bluuebunny/crossref_metadata_2025_split huggingface dataset:
Point-of-Care Ultrasound Predictors for the Diagnosis of Tuberculosis in HIV-Positive Patients Presenting to an Emergency Center
Authors: Van Hoving Daniël Jacobus , Kenge Andre P. , Maartens Gary , Meintjes Graeme 
Published: January 2020

Background:
The performance of point-of-care ultrasound (PoCUS) to diagnose HIV-associated tuberculosis has not been evaluated in large prospective studies. We determined the diagnostic accuracy of individual PoCUS features, performed an external validation of the focused assessment with sonography for HIV/TB (FASH) protocol, and determined independent PoCUS predictors of HIV-associated tuberculosis appropriate for use by emergency center practitioners.

Setting:
A cross-sectional diagnostic study was performed at the emergency center of Khayelitsha Hospital (Cape Town, South Africa).

Methods:
HIV-positive adults with the suspicion of having tuberculosis were prospectively enrolled. PoCUS was performed according to a standardized protocol. Reference standard was the detection of Mycobacterium tuberculosis using Xpert MTB/RIF or culture.

Results:
We enrolled 414 participants: 243 female, median age 36 years, median CD4 cell count 86/mm3, and 172 (42%) had tuberculosis. Sensitivity and specificity were ≥1 individual PoCUS feature [73% (95% CI: 65 to 79), 54% (95% CI: 47 to 60)], FASH protocol [71% (95% CI: 64 to 78), 57% (95% CI: 50 to 63)]. Independent PoCUS predictors identified were intra-abdominal lymphadenopathy of any size (aDOR 3.7 (95% CI: 2.0 to 6.7)], ascites [aDOR 3.0 (95% CI: 1.5 to 5.7)], and pericardial effusion of any size [aDOR 1.9 (95% CI: 1.2 to 3.0)]. The c-statistic for the derivation model was 0.680 (95% CI: 0.631 to 0.729), compared with 0.630 (95% CI: 0.576 to 0.684) of the FASH protocol. Two or more independent PoCUS predictors had 91% (95% CI: 86 to 94) specificity.

Conclusion:
The presence of 2 or more independent PoCUS predictors (intra-abdominal lymphadenopathy, ascites, and pericardial effusion) had moderate discrimination for HIV-associated tuberculosis in patients presenting to the emergency center.
Higher Acuity Resource Utilization With Older Age and Poorer HIV Control in Adolescents and Young Adults in the HIV Research Network
Authors: Neilan Anne M. , Lu Frances , Gebo Kelly A. , Diaz-Reyes Rebeca , Huang Mingshu , Parker Robert A. , Karalius Brad , Patel Kunjal , Voss Cindy , Ciaranello Andrea L. , Agwu Allison L. 
Published: January 2020

Background:
Adolescents and young adults (AYA) with HIV experience poorer health outcomes compared with adults. To improve care for AYA with HIV, information about patterns of costly health care resource utilization is needed.

Methods:
Among 13–30 year olds in the US HIV Research Network, we stratified outpatient visits, emergency department (ED) visits, and inpatient days/person-year (PY) by HIV acquisition model [perinatal (PHIVY) and nonperinatal (NPHIVY)], age (13–17, 18–23, and 24–30 years), CD4 strata (<200, 200–499, and ≥500 cells/µL), and viral load (VL) suppression (<, ≥400 copies/mL [c/mL]) combined with antiretroviral (ARV) use.

Results:
Among 4540 AYA (PHIVY: 15%; NPHIVY: 85%), mean follow-up was 2.8 years. Among PHIVY, most person-time (PT) was spent between ages 13 and 23 years (13–17 years: 43%; 18–23 years: 45%), CD4 ≥500/µL (61%), and VL <400 c/mL (69%). Among NPHIVY, most PT was spent between ages 24 and 30 years (56%), with CD4 ≥500/µL (54%), and with VL <400 c/mL (67%). PT spent while prescribed ARVs and with VL ≥400 c/mL was 29% (PHIVY) and 24% (NPHIVY). For PHIVY and NPHIVY, outpatient visit rates were higher at younger ages (13–17 years and 18–23 years), lower CD4 (<200 and 200–499/µL), and among those prescribed ARVs. Rates of ED visits and inpatient days were higher during PT spent at older ages (18–23 years and 24–30 years), lower CD4 (<200 and 200–499/µL), and VL ≥400 c/mL. Utilization was higher among PHIVY than NPHIVY (outpatient: 12.1 vs. 6.0/PY; ED: 0.4 vs. 0.3/PY; inpatient: 1.5 vs. 0.8/PY).

Conclusions:
More ED visits and inpatient days were observed during time spent at older ages, lower CD4 count, and VL ≥400 c/mL. Interventions to improve virologic suppression and immune response may improve outcomes, and thus decrease costly resource utilization, for AYA with HIV.
A Classifier to Predict Viral Control After Antiretroviral Treatment Interruption in Chronic HIV-1–Infected Patients
Authors: Fehér Csaba , Plana Montserrat , Crespo Guardo Alberto , Climent Nuria , Leal Lorna , Ugarte Ainoa , Fernández Irene , Etcheverry María F. , Gatell Josep M. , Sánchez-Palomino Sonsoles , García Felipe , Aloy Patrick 
Published: January 2020

Objectives:
To construct a classifier that predicts the probability of viral control after analytical treatment interruptions (ATI) in HIV research trials.

Methods:
Participants of a dendritic cell–based therapeutic vaccine trial (DCV2) constituted the derivation cohort. One of the primary endpoints of DCV2 was the drop of viral load (VL) set point after 12 weeks of ATI (delta VL12). We classified cases as “controllers” (delta VL12 > 1 log10 copies/mL, n = 12) or “noncontrollers” (delta VL12 < 0.5 log10 copies/mL, n = 10) and compared 190 variables (clinical data, lymphocyte subsets, inflammatory markers, viral reservoir, ELISPOT, and lymphoproliferative responses) between the 2 groups. Naive Bayes classifiers were built from combinations of significant variables. The best model was subsequently validated on an independent cohort.

Results:
Controllers had significantly higher pre–antiretroviral treatment VL [110,250 (IQR 71,968–275,750) vs. 28,600 (IQR 18737–39365) copies/mL, P = 0.003] and significantly lower proportion of some T-lymphocyte subsets than noncontrollers: prevaccination CD4+CD45RA+RO+ (1.72% vs. 7.47%, P = 0.036), CD8+CD45RA+RO+ (7.92% vs. 15.69%, P = 0.017), CD4+CCR5+ (4.25% vs. 7.40%, P = 0.011), and CD8+CCR5+ (14.53% vs. 27.30%, P = 0.043), and postvaccination CD4+CXCR4+ (12.44% vs. 22.80%, P = 0.021). The classifier based on pre–antiretroviral treatment VL and prevaccine CD8+CD45RA+RO+ T cells was the best predictive model (overall accuracy: 91%). In an independent validation cohort of 107 ATI episodes, the model correctly identified nonresponders (negative predictive value = 94%), while it failed to identify responders (positive predictive value = 20%).

Conclusions:
Our simple classifier could correctly classify those patients with low probability of control of VL after ATI. These data could be helpful for HIV research trial design.
Immediate Reconstruction After Colorectal Cancer Resection
Authors: Crystal Dustin T. , Zwierstra Myrthe J. , Blankensteijn Louise L. , Ibrahim Ahmed M. S. , Sieber Brady A. , Lee Bernard T. , Lin Samuel J. 
Published: January 2020

Background
Colorectal cancer is one of the most common and fatal malignancies in the United States. When localized to the distal gastrointestinal tract, surgical therapy includes abdominoperineal resection (APR) or pelvic exenteration (PEX). Subsequent ablative defects are considerable, impart concerning morbidity, and often necessitate autologous reconstruction. The aim of this study was to assess postoperative outcomes after reconstruction of APR and PEX defects.

Methods
The American College of Surgeons National Surgical Quality Improvement Program (2005–2017) was queried for patients undergoing APR for lower gastrointestinal malignancies with concurrent autologous reconstructions. Cases of disseminated cancer were excluded. Postoperative adverse event profiles, including rates of wound and systemic complications, were evaluated. Multivariate regression analysis controlling for age, sex, body mass index, and operative time was performed to calculate adjusted odds ratios (ORs).

Results
A total of 1309 patients were identified as undergoing APR/PEX with concomitant reconstruction. The majority (96.9%) of reconstructions consisted of muscle, myocutaneous, fasciocutaneous, or omental pedicled flaps. Of the cohort, 45.7% experienced at least 1 all-cause complication within 30-days of the procedure. Having a limited or moderate frailty (frailty index of “1” or “2”) was identified as a predictor of all-cause complications [OR, 1.556; 95% confidence interval (CI), 1.187–2.040, P = 0.001; and OR, 1.741; 95% CI, 1.193–2.541, P = 0.004, respectively], whereas smoking was a predictor of wound complications (OR, 1.462; 95% CI, 1.070–1.996, P = 0.017) and steroid use was a predictor of mild systemic complications (OR, 2.006; 95% CI, 1.058–3.805, P = 0.033).

Conclusion
Anorectal cancer resection often necessitates reconstruction secondary to postexenteration perineal defects. The incidence of postoperative complications is relatively high, and several risk factors are identified to help refine patient optimization.
A Comparison of Case Volume in Craniofacial Surgery by Plastic Surgery Residency Training Model
Authors: Silvestre Jason , Doss Linden R. , Hernandez Jade M. , Serletti Joseph M. , Chang Benjamin 
Published: January 2020

Background
Plastic surgeons in the United States are trained under 2 residency training models: integrated and independent. This study analyzes the variability of craniofacial surgery cases performed both between and within training models.

Methods
Case volume data from national data reports of 5 plastic surgery resident cohorts were analyzed (2011–2015). Craniofacial surgery case volumes across 4 major categories and 23 subcategories were compared between training models via t tests. Differences in intramodel variability were compared with F tests. Fold differences were calculated between mean case volumes and minimum requirements in craniofacial surgery.

Results
A total of 526 independent/combined (64%) and 292 integrated (36%) plastic surgery residents were included. Integrated residents reported more cases classified as congenital defect (118.8 ± 49.3 vs 110.3 ± 42.9, P = 0.013), neoplasm (202.0 ± 79.7 vs 163.2 ± 60.8, P < 0.001), and trauma (149.0 ± 61.8 vs 127.0 ± 52.0, P < 0.001), but not aesthetic (122.3 ± 68.6 vs 116.5 ± 50.5, P = 0.201). Integrated residents reported more case volume in 12 case subcategories, whereas independent/combined residents reported more cases in 3 case subcategories. Integrated residents had greater intramodel variability in 12 case subcategories, whereas independent/combined residents had greater intramodel variability in 2 case subcategories. Fold differences between mean case volumes and minimum requirements ranged from 1.8 times to 6.0 times.

Conclusions
Integrated residents tended to report significantly more craniofacial surgery cases and exhibit greater intrapathway variability. More research is needed to understand the impact of disparate case volume on core competency training in craniofacial surgery during plastic surgery residency.
Inferiorly Based Preauricular Flap for Anterior Ear Reconstruction
Authors: Sorkin Alex , Heller Lior , Landau Geva , Sherf Matan , Hartstein Morris E. , Hadad Eran 
Published: January 2020

Background
The anterior aspect of the auricle is a complex 3-dimensional structure. Each anatomical component in this region has an essential role in the aesthetic appearance of the ear and face. The reconstruction of defects in this region is challenging because of the lack of mobile, excess skin for primary closure, and the inability to skin graft overexposed cartilage.

Objective
The aim of the study was to present the planning and surgical technique of a simple, reproducible, 1-stage flap, for the reconstruction of the anterior aspect of the auricle.

Patients and Methods
A series of 11 patients, who underwent reconstruction of the anterior aspect of the auricle with 1-stage, inferiorly based, preauricular, cutaneous flap. All reconstructions were conducted under local anesthesia, and the defects were mainly due to tumor resections or skin necrosis after otoplasty. The average defect size was 1.5 cm. The flap was applied to different sites of the anterior auricle.

Results
All flaps survived except one, where there was partial flap loss. The aesthetic results were excellent, with no auricular deformity.

Conclusions
The inferiorly based, preauricular flap is a versatile flap for a safe, simple, and reproducible, 1-stage reconstruction for almost every region of anterior ear defect, with excellent aesthetic results.
Mass Spectrometric Characterization of Metabolites in Ear Cartilage
Authors: Yang Jinxiu , He Leren 
Published: January 2020

Objective
The aims of the study were to perform mass spectrometric characterization of metabolites in microtic and healthy ear auricular cartilage tissue, to screen the differential metabolites and pathways in these tissues, and to find a connection between the changes in the metabolic pathways and the biochemical properties of the cartilage tissue.

Methods
According to the inclusion criteria, patients with simple microtia admitted to the hospital between June 2017 and January 2018 were selected upon admission. During ear reconstruction surgery, residual auricle cartilage tissues of the patients were harvested as the case group (18 cases), and normal auricle cartilage tissues (18 cases) were taken as the control group. The mass spectrometry technique gas chromatography time-of-flight mass spectrometry and the XploreMET platform were used to identify and characterize the metabolites in the ear cartilage samples. Then, differential metabolites and key pathways were identified and analyzed.

Results
In total, 277 metabolites were detected, but only 132 metabolites were annotated in the JiaLib (one of the largest metabolomics libraries in the world). Of those, 14 differential metabolites and 3 metabolic pathways were identified between microtia and healthy ear cartilage, including the pathways of arginine metabolism, taurine metabolism, and pantothenate and CoA metabolism, P < 0.05.

Conclusions
Arginine, taurine, and l-cysteine may have an association with the development of microtia ear cartilage, and arginine succinate synthase and argininosuccinate lyase may be the key enzyme in microtia. This new direction on microtia can help us understand the pathogenesis of microtia and propose some new ideas for its etiology.
Dermal Autografts in Breast Reconstruction
Authors: Davis Claire , Boyd Carter , Mateo de Acosta Andino David A. , Kumbla Pallavi A. , Sanchez Ruston J. , Kurapati Srikanth , King Timothy W. , de la Torre Jorge I. 
Published: January 2020

Abstract
Breast cancer affects 1 in 8 women. As the treatment of breast cancer evolves, breast reconstruction does as well. Implant-based reconstructions are increasing, leading to increased use of acellular dermal matrix (ADM) for better implant positioning. Acellular dermal matrices are derived from cadaveric skin and are processed to be immunologically inert. However, ADM can be costly and can have complications such as seroma and infection. This has led to the development of dermal autografts. These were first used in postmastectomy breast reconstruction in women with redundant breast skin that was deepithelialized and used for lower pole coverage of tissue expanders and implants. This evolved into harvesting dermal autografts from the abdomen. Later studies evaluated the use of meshed dermal autografts. Histological analysis of ADM versus dermal autografts shows that there are increased vessels within dermal autografts compared with ADM. This potentially contributes to the decreased complication rate seen with autografts. In addition, one study showed equivalent results in aesthetic outcomes and capsular contracture between ADM and dermal autograft. Analysis of cost has shown that ADM is significantly more costly than harvesting a dermal autograft. Physician reimbursement is also higher for dermal autografts. This review article seeks to summarize key studies that highlight the feasibility of using dermal autografts in breast reconstruction.
Versatility of Pedicled Perforator-Based V-Y Advancement Flaps for Reconstruction of the Upper Limb
Authors: Kennedy Anne-Marie , Lloyd Mark Sheldon , Niranjan Niri S. 
Published: January 2020

Introduction
The aim of any reconstruction is to provide a robust and cosmetically pleasing result that does not significantly alter function. We describe our experience of using the V-Y principle in advancement flaps designed around a distinct perforator to reconstruct soft tissue defects of the upper limb. The shortcomings of fasciocutaneous and fascial flaps requiring skin grafting can be eliminated.

Methods
This was a 10-year retrospective review of patients who had V-Y flaps based on a distinct perforator for defects of the shoulder, axilla, arm, elbow, forearm, wrist, and hand. Defects of the digits and thumb were excluded.

Results
There were 59 flaps in 52 patients with an average age of 44 years (18–72 years). Skin malignancy was the most common primary etiology. The average defect size was 35 cm2 (9–80 cm2). There were no total flap failures; however, there were 4 partial losses, which healed by secondary intention. Seven flaps had to be explored for the hematoma evacuation.

Conclusions
The use of V-Y flaps based on distinct perforators in the upper limb retains limb aesthetics, allows early mobility and is a safe and reliable technique.
The Effects of Dextran on Postoperative Thrombosis and Hemodilution in Microvascular Head and Neck Reconstruction
Authors: Filipan Dorotea , Dediol Emil , Blivajs Igor , Milic Morena 
Published: January 2020

Background
Free tissue transfer is an integral part of reconstructive head and neck surgery today. Although increased experience and refinements in techniques have minimized flap loss, pharmacological agents have been used to prevent thrombus formation and flap failures, despite their questionable effectiveness. The aim of this study is to investigate the use of dextran 40 in thrombosis prophylaxis, as well as its effects on blood coagulability and flap survival.

Methods
This is a retrospective analysis of 176 free flaps performed at University Hospital Dubrava, Zagreb, Croatia, during a 4-year period. A comparison was made between 2 patient groups, based on their respective postoperative prophylaxis protocols. All patients were treated with low-molecular-weight heparin as deep vein thrombosis prevention, until patient mobilization. Group 1 was on dextran 40 protocol, whereas group 2 did not receive additional treatment. Primary outcome of the study was determined as flap loss rate, whereas secondary outcome was evaluated as the rate of thrombosis or hemorrhage. The hemodilution potential of dextran 40 was examined through blood count laboratory values.

Results
Total flap survival rate was 90.34%. There were 16 free flap losses and 1 partial loss overall. Anastomoses were re-explored in a total of 27 cases, of which 17 were salvaged. There were 29 events of hemorrhage or arterial or venous thrombosis: 17 in group 1 and 12 in group 2. A sum of 26 incidences of other postoperative complications was recorded, 13 in each group. Hemodilution status showed a statistically significant reduction in erythrocyte count and hemoglobin and hematocrit levels in the group receiving dextran 40, on postoperative days 1 and 3, but no such effect was observed on postoperative platelet count.

Conclusions
Although dextran 40 has been shown to have a valuable effect on hemodilution, which is beneficial in microsurgery, it did not demonstrate better outcomes in terms of flap survival. Because it can cause serious systemic complications, it is better not to administer it routinely. However, its important influence on reduction in erythrocyte count and hemoglobin and hematocrit levels should be further investigated.
Integrated physical and mental healthcare: an overview of models and their evaluation findings
Authors: Coates Dominiek , Coppleson Danielle , Schmied Virginia 
Published: January 2020

ABSTRACT

Background:
Comorbid physical and mental health problems are common across the age spectrum. However, services addressing these health concerns are typically siloed and disconnected. Over the past 2 decades efforts have been made to design integrated services to address the physical and mental health needs of the population but little is known about the characteristics of effective integrated care models. The aim of the review was to map the design of integrated care initiatives/models and to describe how the models were evaluated and their evaluation findings.

Method:
Using a scoping review methodology, quantitative and qualitative evidence was systematically considered. To identify studies, Medline, PubMed, PsychINFO, CINAHL were searched for the period from 2003 to 2018, and reference lists of included studies and review articles were examined.

Results:
The current review identified 43 studies, describing 37 models of integrated physical and mental healthcare. Although modest in terms of evaluation design, it is evident that models are well received by consumers and providers, increase service access, and improve physical and mental health outcomes. Key characteristics of models include shared information technology, financial integration, a single-entry point, colocated care, multidisciplinary teams, multidisciplinary meetings, care coordination, joint treatment plan, joint treatment, joint assessment/joint assessment document, agreed referral criteria and person-centred care. Although mostly modest in term of research design, models were well received by consumers and providers, increased service access and improved physical and mental health outcomes. There was no clear evidence regarding whether models of integrated care are cost neutral, increase or reduce costs.

Conclusion:
Future research is needed to identify the elements of integrated care that are associated with outcomes, measure cost implications and identify the experiences and priorities of consumers and clinicians.
Accucopy: Accurate and Fast Inference of Allele-specific Copy Number Alterations from Low-coverage Low-purity Tumor Sequencing Data
Authors: Fan Xinping , Luo Guanghao , Huang Yu S. 
Published: January 2020

AbstractBackgroundCopy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task.ResultsWe introduce Accucopy, a method to infer total copy numbers (TCNs) and allele-specific copy numbers (ASCNs) from challenging low-purity and low-coverage tumor samples. Accucopy adopts many robust statistical techniques such as kernel smoothing of coverage differentiation information to discern signals from noise and combines ideas from time-series analysis and the signal-processing field to derive a range of estimates for the period in a histogram of coverage differentiation information. Statistical learning models such as the tiered Gaussian mixture model, the Expectation-Maximization (EM) algorithm, and Sparse Bayesian Learning (SBL) were customized and built into the model. Accucopy is implemented in C++/Rust, packaged in a docker image, and supports non-human samples, more athttp://www.yfish.org/software/.ConclusionsWe describe Accucopy, a method that can predict both TCNs and ASCNs from low-coverage low-purity tumor sequencing data. Through comparative analyses in both simulated and real-sequencing samples, we demonstrate that Accucopy is more accurate than Sclust, ABSOLUTE, and Sequenza.