bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiology of Bloodstream Infections Caused by Escherichia coli and Klebsiella pneumoniae That Are Piperacillin-Tazobactam-Nonsusceptible but Ceftriaxone-Susceptible
Authors: Baker Thomas M , Rogers Wesley , Chavda Kalyan D , Westblade Lars F , Jenkins Stephen G , Nicolau David P , Kreiswirth Barry N , Calfee David P , Satlin Michael J 
Published: November 2018

AbstractBackgroundPiperacillin-tazobactam-nonsusceptible (TZP-NS) Enterobacteriaceae are typically also resistant to ceftriaxone. We recently encountered bacteremias due to Escherichia coli (Ec) and Klebsiella pneumoniae (Kp) that were TZP-NS but ceftriaxone-susceptible (CRO-S).MethodsWe reviewed all Ec and Kp bacteremias from 2011 to 2015 at our center and assessed the prevalence, antimicrobial susceptibilities, genetic profiles, patient characteristics, treatments, and outcomes of TZP-NS/CRO-S infections. We identified risk factors for TZP-NS/CRO-S infections compared with Ec and Kp bacteremias that were TZP-S and CRO-S (Control Group 1) and compared outcomes of patients with TZP-NS/CRO-S bacteremias, Control Group 1, and patients bacteremic with extended-spectrum β-lactamase (ESBL)–producing Ec and Kp.ResultsThere were 1857 Ec and Kp bacteremia episodes, of which 78 (4.2%) were TZP-NS/CRO-S (Ec: 50/1227 [4.1%]; Kp: 28/630 [4.4%]). All TZP-NS/CRO-S isolates were also ampicillin-sulbactam-NS. Of 32 TZP-NS/CRO-S isolates that were sequenced, 28 (88%) harbored blaTEM-1 or blaSHV-1, none had an ESBL or AmpC β-lactamase gene, and many sequence types were represented. Independent risk factors for TZP-NS/CRO-S bacteremia were exposure to β-lactam/β-lactamase inhibitors (BL/BLIs; adjusted odds ratio [aOR], 5.5; P &lt; .001) and cephalosporins (aOR, 3.0; P = .04). Thirty-day mortality after TZP-NS/CRO-S bacteremia was 25%, which was similar to control groups and was similar in patients treated empirically with BL/BLIs compared with those treated with cephalosporins or carbapenems. Targeted therapy with cephalosporins did not yield a higher 30-day mortality rate than carbapenem therapy.ConclusionsTZP-NS/CRO-S Ec and Kp are emerging causes of bacteremia, and further research is needed to better understand the epidemiology, resistance mechanisms, and clinical impact of these strains.
Seroprevalence of Hepatitis E Virus Infection Among People Living With HIV in the Central African Republic
Authors: Demi Sibiro Ornella Anne , Manirakiza Alexandre , Komas Narcisse Patrice 
Published: November 2018

Abstract

Background
Hepatitis E virus (HEV) is a waterborne virus that causes acute hepatitis in immunocompromised patients and those who are immunocompetent. Few cases of chronic HEV have been described in industrialized countries. The Central African Republic is 1 of the few countries in the world that is endemic for both HIV and HEV. The prevalence of HIV infection is estimated to be 4.9% among adults aged 15–49 years, and hepatitis E is epidemo-endemic. The aim of this study was to characterize the epidemiology of HEV infection in people living with HIV (PLHIV) in Bangui.

Methods
A cross-sectional study was conducted between April and September 2015 based on answers to a questionnaire, and blood samples were collected for determination of immunological markers by enzyme-linked immunosorbent assay and molecular tests.

Results
Of the 200 PLHIV included, 15 (7.5%) had the IgM that characterizes acute HEV infection; 8.9% were women, and 2.2% were men. The overall seroprevalence of IgG was 68% (48% women and 70.4% men), indicating that men are statistically significantly more exposed to HEV than women. HEV infection had no effect on transaminase or T-CD4+ lymphocyte cell levels. The origin of infection could not be identified.

Conclusions
The seroprevalence of HEV is very high among PLHIV and in the general population of Bangui. This must be taken into account in studies of the risk factors of PLHIV infected with HEV.
Identification of Somatotopic Organization and Optimal Stimulation Site Within the Subthalamic Nucleus for Parkinson's Disease
Authors: Sasaki Tatsuya , Kuwahara Ken , Kin Ittetsu , Okazaki Mihoko , Sasada Susumu , Shinko Aiko , Kameda Masahiro , Yasuhara Takao , Agari Takashi , Date Isao 
Published: November 2018

Abstract

BACKGROUND
Details of the somatotopy within the subthalamic nucleus (STN) are still poorly understood; however, the STN is a common target of deep brain stimulation (DBS) for Parkinson disease.

OBJECTIVE
To examine somatotopic organization within the STN and identify optimal stimulation sites from 77 surgical cases with microelectrode recording.

METHODS
STN-DBS was performed for 77 patients with Parkinson disease between 2010 and 2014. We performed passive movements of each joint and captured single neuronal activities to identify movement-related cells (MRCs). The sites of MRCs and active contacts were determined by measuring their distances from the first contact of DBS electrode. Their positional correlations were directly and indirectly analyzed.

RESULTS
The number of obtained MRCs was 264, of which 151 responded to multiple joints. The average x-, y-, and z-coordinates of the cells of the upper and lower limbs from the midcommisural point were 13.1 ± 1.1 and 12.7 ± 1.2, 0.22 ± 1.3 and −0.45 ± 1.5, and −2.5 ± 1.1 and −3.0 ± 1.4 mm, respectively. Most MRCs were distributed in the upper third of the STN, in its superior, lateral, and posterior regions, along the DBS electrode routes. Active contacts were observed to lie slightly inferior, medial, and posterior to the average MRC position.

CONCLUSION
Somatotopic organization of the STN was easier to observe in the present study than in previous studies. Optimal stimulation sites were located inferior, medial, and posterior to the average MRC location. The sites may correspond to associative or motor parts through which fibers from the supplementary motor area pass.
Opioid-Induced Reductions in Gait Variability in Healthy Volunteers and Individuals with Knee Osteoarthritis
Authors: Henriksen Marius , Alkjær Tine , Raffalt Peter C , Jørgensen Louse , Bartholdy Cecilie , Hansen Steen Honoré , Bliddal Henning 
Published: November 2018

Abstract
Objective. To investigate differences in gait variability induced by two different single-dose opioid formulations and an inert placebo in healthy volunteers and knee osteoarthritis patients. Design. Experimental, randomized, double-blinded, crossover study of inert placebo (calcium tablets), 50 mg of tapentadol, and 100 mg of tramadol. Setting. Laboratory setting. Subjects. Healthy volunteers and knee osteoarthritis patients. Methods. At three visits, separated by seven days, one tablet was administered per visit according to the randomization code. At each visit, a baseline measurement was done before tablet administration, after which hourly measurements were performed for six hours, yielding a total of seven measurements per visit. Gait variability was measured by three-dimensional gait analysis, recorded during six minutes of continuous treadmill walking at self-selected speed. One hundred seventy gait cycles were identified from detection of clear events of the knee joint angle trajectories. Gait variability was assessed as average standard deviations over a gait cycle of the sacrum displacements and accelerations; sagittal plane ankle, knee, and hip joint angles; step widths; and stride times. Results. Twenty-four opioid-naïve and neurologically intact participants (12 healthy volunteers and 12 knee osteoarthritis patients) were included and completed the experiment. Tapentadol reduced the variability of sacrum displacements and accelerations compared with placebo and tramadol. There were no differences between experimental conditions regarding the variability in lower-extremity joint angle variability, step widths, or stride times. Conclusions. In opioid-naïve and neurologically intact individuals, tapentadol seems to reduce movement variability during treadmill walking, compared with placebo and tramadol. This can be interpreted as a loss of adaptability that might increase the risk of falling if the system is perturbed.
Practice Variations in Exercise Training Programs in Dutch Cardiac Rehabilitation Centers: Prospective, Observational Study
Authors: Vromen Tom , Peek Niels , Abu-Hanna Ameen , Kemps Hareld M 
Published: November 2018

Abstract

Background
A recent survey among Dutch cardiac rehabilitation centers demonstrated considerable between-center variations in the contents of exercise training programs. For patients entering cardiac rehabilitation, current guidelines recommend tailored exercise training programs based on patient characteristics and rehabilitation goals.

Objective
This study was to analyze to what extent these patient characteristics are determinants of variations in training programs.

Design
This was a prospective, observational study with cross-sectional measurements among 10 cardiac rehabilitation centers.

Methods
The following data were obtained about patients entering cardiac rehabilitation: referral diagnosis, rehabilitation goals, and exercise training variables. Primary outcomes were variations in total aerobic training time, intensity, and volume before and after case-mix correction for population differences between centers. Secondary outcomes were variations in other training characteristics and the role of exercise testing in the determination of training intensity. Also, the roles of diagnosis and training goals in determining aerobic training time and intensity were studied.

Results
Data from 700 participants were analyzed. There were significant variations between centers in all aerobic and most resistance training characteristics. For aerobic training intensity, time, and volume, great variations remained after case-mix correction. An exercise test was performed for 656 participants (93.7%) but was used to determine training intensity in only 344 (52.4%) of these participants. In most centers, referral diagnosis and rehabilitation goals were unrelated to aerobic training time or intensity.

Limitations
Some form of selection bias cannot be excluded because the competing centers represented a minority of Dutch exercise-based cardiac rehabilitation centers.

Conclusions
This study showed that the contents of training programs varied considerably between cardiac rehabilitation centers, independent of population differences. Furthermore, aerobic training time and intensity were mostly unrelated to rehabilitation goals and referral diagnosis.
Distant Reading the Body, 1640–1699
Authors: Mann Rachel , Gavin Michael 
Published: November 2018

Abstract
This paper analyses seventeenth-century discourse of the human body over the Early English Books Online full-text corpus. Anatomy and medicine depict the body as a physiological object, knowable mainly through its parts and processes. Fiction and poetry tend to represent the body as a social entity, knowable primarily through intersubjective action and ethical ideals. In both contexts, bodies are perceived and described through close attention to their parts, but when bodies are conceived as such, they are described as abstract entities that organize the whole. This distinction is difficult to see at the level of close reading but unmistakable at larger scale. Deep conceptual structures at work underneath both anatomy and fiction, we argue, underlie a conception of the body that informs more particularized notions of mobility, sociality, and physicality.
The Effect of Foot Massage on Pain Intensity and Anxiety in Patients Having Undergone a Tibial Shaft Fracture Surgery: A Randomized Clinical Trial
Authors: Pasyar Nilofar , Rambod Masoume , Kahkhaee Fateme Rezaee 
Published: November 2018

Objective:
To determine the effect of massage therapy on pain intensity and anxiety in patients who have undergone tibial shaft fracture surgery.

Design:
This study was a randomized clinical trial with a pre–post design. As the study included 2 treatment groups, it was a parallel study.

Setting:
Khatam-Al-Anbia Hospital in Zahedan, Iran, between July and August 2017.

Patients:
In all, 66 patients who underwent a tibial shaft fracture surgery were enrolled and randomly assigned to intervention and control groups (33 patients each).

Intervention:
The intervention included a 10-minute foot massage (5 minutes per leg) using sweet almond oil, the most common lubricant used in massage therapy.

Main Outcome Measurements:
Data were collected using pain numeric rating scale and Spielberger State-Trait Anxiety Inventory before and after intervention.

Results:
After intervention, the mean scores for pain intensity, and anxiety in the intervention and control groups were 4.72 (0.97) and 5.72 (0.91), and 42.84 (6.50) and 58.36 (10.37), respectively. A significant difference was noted between the intervention and control groups concerning pain intensity and anxiety.

Conclusions:
The results indicated that massage therapy reduced pain intensity and anxiety in patients who underwent tibial shaft fracture surgery. Therefore, using massage as a noninvasive and acceptable intervention is suggested in orthopaedic surgery, especially after tibial shaft fracture surgeries.

Level of Evidence:
Therapeutic Level I. See Instructions for Authors for a complete description of levels of evidence.
Prevalence of Asymptomatic Intraductal Papillary Mucinous Neoplasms in Healthy and Ill Populations Detected by Ultrasonography
Authors: Ricci Claudio , Migliori Marina , Imbrogno Andrea , Mazzotta Elena , Felicani Cristina , Serra Carla , Bergonzoni Barbara , Calculli Lucia , Casadei Riccardo 
Published: November 2018

Objectives
The aim of this study was to establish the prevalence of intraductal papillary mucinous neoplasms (IPMNs) without and with high-risk stigmata (HRS)/worrisome features (WF) and the epidemiologic association between IPMNs and other diseases.

Methods
Ultrasound examinations of outpatients were evaluated. The IPMN was confirmed by magnetic resonance imaging. The prevalence of IPMNs and HRS/WF IPMNs was calculated. The association between IPMNs and other diseases was studied.

Results
The prevalence rate of IPMNs was 3.4%. A total of 1,531,264 IPMNs were expected in Italian population (2.5%), whereas 2257 per 100,000 citizens (2.3%) were expected in the European standard population (ESP2013). The prevalence rates of HRS/WF IPMNs were 0.5%, 0.7%, and 0.6%, in our, the Italian, and the ESP2013 populations, respectively. A total of 432,881 and 620 HRS/WF IPMNs per 100,000 residents were expected in the Italian and the ESP2013 populations, respectively. The IPMN prevalence increased over 50 years of age (odds ratio [OR], 3.2; P < 0.001) and over 70 years of age (OR, 1.9; P < 0.001). Female sex was related to the presence of IPMNs (OR, 1.9; P < 0.001).

Conclusions
Intraductal papillary mucinous neoplasms had a high prevalence in asymptomatic nonhospitalized populations. Age older than 50 years identified a possible risk category.
The use and misuse of herbarium specimens in evaluating plant extinction risks
Authors: Nic Lughadha Eimear , Walker Barnaby E. , Canteiro Cátia , Chadburn Helen , Davis Aaron P. , Hargreaves Serene , Lucas Eve J. , Schuiteman André , Williams Emma , Bachman Steven P. , Baines David , Barker Amy , Budden Andrew P. , Carretero Julia , Clarkson James J. , Roberts Alexandra , Rivers Malin C. 
Published: November 2018

Herbarium specimens provide verifiable and citable evidence of the occurrence of particular plants at particular points in space and time, and are vital resources for assessing extinction risk in the tropics, where plant diversity and threats to plants are greatest. We reviewed approaches to assessing extinction risk in response to the Convention on Biological Diversity's Global Strategy for Plant Conservation Target 2: an assessment of the conservation status of all known plant species by 2020. We tested five alternative approaches, using herbarium-derived data for trees, shrubs and herbs in five different plant groups from temperate and tropical regions. All species were previously fully assessed for the IUCN Red List. We found significant variation in the accuracy with which different approaches classified species as threatened or not threatened. Accuracy was highest for the machine learning model (90%) but the least data-intensive approach also performed well (82%). Despite concerns about spatial, temporal and taxonomic biases and uncertainties in herbarium data, when specimens represent the best available evidence for particular species, their use as a basis for extinction risk assessment is appropriate, necessary and urgent. Resourcing herbaria to maintain, increase and disseminate their specimen data is essential to guide and focus conservation action.
This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.
Results dissemination from clinical trials conducted at German university medical centres was delayed and incomplete
Authors: Wieschowski Susanne , Riedel Nico , Wollmann Katharina , Kahrass Hannes , Müller-Ohlraun Stephanie , Schürmann Christopher , Kelley Sean , Kszuk Ute , Siegerink Bob , Dirnagl Ulrich , Meerpohl Jörg , Strech Daniel 
Published: November 2018

AbstractObjectiveTimely and comprehensive reporting of clinical trial results build the backbone of evidence-based medicine and responsible research. The proportion of timely disseminated trial results can inform alternative national and international benchmarking of university medical centers (UMCs).Study Design and SettingFor all German UMCs we tracked all registered trials completed between 2009 and 2013. The results and an interactive website benchmark German UMCs regarding their performance in results dissemination.ResultsWe identified and tracked 2,132 clinical trials. For 1,509 trials, one of the German UMCs took the academic lead. Of these 1,509 “lead trials”, 39% published their results (mostly via journal publications) in a timely manner (<24 months after completion). More than six years after study completion, 26% of all eligible lead trials still had not disseminated results.ConclusionDespite substantial attention from many stakeholders to the topic, there is still a strong delay or even absence of results dissemination for many trials. German UMCs have several opportunities to improve this situation. Further research should evaluate whether and how a transparent benchmarking of UMC performance in results dissemination helps to increase value and reduce waste in medical research.
Bone marrow-on-a-chip: Emulating the human bone marrow
Authors: Sieber Stefan , Winter Annika , Wachsmuth Johanna , David Rhiannon , Stecklum Maria , Hellmeyer Lars , Ewart Lorna , Marx Uwe , Lauster Roland , Rosowski Mark 
Published: November 2018

AbstractMultipotent hematopoietic stem and progenitor cells HSPC reside in specialized stem cell niches within the bone marrow, that provide a suitable microenvironment for lifelong maintenance of the stem cells. Meaningful in vitro models recapitulating the in vivo stem cell niche biology can be employed for both basic research as well as for applied sciences and represent a powerful tool to reduce animal tests in preclinical studies. Recently we published the generation of an in vitro bone marrow niche model, capable of long-term cultivation of HSC based on an organ-on-a-chip platform. This study provides a detailed analysis of the 3D culture system including matrix environment analysis by SEM, transcriptome analysis and system intrinsic differentiation induction. Furthermore, the bone marrow on a chip model can serve to multiply and harvest HSPC, since repeated cell removal not compromised the functionality of the culture system. The prolongation of the culture time to 8 weeks demonstrate the capacity to apply the model in repeated drug testing experiments. The quality of the presented system is emphasized by the differentiation capacity of long-term cultivated HSPC in vitro and in vivo. Transplanted human HSPC migrated actively into the bone marrow of irradiated mice and contributed to the long-term reconstitution of the hematopoietic system after four and eight weeks of in vitro cultivation.The introduced system offers a multitude of possible applications to address a broad spectrum of questions regarding HSPC, the corresponding bone marrow niche biology, and pathological aberrations.
Proteostasis environment shapes higher-order epistasis operating on antibiotic resistance
Authors: Guerrero Rafael F. , Scarpino Samuel V. , Rodrigues João V. , Hartl Daniel L. , Ogbunugafor C. Brandon 
Published: November 2018

ABSTRACTRecent studies have shown that higher-order epistasis is ubiquitous and can have large effects on complex traits. Yet, we lack frameworks for understanding how epistatic interactions are influenced by basic aspects of cell physiology. In this study, we assess how protein quality control machinery—a critical component of cell physiology—affects epistasis for different traits related to bacterial resistance to antibiotics. Specifically, we attempt to disentangle the interactions between different protein quality control genetic backgrounds and two sets of mutations: (i) SNPs associated with resistance to antibiotics in an essential bacterial enzyme (dihydrofolate reductase, or DHFR) and (ii) differing DHFR bacterial species-specific amino acid background sequences (Escherichia coli, Listeria grayi, andChlamydia muridarum). In doing so, we add nuance to the generic observation that non-linear genetic interactions are widespread and capricious in nature, by proposing a mechanistically-grounded analysis of how proteostasis shapes epistasis. These findings simultaneously fortify and demystify the role of environmental context in modulating higher-order epistasis, with direct implications for evolutionary theory, genetic modification technology, and efforts to manage antimicrobial resistance.
DNA microscopy: Optics-free spatio-genetic imaging by a stand-alone chemical reaction
Authors: Weinstein Joshua A. , Regev Aviv , Zhang Feng 
Published: November 2018

AbstractAnalyzing the spatial organization of molecules in cells and tissues is a cornerstone of biological research and clinical practice. However, despite enormous progress in profiling the molecular constituents of cells, spatially mapping these constituents remains a disjointed and machinery-intensive process, relying on either light microscopy or direct physical registration and capture. Here, we demonstrate DNA microscopy, a new imaging modality for scalable, optics-free mapping of relative biomolecule positions. In DNA microscopy of transcripts, transcript molecules are tagged in situ with randomized nucleotides, labeling each molecule uniquely. A second in situ reaction then amplifies the tagged molecules, concatenates the resulting copies, and adds new randomized nucleotides to uniquely label each concatenation event. An algorithm decodes molecular proximities from these concatenated sequences, and infers physical images of the original transcripts at cellular resolution. Because its imaging power derives entirely from diffusive molecular dynamics, DNA microscopy constitutes a chemically encoded microscopy system.