphy
Authors: Fernandes Anjali M. , Törnqvist Torbjörn E. , Straub Kyle M. , Mohrig David 
Published: October 2016

Abstract
Fluvial channels encounter a backwater reach when they approach a standing body of water, and recent studies have shown that the transition from normal flow to backwater-influenced flow is associated with sediment mass extraction through deposition. Here we test the hypothesis that systematic changes in the geometry of channel-belt deposits and sedimentary architecture occur across this transition, using data from the late Holocene Mississippi (southern USA) and Rhine (The Netherlands) fluvio-deltaic systems. We use the estimated backwater length and average channel width as characteristic length scales to non-dimensionalize the downstream trends in channel-belt width for these systems. The collapsed data follow similar trends, suggesting that the observed variations in channel-belt geometry and fluvio-deltaic stratigraphy are tied to the location of the backwater transition zone. These findings suggest a unifying hydraulic control on fluvio-deltaic channel belts and provide a new framework for predicting and understanding the properties of ancient rivers in the coastal zone.
Investigation of surfactant protein-D and interleukin-6 levels in patients with blunt chest trauma with multiple rib fractures and pulmonary contusions: a cross-sectional study in Black Sea Region of Turkey
Authors: Kurt Aysel , Turut Hasan , Acipayam Ahmet , Kirbas Aynur , Yuce Suleyman , Cumhur Cure Medine , Cure Erkan 
Published: October 2016

ObjectiveMultiple rib fractures (RFs) and pulmonary contusions (PCs), with resulting systemic lung inflammation, are the most common injuries caused by blunt chest trauma (BCT) in motor vehicle accidents. This study examined levels of the inflammation marker interleukin (IL)-6 and those of the acute-phase reactant surfactant protein (SP)-D in patients with BCT.DesignProspective, cross-sectional, observational study.SettingSingle-centre, tertiary care hospital in the Black Sea Region of Turkey.ParticipantsThe study included 60 patients with BCT who were hospitalised in our thoracic surgery department.Parameters measuresThe SP-D and IL-6 serum levels of patients with RFs (two or more RFs) (n=30) and patients with PCs (n=30) were measured after 6 hours, 24 hours and 7 days, and compared with those of age-matched and gender-matched healthy participants.ResultsThe 6-hour serum SP-D levels of the RFs (p=0.017) and PCs (p<0.001) groups were significantly higher than those of the healthy controls. The 24-hour and 7-day SP-D levels of both groups were also higher than the control group. The serum IL-6 levels of both groups were significantly higher than those of the control group. We have found Injury Severity Score to be independently related to 6-hour IL-6 (β=1.414, p<0.001) and 24-hour IL-6 levels (β=1.067, p<0.001). The development of complications was independently related to 6-hour SP-D level (β=0.211, p=0.047).ConclusionsRFs and PCs after BCT lead to local and systemic inflammation due to lung injury. The levels of the systemic inflammation marker IL-6 and those of the acute-phase reactant SP-D were elevated in the present study. The SP-D level may be used as a marker in the follow-up of BCT-related complications.
Effectiveness of screening colonoscopy in reducing the risk of death from right and left colon cancer: a large community-based study
Authors: Doubeni Chyke A , Corley Douglas A , Quinn Virginia P , Jensen Christopher D , Zauber Ann G , Goodman Michael , Johnson Jill R , Mehta Shivan J , Becerra Tracy A , Zhao Wei K , Schottinger Joanne , Doria-Rose V Paul , Levin Theodore R , Weiss Noel S , Fletcher Robert H 
Published: October 2016

ObjectiveScreening colonoscopy's effectiveness in reducing colorectal cancer mortality risk in community populations is unclear, particularly for right-colon cancers, leading to recommendations against its use for screening in some countries. This study aimed to determine whether, among average-risk people, receipt of screening colonoscopy reduces the risk of dying from both right-colon and left-colon/rectal cancers.DesignWe conducted a nested case–control study with incidence-density matching in screening-eligible Kaiser Permanente members. Patients who were 55–90 years old on their colorectal cancer death date during 2006–2012 were matched on diagnosis (reference) date to controls on age, sex, health plan enrolment duration and geographical region. We excluded patients at increased colorectal cancer risk, or with prior colorectal cancer diagnosis or colectomy. The association between screening colonoscopy receipt in the 10-year period before the reference date and colorectal cancer death risk was evaluated while accounting for other screening exposures.ResultsWe analysed 1747 patients who died from colorectal cancer and 3460 colorectal cancer-free controls. Compared with no endoscopic screening, receipt of a screening colonoscopy was associated with a 67% reduction in the risk of death from any colorectal cancer (adjusted OR (aOR)=0.33, 95% CI 0.21 to 0.52). By cancer location, screening colonoscopy was associated with a 65% reduction in risk of death for right-colon cancers (aOR=0.35, CI 0.18 to 0.65) and a 75% reduction for left-colon/rectal cancers (aOR=0.25, CI 0.12 to 0.53).ConclusionsScreening colonoscopy was associated with a substantial and comparably decreased mortality risk for both right-sided and left-sided cancers within a large community-based population.
Single-center experience in the endovascular treatment of wide-necked intracranial aneurysms with a bridging intra-/extra-aneurysm implant (pCONus)
Authors: Fischer S , Weber A , Titschert A , Brenke C , Kowoll A , Weber W 
Published: October 2016

PurposeTo retrospectively evaluate the safety and efficacy of the endovascular treatment of wide-necked intracranial aneurysms assisted by a novel intra-/extra-aneurysm stent-like implant (pCONus).MethodsInitial and follow-up angiographic and clinical results are presented of 25 patients with 25 unruptured and ruptured wide-necked intracranial aneurysms treated by reconstruction of the aneurysm neck using the pCONus implant followed by coil occlusion of the fundus.ResultsSuccessful intra-/extra-aneurysm deployment of the pCONus with coil occlusion of the fundus was achieved in all but one case. Procedure-related ischemic complications were observed in three cases with permanent deterioration in one. Acceptable aneurysm occlusion was achieved in all cases. Follow-up angiography revealed sufficient occlusion in 81.0% of the aneurysms. Intimal hyperplasia in the stented segment of the parent artery or device migration has not been observed to date.ConclusionsThe pCONus device offers a promising treatment option for complex wide-necked bifurcation intracranial aneurysms. Acute or delayed dislocations of coils into the parent artery are successfully avoided.
Lag screw and tension band wire arthrodesis of the scapulohumeral joint in a miniature bull calf
Authors: Cypher Elizabeth , van Amstel Sarel , Lyons Rachel , Anderson David E 
Published: October 2016

An eight‐month‐old miniature zebu bull calf, 50 kg, was presented for evaluation of a moderate (grade 4 out of 5) right forelimb lameness of eight weeks’ duration. Clinical and radiographic findings revealed a marked degenerative osteoarthritis of the right scapulohumeral joint. Arthrodesis of the right scapulohumeral joint via placement of two transarticular cancellous bone screws in lag fashion and a dorsolateral figure‐of‐eight tension band wire was performed. Final angle of arthrodesis was 122°. Short‐term morbidity was minimal. The patient remained comfortable on the limb throughout the eight‐day hospitalisation. By discharge, the lameness had improved (grade 3 out of 5). Long‐term follow‐up at six months was considered good for breeding soundness, though a gait deficit was present in the affected limb. Lag screw and tension band wire arthrodesis of the scapulohumeral joint should be considered a viable less invasive option in small ruminants with terminal scapulohumeral joint disease.
Automatic generation of efficient accelerators for reconfigurable hardware
Authors: Koeplinger David , Delimitrou Christina , Prabhakar Raghu , Kozyrakis Christos , Zhang Yaqi , Olukotun Kunle 
Published: October 2016

Acceleration in the form of customized datapaths offer large performance and energy improvements over general purpose processors. Reconfigurable fabrics such as FPGAs are gaining popularity for use in implementing application-specific accelerators, thereby increasing the importance of having good high-level FPGA design tools. However, current tools for targeting FPGAs offer inadequate support for high-level programming, resource estimation, and rapid and automatic design space exploration.
We describe a design framework that addresses these challenges. We introduce a new representation of hardware using parameterized templates that captures locality and parallelism information at multiple levels of nesting. This representation is designed to be automatically generated from high-level languages based on parallel patterns. We describe a hybrid area estimation technique which uses template-level models and design-level artificial neural networks to account for effects from hardware place-and-route tools, including routing overheads, register and block RAM duplication, and LUT packing. Our runtime estimation accounts for off-chip memory accesses. We use our estimation capabilities to rapidly explore a large space of designs across tile sizes, parallelization factors, and optional coarse-grained pipelining, all at multiple loop levels. We show that estimates average 4.8% error for logic resources, 6.1% error for runtimes, and are 279 to 6533 times faster than a commercial high-level synthesis tool. We compare the best-performing designs to optimized CPU code running on a server-grade 6 core processor and show speedups of up to 16.7×.
APRES
Authors: Oh Yunho , Kim Keunsoo , Yoon Myung Kuk , Park Jong Hyun , Park Yongjun , Ro Won Woo , Annavaram Murali 
Published: October 2016

Long memory latency and limited throughput become performance bottlenecks of GPGPU applications. The latency takes hundreds of cycles which is difficult to be hidden by simply interleaving tens of warp execution. While cache hierarchy helps to reduce memory system pressure, massive Thread-Level Parallelism (TLP) often causes excessive cache contention. This paper proposes Adaptive PREfetching and Scheduling (APRES) to improve GPU cache efficiency. APRES relies on the following observations. First, certain static load instructions tend to generate memory addresses having very high locality. Second, although loads have no locality, the access addresses still can show highly strided access pattern. Third, the locality behavior tends to be consistent regardless of warp ID.
APRES schedules warps so that as many cache hits generated as possible before any cache misses generated. This is to minimize cache thrashing when many warps are contending for a cache line. However, to realize this operation, it is required to predict which warp will hit the cache in the near future. Without directly predicting future cache hit/miss for each warp, APRES creates a group of warps that will execute the same load instruction in the near future. Based on the third observation, we expect the locality behavior is consistent over all warps in the group. If the first executed warp in the group hits the cache, then the load is considered as a high locality type, and APRES prioritizes all warps in the group. Group prioritization leads to consecutive cache hits, because the grouped warps are likely to access the same cache line. If the first warp missed the cache, then the load is considered as a strided type, and APRES generates prefetch requests for the other warps in the group. After that, APRES prioritizes prefetch targeted warps so that the demand requests are merged to Miss Status Holding Register (MSHR) or prefetched lines can be accessed. On memory-intensive applications, APRES achieves 31.7% performance improvement compared to the baseline GPU and 7.2% additional speedup compared to the best combination of existing warp scheduling and prefetching methods.
Temporal coordination of olfactory cortex sharp-wave activity with up- and downstates in the orbitofrontal cortex during slow-wave sleep
Authors: Onisawa Naomi , Manabe Hiroyuki , Mori Kensaku 
Published: October 2016

During slow-wave sleep, interareal communications via coordinated, slow oscillatory activities occur in the large-scale networks of the mammalian neocortex. Because olfactory cortex (OC) areas, which belong to paleocortex, show characteristic sharp-wave (SPW) activity during slow-wave sleep, we examined whether OC SPWs in freely behaving rats occur in temporal coordination with up- and downstates of the orbitofrontal cortex (OFC) slow oscillation. Simultaneous recordings of local field potentials and spike activities in the OC and OFC showed that during the downstate in the OFC, the OC also exhibited downstate with greatly reduced neuronal activity and suppression of SPW generation. OC SPWs occurred during two distinct phases of the upstate of the OFC: early-phase SPWs occurred at the start of upstate shortly after the down-to-up transition in the OFC, whereas late-phase SPWs were generated at the end of upstate shortly before the up-to-down transition. Such temporal coordination between neocortical up- and downstates and olfactory system SPWs was observed between the prefrontal cortex areas (OFC and medial prefrontal cortex) and the OC areas (anterior piriform cortex and posterior piriform cortex). These results suggest that during slow-wave sleep, OC and OFC areas communicate preferentially in specific time windows shortly after the down-to-up transition and shortly before the up-to-down transition. NEW & NOTEWORTHY Simultaneous recordings of local field potentials and spike activities in the anterior piriform cortex (APC) and orbitofrontal cortex (OFC) during slow-wave sleep showed that APC sharp waves tended to occur during two distinct phases of OFC upstate: early phase, shortly after the down-to-up transition, and late phase, shortly before the up-to-down transition, suggesting that during slow-wave sleep, olfactory cortex and OFC areas communicate preferentially in the specific time windows.
Changes in activity of fast-spiking interneurons of the monkey striatum during reaching at a visual target
Authors: Marche Kévin , Apicella Paul 
Published: October 2016

Recent works highlight the importance of local inhibitory interneurons in regulating the function of the striatum. In particular, fast-spiking interneurons (FSIs), which likely correspond to a subgroup of GABAergic interneurons, have been involved in the control of movement by exerting strong inhibition on striatal output pathways. However, little is known about the exact contribution of these presumed interneurons in movement preparation, initiation, and execution. We recorded the activity of FSIs in the striatum of monkeys as they performed reaching movements to a visual target under two task conditions: one in which the movement target was presented at unsignaled left or right locations, and another in which advance information about target location was available, thus allowing monkeys to react faster. Modulations of FSI activity around the initiation of movement (53% of 55 neurons) consisted mostly of increases reaching maximal firing immediately before or, less frequently, after movement onset. Another subset of FSIs showed decreases in activity during movement execution. Rarely did movement-related changes in FSI firing depend on response direction and movement speed. Modulations of FSI activity occurring relatively early in relation to movement initiation were more influenced by the preparation for movement, compared with those occurring later. Conversely, FSI activity remained unaffected, as monkeys were preparing a movement toward a specific location and instead moved to the opposite direction when the trigger occurred. These results provide evidence that changes in activity of presumed GABAergic interneurons of the primate striatum could make distinct contributions to processes involved in movement generation. NEW & NOTEWORTHY We explored the functional contributions of striatal fast-spiking interneurons (FSIs), presumed GABAergic interneurons, to distinct steps of movement generation in monkeys performing a reaching task. The activity of individual FSIs was modulated before and during the movement, consisting mostly of increased in firing rates. Changes in activity also occurred during movement preparation. We interpret this variety of modulation types at different moments of task performance as reflecting differential FSI control over distinct phases of movement.