bluuebunny/crossref_metadata_2025_split huggingface dataset:
An MLST approach to support tracking of plasmids carrying OXA-48-like carbapenemase
Authors: Brehony Carina , McGrath Elaine , Brennan Wendy , Tuohy Alma , Whyte Thomas , Brisse Sylvain , Maiden Martin , Jolley Keith , Morris Dearbháile , Cormican Martin 
Published: March 2019

AbstractObjectivesThe prevalence of infections caused by OXA-48-like carbapenemase-producing organisms in Ireland has increased dramatically since 2011 and is an urgent public health issue. Genome-based high-resolution genotyping was used to analyse clinical isolates submitted to the Irish Carbapenemase-Producing Enterobacteriaceae Reference Laboratory Service for a 13 month period (2016–17).MethodsA total of 109 OXA-48-producing non-duplicate clinical isolates from 16 submitting centres were sequenced. Using a gene-by-gene approach, isolate genomes were characterized by MLST and core genome MLST, and the presence of antimicrobial resistance determinants was determined. Reference mapping and a novel plasmid MLST-type approach was applied to determine plasmid background.ResultsThe OXA-48-like-producing isolates were Escherichia coli (n = 56), Klebsiella spp. (n = 46) and Enterobacter cloacae (n = 7). Amongst the E. coli isolates there were 37 different STs and amongst the Klebsiella spp. isolates there were 27 different STs. blaOXA-48 was present in 105/109 (96.3%) of isolates. Based on mapping analysis and detection of the pOXA-48 IncL-type plasmid replicon and backbone genes, a pOXA-48-like plasmid was identified in 93/109 isolates (85.3%). The remaining isolates (n = 16; 14.7%) harboured blaOXA-48-like genes in unknown environments. Using a gene-by-gene approach two pOXA-48-like plasmid groups with 2/71 pOXA-48-like locus differences between them were identified.ConclusionsIn Ireland we found a diversity of genotypes associated with OXA-48-like-producing clinical isolates with the IncL pOXA-48 plasmid type predominating as the blaOXA-48 genetic environment. A plasmid MLST approach can rapidly identify plasmids associated with outbreaks and monitor spread of types temporally and geographically.
Analytical treatment interruption in chronic HIV-1 infection: time and magnitude of viral rebound in adults with 10 years of undetectable viral load and low HIV-DNA (APACHE study)
Authors: Castagna Antonella , Muccini Camilla , Galli Laura , Bigoloni Alba , Poli Andrea , Spagnuolo Vincenzo , Nozza Silvia , Racca Sara , Galli Andrea , Cinque Paola , Carini Elisabetta , Lazzarin Adriano 
Published: March 2019

AbstractObjectivesDespite the fact that there are individuals who have chronic HIV infection, few studies have investigated ART interruption in this setting. The aim of this study was to evaluate the ability to spontaneously control viral replication during analytical treatment interruption (ATI) in adults with chronic HIV-1 infection, on ART, with suppressed viraemia for >10 years and with a low reservoir.Patients and methodsThis was a prospective, open-label, single-arm, non-randomized, proof-of-concept study (NCT03198325) of subjects with chronic HIV-1 infection, HIV-RNA <50 copies/mL for ≥10 years, without residual viraemia for ≥5 years, CD4+ >500 cells/mm3, HIV-DNA <100 copies/106 PBMCs and without comorbidities or AIDS-defining diseases. Enrolled patients were strictly monitored. The ART regimen in use at ATI was resumed in the case of confirmed viral rebound (CVR, two consecutive HIV-RNA >50 copies/mL). Results are reported as median (IQR).ResultsNine patients underwent ATI. All participants experienced CVR [4.84 (IQR: 3.47–6.47) HIV-RNA log10 copies/mL] after ATI at a median time of 21 days (range 14–56) and restarted ART. After ART resumption, all the subjects achieved HIV-RNA <50 copies/mL in a median of 88 days (range 15–197). No serious adverse event occurred; one subject experienced acute retroviral syndrome. No significant correlation between baseline factors and time to viral rebound was observed, while the magnitude of viral rebound was significantly associated with pre-ART HIV-1 RNA (Spearman r = 0.786, P = 0.036), nadir CD4+ (Spearman r = −0.800, P = 0.010), baseline CD4+ (Spearman r = −0.667, P = 0.049) and years with undetectable viral load (Spearman r = −0.717, P = 0.030).ConclusionsDespite a long period of HIV viral load suppression and a low viral reservoir, early and consistent viral rebound was observed during ATI in all subjects.
Researching Human Rights Professionals: Tracing the Networks of Human Rights Practice
Authors: Bruch Elizabeth M 
Published: March 2019

AbstractHuman rights professionals are significant actors in international institutions, humanitarian interventions, and other dimensions of global governance. Despite their significance, they remain part of an under-researched global elite of international expert practitioners. This article explores the challenges of conducting transnational research involving human rights professionals in exploring the networks of institutions, actors and relationships in human rights fieldwork. It raises practical and methodological issues related to research relationships, access to participants and information, and the larger contexts of geopolitical and structural power. Using insights from human rights professionals themselves, it illuminates questions of expertise, identity and location, as well as the mediating roles of texts and technology in the research and in the network of practice.
Characterization of Corn Root Factors to Improve Artificial Diet for Western Corn Rootworm (Coleoptera: Chrysomelidae) Larvae
Authors: Huynh Man P , Bernklau Elisa J , Coudron Thomas A , Shelby Kent S , Bjostad Louis B , Hibbard Bruce E 
Published: March 2019

Abstract
The western corn rootworm, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), is an important economic pest of maize (Zea mays L.) in North America and Europe. Previous efforts to formulate an artificial diet for western corn rootworm larvae highlighted an important role of corn root powder, which had a significant positive impact on several larval developmental traits. Unfortunately, this ingredient is not available for purchase. Toward the goal of developing an artificial diet for western corn rootworm larvae with all ingredients readily accessible, we conducted research to isolate essential growth factors for larval development from corn root powder to improve the performance of diet without corn root powder. For all experiments, multiple life history parameters (survival, weight, and molting) were recorded from 15-d diet bioassays. Corn roots may contain factors that assist in larval growth, but some of these factors were not fully extracted by methanol and remained in the extracted root. Methanolic extracts significantly increased molting to second instar, but did not significantly increase survival, dry weight, or molting to third instar, suggesting the primary corn root substituents affecting these factors cannot be extracted or other extraction methods may be required to extract the essential factors from corn roots. We showed that whole corn root powder was best when used in combination with all the other nutrient sources in the published western corn rootworm formulation. Corn root powder made from proprietary seed and Viking seed has similar value.
Measuring mobility, disease connectivity and individual risk: a review of using mobile phone data and mHealth for travel medicine
Authors: Lai Shengjie , Farnham Andrea , Ruktanonchai Nick W , Tatem Andrew J 
Published: March 2019

Abstract

Rationale for review
The increasing mobility of populations allows pathogens to move rapidly and far, making endemic or epidemic regions more connected to the rest of the world than at any time in history. However, the ability to measure and monitor human mobility, health risk and their changing patterns across spatial and temporal scales using traditional data sources has been limited. To facilitate a better understanding of the use of emerging mobile phone technology and data in travel medicine, we reviewed relevant work aiming at measuring human mobility, disease connectivity and health risk in travellers using mobile geopositioning data.

Key findings
Despite some inherent biases of mobile phone data, analysing anonymized positions from mobile users could precisely quantify the dynamical processes associated with contemporary human movements and connectivity of infectious diseases at multiple temporal and spatial scales. Moreover, recent progress in mobile health (mHealth) technology and applications, integrating with mobile positioning data, shows great potential for innovation in travel medicine to monitor and assess real-time health risk for individuals during travel.

Conclusions
Mobile phones and mHealth have become a novel and tremendously powerful source of information on measuring human movements and origin–destination-specific risks of infectious and non-infectious health issues. The high penetration rate of mobile phones across the globe provides an unprecedented opportunity to quantify human mobility and accurately estimate the health risks in travellers. Continued efforts are needed to establish the most promising uses of these data and technologies for travel health.
Estimates for the impact of ultraviolet background fluctuations on galaxy clustering measurements
Authors: Upton Sanderbeck Phoebe , Iršič Vid , McQuinn Matthew , Meiksin Avery 
Published: March 2019

ABSTRACT
Spatial fluctuations in ultraviolet backgrounds can subtly modulate the distribution of extragalactic sources, a potential signal and systematic for large-scale structure surveys. While this modulation has been shown to be significant for 3D Ly α forest surveys, its relevance for other large-scale structure probes has been hardly explored, despite being the only astrophysical process that likely can affect clustering measurements on the scales of ≳Mpc. We estimate that the background fluctuations, modulating the amount of H i, have a fractional effect of (0.03–0.3) × (k/[10−2 Mpc−1])−1 on the power spectrum of 21 cm intensity maps at z = 1–3. We find a smaller effect for H α and Ly α intensity mapping surveys of (0.001–0.1) × (k/[10−2 Mpc−1])−1 and even smaller effect for more traditional surveys that correlate the positions of individual H α or Ly α emitters. We also estimate the effect of backgrounds on low-redshift galaxy surveys in general based on a simple model in which background fluctuations modulate the rate halo gas cools, modulating star formation: We estimate a maximum fractional effect on the power of ∼0.01 (k/[10−2 Mpc−1])−1 at z = 1. We compare sizes of these imprints to cosmological parameter benchmarks for the next generation of redshift surveys: We find that ionizing backgrounds could result in a bias on the squeezed triangle non-Gaussianity parameter fNL that can be larger than unity for power spectrum measurements with a SPHEREx-like galaxy survey, and typical values of intensity bias. Marginalizing over a shape of the form k−1PL, where PL is the linear matter power spectrum, removes much of this bias at the cost of ${\approx } 40{{\ \rm per\ cent}}$ larger statistical errors.
ETHOS – an effective theory of structure formation: formation of the first haloes and their stars
Authors: Lovell Mark R , Zavala Jesús , Vogelsberger Mark 
Published: March 2019

Abstract
A cut-off in the linear matter power spectrum at dwarf galaxy scales has been shown to affect the abundance, formation mechanism and age of dwarf haloes, and their galaxies at high and low redshifts. We use hydrodynamical simulations of galaxy formation within the ETHOS framework in a benchmark model that has such a cut-off and that has been shown to be an alternative to the cold dark matter (CDM) model that alleviates its dwarf-scale challenges. We show how galaxies in this model form differently to CDM, on a halo-by-halo basis, at redshifts z ≥ 6. We show that when CDM haloes with masses around the ETHOS half-mode mass scale are resimulated with the ETHOS matter power spectrum, they form with 50 per cent less mass than their CDM counterparts due to their later formation times, yet they retain more of their gas reservoir due to the different behaviour of gas and dark matter during the monolithic collapse of the first haloes in models with a galactic-scale cut-off. As a result, galaxies in ETHOS haloes near the cut-off scale grow rapidly between z = 10 and 6 and by z = 6 end up having very similar stellar masses, higher gas fractions and higher star formation rates relative to their CDM counterparts. We highlight these differences by making predictions for how the number of galaxies with old stellar populations is suppressed in ETHOS for both z = 6 galaxies and for gas-poor Local Group fossil galaxies. Interestingly, we find an age gradient in ETHOS between galaxies that form in high- and low-density environments.
Synthesizing the Strength of the Evidence of Complementary and Integrative Health Therapies for Pain
Authors: Giannitrapani Karleen F , Holliday Jesse R , Miake-Lye Isomi M , Hempel Susanne , Taylor Stephanie L 
Published: March 2019

Abstract

Objective
Pain and opioid use are highly prevalent, leading for calls to include nonpharmacological options in pain management, including complementary and integrative health (CIH) therapies. More than 2,000 randomized controlled trials (RCTs) and many systematic reviews have been conducted on CIH therapies, making it difficult to easily understand what type of CIH therapy might be effective for what type of pain. Here we synthesize the strength of the evidence for four types of CIH therapies on pain: acupuncture, therapeutic massage, mindfulness techniques, and tai chi.

Design
We conducted searches of English-language systematic reviews and RCTs in 11 electronic databases and previously published reviews for each type of CIH. To synthesize that large body of literature, we then created an “evidence map,” or a visual display, of the literature size and broad estimates of effectiveness for pain.

Results
Many systematic reviews met our inclusion criteria: acupuncture (86), massage (38), mindfulness techniques (11), and tai chi (21). The evidence for acupuncture was strongest, and largest for headache and chronic pain. Mindfulness, massage, and tai chi have statistically significant positive effects on some types of pain. However, firm conclusions cannot be drawn for many types of pain due to methodological limitations or lack of RCTs.

Conclusions
There is sufficient strength of evidence for acupuncture for various types of pain. Individual studies indicate that tai chi, mindfulness, and massage may be promising for multiple types of chronic pain. Additional sufficiently powered RCTs are warranted to indicate tai chi, mindfulness, and massage for other types of pain.
Prevalence and lameness-associated risk factors in Alberta feedlot cattle
Authors: Davis-Unger Jessica , Schwartzkopf-Genswein Karen S G , Pajor Ed A , Hendrick Steve , Marti Sonia , Dorin Craig , Orsel Karin 
Published: March 2019

AbstractLameness in cattle is a health and welfare concern; however, limited information is available on risk factors and the relationship between lameness and common diseases like bovine respiratory disease (BRD). Therefore, the objectives of this study were to: 1) identify prevalence of lameness in feedlot cattle and related risk factors of cattle diagnosed as lame; and 2) determine associations between BRD occurrence and lameness. Feedlot cattle health records were available from 28 feedlots for 10 yr. The data set consisted of 663,838 cattle records, with 13.9% (92,156) diagnosed with a disease, including 32.3%, 46.0%, and 22.0% with lameness, BRD, and other diagnoses, respectively. Lameness was classified into four categories: foot rot (FR), joint infections (JI), lame with no visible swelling (LNVS), and injuries (INJ), with a prevalence of 74.5%, 16.1%, 6.1%, and 3.1%, respectively. Lameness was compared across cattle types (arrival date and weight) as well as age classification (calf vs. yearling), gender (steer vs. heifer), and season of placement in the feedlot (spring, summer, fall, and winter). Within the disease-diagnosed population, lameness represented 28.5% of treated fall-placed calves, 38.5% of winter-placed calves, and 40.8% of treated yearlings. Foot rot was the most common diagnosis with 74.5% of all lameness diagnoses, with winter- and fall-placed calves more likely to be diagnosed with FR compared to yearlings (OR: 1.19, 95% CI: 1.10–1.30 and OR: 1.46, 95% CI: 1.38–1.55, respectively). Joint infections were the second most common diagnosis (16.1%). Compared to yearlings, fall-placed calves had a higher odds (OR: 3.64, 95% CI: 3.12–4.24) for JI. Injuries and LNVS were the least common but again fall-placed calves had higher odds of this diagnosis compared to yearlings (OR: 2.26, 95% CI: 1.70–2.99 and OR: 9.10, 95% CI: 6.26–13.2, respectively). Gender was significantly different for JI as steers were less likely affected compared to heifers (OR: 0.687, 95% CI: 0.545–0.867), and more likely affected by LNVS (OR: 2.46, 95% CI: 1.57–3.84). Of all lameness-associated deaths, JI accounted for almost 50%. Finally, cattle diagnosed with BRD were subsequently more likely to be diagnosed with INJ, JI, or LNVS (P &lt; 0.001 for all comparisons). In conclusion, animal type and gender were associated with type of lameness diagnoses, allowing feedlots to allocate resources to groups at highest risk and focus on early intervention strategies.
A Percutaneous Threaded Wire as a Clamp Technique for Avoiding Wedge Deformity While Nailing Intertrochanteric Femur Fractures
Authors: Maupin Jeremiah J. , Steinmetz Raymond G. , Hickerson Lindsay E. 
Published: March 2019

Summary:
Hip fractures are common injuries managed by the orthopaedic surgeon, and within the umbrella of hip fractures, intertrochanteric femur fractures constitute a significant portion of these injuries. Recent trends have shown an increased usage of cephalomedullary nails for these injuries. A known potential complication of this technique is the generation of a wedge deformity creating a varus alignment, especially when the cranial portion of the intertrochanteric fracture exits at or near the starting point of the nail. Although the biomechanics of this phenomenon are well described, few reports have shown techniques to help avoid this phenomenon. Here, we present a novel technique we have found useful to help prevent the wedge deformity incorporating commonly available instruments.
Uncemented Reverse Total Shoulder Arthroplasty as Initial Treatment for Comminuted Proximal Humerus Fractures
Authors: Wright Jon O. , Ho Anthony , Kalma Jeremy , Koueiter Denise , Esterle Jason , Marcantonio David , Wiater J. Michael , Wiater Brett 
Published: March 2019

Objectives:
To determine whether uncemented implants would provide similar outcomes while avoiding the complications associated with cement in the treatment of elderly patients with proximal humerus fractures (PHFs) with primary reverse total shoulder arthroplasty (RTSA).

Design:
Case series.

Setting:
A single Level I trauma center.

Patients/Participants:
A prospectively obtained cohort of 30 patients who underwent uncemented RTSA as initial treatment for a comminuted PHF: 4 male, 26 female; average age 71 ± 11 years.

Intervention:
Uncemented RTSA.

Main Outcome Measures:
(1) Radiographic analysis, (2) postoperative clinical range of motion, and (3) functional outcome scores: the American Shoulder and Elbow Surgeons Shoulder score and the Simple Shoulder Test score.

Results:
Radiographic analysis showed 97% achieved stable humeral stem fixation and 70% had healing of the tuberosities in anatomical position. Average range of motion was 130 ± 31 degrees of forward flexion, 32 ± 18 degrees of external rotation, and internal rotation to the midlumbar spine. Average American Shoulder and Elbow Surgeons Shoulder score was 82.0 ± 13.5 (with an average pain rating of 0.8 ± 1.3), and average Simple Shoulder Test score was 69.4% ± 19.1%.

Conclusions:
Our data show that treatment of comminuted PHFs in elderly patients with uncemented RTSA can consistently produce good clinical outcomes with a low rate of complications and suggest that cement may not be necessary for RTSA in the trauma setting.

Level of Evidence:
Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Screening in adrenal tumors
Authors: Corssmit Eleonora P.M. , Dekkers Olaf M. 
Published: March 2019

Purpose of review
Adrenal tumors are mostly encountered as incidentalomas in patients undergoing imaging not performed for suspected adrenal disease; although the majority are benign and nonfunctioning, malignant tumors and functioning tumors need to be excluded. The purpose of this review is to highlight recent advances in the evaluation of adrenal tumors.

Recent findings
As a consequence of increased use of technologically improved imaging techniques, the detection of adrenal incidentalomas has continued to increase. The vast majority of adrenal tumors are adrenocortical adenomas. To discriminate malignant from benign tumors and to identify clinically relevant functioning tumors, necessitating therapeutic intervention, adrenal tumors are best evaluated with unenhanced computed tomography (CT) attenuation and 1 mg dexamethasone overnight suppression test. An unenhanced CT attenuation value of 10 Hounsfield units or less excludes adrenocortical carcinoma and pheochromocytoma. Testing for hyperaldosteronism should be performed in hypertensive and/or hypokalemic patients, sex hormones, and steroid precursors in patients with clinical features suggestive of adrenocortical carcinoma. In patients with active extraadrenal malignancy and a single adrenal lesion without suspicion for metastasis elsewhere, CT-guided biopsy can be considered to rule out metastatic disease.

Summary
All patients with an adrenal tumor and without a prior history of cancer should be initially evaluated by unenhanced CT attenuation and 1 mg overnight dexamethasone suppression test, and additional hormone testing when indicated.
Challenges of denosumab in giant cell tumor of bone, and other giant cell-rich tumors of bone
Authors: Lipplaa Astrid , Dijkstra Sander , Gelderblom Hans 
Published: March 2019

Purpose of review
Giant cell tumor of bone (GCTB) is an uncommon benign primary bone tumor, consisting of receptor activator of nuclear factor kappa-B (RANK) expressing reactive osteoclast-like giant cells and neoplastic spindle-shaped cells. Denosumab was approved by FDA in 2013 and by EMA in 2014 to treat adults and skeletally mature adolescents with unresectable GCTB or when resection is likely to result in severe morbidity. However, there is much discussion regarding the optimal applied treatment strategy.

Recent findings
Neoadjuvant treatment of GCTB with denosumab can effectively downstage tumors to facilitate less morbid surgery or completely avoid the need for resection, but there is concern about local recurrence postsurgery. Definitive treatment of unresectable GTCB improves symptoms and halts tumor progression. The optimal treatment duration is unclear and long-term treatment is associated with adverse events like osteonecrosis of the jaw (ONJ) and atypical femoral fractures. Denosumab maintenance dose interval is currently being investigated.

Summary
For the related but heterogenous group of giant cell rich tumors of bone, like aneurysmal bone cysts (ABC) and central giant cell granuloma (CGCG), denosumab is a new treatment modality under investigation. Given the effectiveness in GCTB, this could be a promising treatment option for selected patients with advanced disease.