bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying Missed Opportunities for Human Immunodeficiency Virus Pre-exposure Prophylaxis During Preventive Care and Reproductive Visits in Adolescents in the Deep South
Authors: Hill Samantha V. , Westfall Andrew O. , Coyne-Beasley Tamera , Simpson Tina , Elopre Latesha 
Published: December 2019

Background
Pre-exposure prophylaxis (PrEP) for individuals at significant risk for Human Immunodeficiency Virus acquisition is approved for individuals weighing at least 35 kg by the Food and Drug Administration. This cross-sectional study analyzed indications for PrEP in a clinical setting.

Methods
There were 429 charts reviewed from adolescents between 15 and 21 years old seen for preventive care visits at an adolescent primary care center in the Deep South during a 1-year timeframe. Univariate and multivariable regression analyses were completed to identify factors associated with indications for PrEP.

Results
Forty-four percent of 429 adolescents (between 15 and 21 years) had a PrEP indication; 77% were women and 95% heterosexual. Significant factors associated with an indication for PrEP included living with a nonparent or nonrelative and polysubstance use. No adolescents with an indication for PrEP were prescribed PrEP. A sensitivity analysis comparing indications for PrEP between the 2014 and 2017 The Centers for Disease Control and Prevention Guidelines revealed no significant differences in percent with an indication (44.5% vs. 42.8%) or factors associated with indications.

Conclusions
Pre-exposure prophylaxis as a biomedical tool for adolescents and young adults (AYAs) may remain underutilized. A key factor in improving utilization involves providers being able to recognize AYAs who may have an indication for PrEP with a specific focus on those AYAs who do not live in households with parents or a surrogate family member and those who are polysubstance users.
Chlamydia trachomatis and Neisseria gonorrhoeae Retesting and Reinfection Rates in New Zealand Health Care Settings: Implications for Sexually Transmitted Infection Control
Authors: Rose Sally B. , Garrett Susan M. , Stanley James , Pullon Susan R.H. 
Published: December 2019

Background
Reinfection with chlamydia or gonorrhea is common and can lead to significant reproductive health complications so testing for reinfection after treatment is recommended. This study described retesting and reinfection rates in regions of New Zealand with higher-than-average population rates of chlamydia.

Methods
This retrospective cohort study analyzed chlamydia and gonorrhea testing data from 2 laboratories providing community testing services for 4 higher-rate regions in the North Island of New Zealand. Three years of data were obtained (2015–2017) to include a minimum of 6-month follow-up for all individuals. Retesting and reinfection rates between 6 weeks and 6 months of a positive result were calculated, and time to retesting was plotted using Kaplan-Meier curves. Logistic regression modeling was used to determine the odds of retesting (outcome 1) and reinfection (outcome 2) between 6 weeks and 6 months of follow-up.

Results
Overall, 34% (3151/9241) of the cohort was retested within the recommended period, of whom 21% retested positive. Significant differences were observed in the odds of retesting by sex, age band, ethnic group, clinic type, and region (P < 0.01). The odds of a subsequent positive on retesting within 6 months differed significantly by sex, age band, and ethnic group (P < 0.01).

Conclusions
These findings reflect substantial gaps in the delivery of best-practice sexually transmitted infection management in New Zealand. There is a clear need to prioritize the implementation of clinic-level processes to support clinicians in the routine delivery of best-practice sexual health care. These should include routine provision of patient advice about retesting and strategies to promote timely and equitable access to retesting.
Evaluation of 2 Commercial Assays for the Detection of Lymphogranuloma Venereum in Rectal Samples
Authors: Bernal-Martínez Samuel , García Sánchez Estefanía , Sivianes Nieves , Padilla Laura , Martin-Mazuelos Estrella 
Published: December 2019

Background
The early identification of the Chlamydia trachomatis variants that cause lymphogranuloma venereum (LGV) is very important to establish an adequate antibiotic treatment. This identification should be made with molecular techniques that are easy to perform and accessible to most microbiology laboratories. The objective of this study was to evaluate 2 real-time polymerase chain reaction (PCR)-based assay (VIASURE Haemophilus ducreyi + C. trachomatis (LGV) real-time PCR detection kit and the Allplex Genital ulcer Assay) for the detection of LGV in rectal samples.

Materials and Methods
Prospective study on positive rectal samples for C. trachomatis. All samples were processed in parallel by both tests. As a molecular reference method and to solve possible discrepancies between both assays, a PCR-based restriction fragment length polymorphism analysis of the major outer membrane protein gene (omp1) was used.

Results
In total, we detected 157 positive rectal samples for C. trachomatis, of which 36 were identified as LGV by PCR-based restriction fragment length polymorphism analysis. The positive percent agreement, negative percent agreement, and overall percent agreement were 88.9%, 100%, and 97.3%, respectively, for the Allplex Genital ulcer assay and 91.6%, 100%, and 97.1%, respectively, for the VIASURE assay. In the direct comparison between the Seegene assay and the VIASURE assay, we obtained a kappa concordance index of 0.98 between both tests.

Conclusions
According to the results obtained, both tests could be used for the detection of LGV in rectal samples.
Three Years of Shared Service HIV Nucleic Acid Testing for Public Health Laboratories: Worthwhile for HIV-1 but Not for HIV-2
Authors: Styer Linda M. , Gaynor Anne M. , Parker Monica M. , Bennett S. Berry , Wesolowski Laura G. , Ethridge Steven , Chavez Pollyanna R. , Sullivan Timothy J. , Fordan Salvacion , Wroblewski Kelly 
Published: December 2019

Background
In 2016, HIV-2 nucleic acid testing (NAT) was added to a shared service program that conducts HIV-1 NAT for public health laboratories performing the recommended algorithm for diagnosing HIV. Here, we evaluate the usefulness of HIV-2 NAT in this program as compared with HIV-1 NAT.

Methods
Specimens eligible for HIV-1 NAT were reactive on an HIV-1/2 antibody or antigen/antibody initial test and nonreactive or indeterminate on a supplemental antibody test or were reactive for HIV-1 antigen-only on an HIV-1/2 antigen/antibody initial test. Specimens eligible for HIV-2 NAT were reactive on an initial test, HIV-2 indeterminate or HIV indeterminate on a supplemental antibody test and had no detectable HIV-1 RNA or were reactive for HIV-2 antibody on an HIV-1/2 antigen/antibody test, and this reactivity was not confirmed with a supplemental antibody assay. All specimens were tested in a reference laboratory using APTIMA HIV-1 qualitative RNA and/or a validated qualitative HIV-2 RNA real-time PCR assay.

Results
During 2016 to 2019, HIV-1 RNA was detected in 234 (14%) of 1731 specimens tested. HIV-2 RNA was not detected in 52 specimens tested. Median time from specimen collection to reporting of HIV-1 and HIV-2 NAT results by year ranged from 9 to 10 days and from 22 to 27 days, respectively. Two specimens with HIV-2 indeterminate results on a supplemental antibody test had detectable HIV-1 RNA.

Conclusions
A shared service model for HIV-1 NAT is both feasible and beneficial for public health laboratories. However, because no HIV-2 infections were detected, our data suggest that this program should reconsider the usefulness of HIV-2 NAT testing.
Patient-Reported Outcomes following Surgical Treatment of Symptomatic Digital Neuromas
Authors: Lans Jonathan , Baker Daniel J. , Castelein René M. , Sood Ravi F. , Chen Neal C. , Eberlin Kyle R. 
Published: December 2019

Background:Many surgical techniques are used to treat symptomatic neuroma, but options are limited for digital neuromas because of a paucity of soft-tissue coverage and/or the absence of the terminal nerve end. The authors assessed factors that influence patient-reported outcomes after surgery for symptomatic digital neuroma.Methods:The authors retrospectively identified 29 patients with 33 symptomatic digital neuromas that were treated surgically. Patients completed the Patient-Reported Outcomes Measurement Information System (PROMIS) Upper Extremity and Pain Interference scales, a numeric rating scale for pain, and the PROMIS Depression scale at a median follow-up of 7.6 years postoperatively (range, 3.2 to 16.8 years). Surgical treatment for neuroma included excision with nerve repair/reconstruction (n=13; 39 percent), neuroma excision alone (n=10; 30 percent), and excision and implantation (n=10; 30 percent). Multivariable linear regression was performed to identify the factors that independently influenced patient-reported outcomes.Results:The mean postoperative PROMIS Upper Extremity score was 45.2 ± 11.2, the mean Pain Interference score was 54.3 ± 10.7, and the mean numeric rating scale pain score was 3 (interquartile range, 1 to 5). Compared with other treatment techniques, neuroma excision with nerve repair/reconstruction was associated with lower numeric rating scale pain scores; lower Pain Interference scores, corresponding to less daily impact of pain; and higher Upper Extremity scores, reflecting better upper extremity function. Older age and higher Depression scores were associated with lower Upper Extremity scores and higher Pain Interference scores. Smoking was associated with higher Pain Interference and numeric rating scale pain scores.Conclusions:Neuroma excision followed by nerve repair/reconstruction resulted in better outcomes compared with neuroma excision alone with or without implantation. Patient age and psychosocial factors influenced patient-reported outcomes.CLINICAL QUESTION/LEVEL OF EVIDENCE:Risk, III.
A Review of Insurance Coverage of Gender-Affirming Genital Surgery
Authors: Ngaage Ledibabari M. , Knighton Brooks J. , Benzel Caroline A. , McGlone Katie L. , Rada Erin M. , Coon Devin , Bluebond-Langner Rachel , Rasko Yvonne M. 
Published: December 2019

Background:
Despite the multiple benefits of gender-affirming surgery for treatment of gender dysphoria, research shows that barriers to care still exist. Third-party payers play a pivotal role in enabling access to transition-related care. The authors assessed insurance coverage of genital reconstructive (“bottom”) surgery and evaluated the differences between policy criteria and international standards of care.

Methods:
A cross-sectional analysis of insurance policies for coverage of bottom surgery was conducted. Insurance companies were selected based on their state enrollment data and market share. A Web-based search and telephone interviews were performed to identify the policies and coverage status. Medical necessity criteria were abstracted from publicly available policies.

Results:
Fifty-seven insurers met inclusion criteria. Almost one in 10 providers did not hold a favorable policy for bottom surgery. Of the 52 insurers who provided coverage, 17 percent held criteria that matched international recommendations. No single criterion was universally required by insurers. Minimum age and definition of gender dysphoria were the requirements with most variation across policies. Almost one in five insurers used proof of legal name change as a coverage requirement. Ten percent would provide coverage for fertility preservation, while 17 percent would cover reversal of the procedure.

Conclusions:
Despite the medical necessity, legislative mandates, and economic benefits, global provision of gender-affirming genital surgery is not in place. Furthermore, there is variable adherence to international standards of care. Use of surplus criteria, such as legal name change, may act as an additional barrier to care even when insurance coverage is provided.
Orbicularis Oculi Muscle Reinnervation Confers Corneal Protective Advantages over Static Interventions Alone in the Subacute Facial Palsy Patient
Authors: Mohanty Ahneesh J. , Perez Justin L. , Hembd Austin , Thrikutam Nikhitha P. , Bartley Jeremy , Rozen Shai M. 
Published: December 2019

Background:
Corneal protection is a priority in flaccid facial palsy patients. Denervation of the orbicularis oculi muscle results in weak palpebral closure and predisposes patients to severe corneal sequelae. While periorbital static procedures enhance corneal coverage in repose, voluntary closure is only regained through dynamic reinnervation of the muscle. This study aims to elucidate the added effect of dynamic reinnervation of the orbicularis oculi muscle on long-term corneal integrity as well as on dynamic closure of the palpebral aperture.

Methods:
Retrospective review was performed on two groups of complete palsy patients: those who received solely periorbital static procedures and those who underwent concomitant orbicularis oculi muscle reinnervation and static lid procedures. Only patients with complete ophthalmic examinations were included. Corneal punctate epithelial erosions in addition to static and dynamic palpebral measurements were serially assessed preoperatively and postoperatively.

Results:
Of 272 facial palsy patients, 26 fit the inclusion criteria. Eleven patients underwent combined muscle reinnervation involving facial–to–masseteric nerve coaptation in addition to static eye procedures, and 15 patients underwent solely static interventions. Analysis revealed a 65.3 percent lower mean punctate epithelial erosion score in reinnervation patients as compared with static patients when evaluated at more than 9 months postoperatively (p < 0.01). Reinnervation patients were also found to have 25.3 percent greater palpebral aperture closure (p < 0.05) and 32.8 percent higher closure velocity (p < 0.01) compared with static patients.

Conclusion:
In patients with subacute facial palsy, dynamic reanimation of the orbicularis oculi muscle with concomitant static interventions provides lasting corneal protection not seen in patients who receive solely static interventions.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
Mid-Term Outcome of Total Hip Arthroplasty in Patients With Progressive Pseudorheumatoid Dysplasia
Authors: Feng Bin , Xiao Ke , Ren Yi , Xia Zenan , Jin Jin , Wu Zhihong , Qiu Guixing , Weng Xisheng 
Published: December 2019

Background
Progressive pseudorheumatoid dysplasia (PPD) is a rare disease that causes musculoskeletal deformities. There has been no detailed report on the outcome of PPD patients who undergo total hip arthroplasty (THA). The aim of this study was to investigate the clinical and radiological outcome of PPD patients undergoing THA after middle-term follow-up.

Methods
This was a medical records review study. Patients with the diagnosis of PPD who underwent THA were enrolled. The PPD diagnosis was confirmed by genetic sequencing. Baseline clinical data were retrieved. The patients were followed for the Harris Hip Score, visual analogue score, range of hip motion, and postoperative complication. Life quality was evaluated with the Short Form 36. Plain x-ray films were used for radiographic evaluation.

Results
Four cases were identified from the patient database in our institute. All the patients presented arthropathy of both hips and underwent 1-stage bilateral THA. All the patients had WISP3 mutation after genetic sequencing. The cases were followed at average 47.9 months (range, 18–93 months). Harris Hip Score increased from 39.67 ± 9.73 points preoperatively to 91.67 ± 4.32 points postoperatively (p < 0.05); Short Form 36 increased from 19.67 ± 1.53 points preoperatively to 71.33 ± 3.06 postoperatively (p < 0.05). The hip range of hip motion was significantly improved after operation. X-ray films showed no obvious radiolucent lines or aseptic loosening at the latest follow-up.

Conclusions
This study indicated that THA was effective to treat the PPD patients complicated with hip arthropathy with satisfactory clinical and radiological outcome after mid-term follow-up.
Role of Interleukin 6 Inhibitors in the Management of Rheumatoid Arthritis
Authors: Yip Ronald Man Lung , Yim Cheuk Wan 
Published: December 2019

Abstract
Rheumatoid arthritis (RA) is a multisystem disease that affects the joints and various organs, resulting in compromised quality of life and increased mortality. A wide spectrum of treatment options is available for RA. Conventional synthetic disease-modifying antirheumatic drugs (csDMARDs) are the first-line of treatment for RA, whereas tumor necrosis factor α inhibitors are commonly used as a second-line biological disease-modifying antirheumatic drug following inadequate response to csDMARDs. However, remission remains difficult to achieve. No single agent is effective for all patients. It is important to consider patients' comorbidities, perspectives, and preferences when selecting treatment.
Interleukin 6 (IL-6) plays a prominent role in the pathophysiology of RA and is an important therapeutic target for RA. Tocilizumab and sarilumab are approved IL-6 inhibitors, which have demonstrated good efficacy and tolerability as combination therapy or monotherapy in RA patients with inadequate response to csDMARDs or tumor necrosis factor α inhibitors. Apart from alleviating joint symptoms, inducing remission, and reducing structural damage, tocilizumab and sarilumab exhibit additional advantages in alleviating extra-articular symptoms, such as fatigue and morning stiffness, and have positive effect on anemia and glucose metabolism. Additionally, evidence showed that certain patient subgroups, such as those with comorbidities including anemia and diabetes mellitus, those with early RA, those with high baseline IL-6 levels, those at high risk of tuberculosis infection, or those intolerant to methotrexate monotherapy, may benefit from IL-6 inhibition. Given these advantages, tocilizumab and sarilumab can be considered earlier as a rational choice for treating RA in suitable patients. Future clinical investigations will help refine the use of these agents.
The Anterolateral Thigh Flap for Reconstruction of the Defect After Maxillectomy
Authors: lin Xiu an , shi You yuan , liu Chang 
Published: December 2019

Objective:This study aimed to investigate the efficacy and success rate of the anterolateral thigh flap (ALT) in reconstructing total maxillectomy defects.Methods:This retrospective study involved patients with total maxillectomy defects, who underwent free ALT reconstruction from June 2005 to October 2014.Results:The study included 72 patients (43 males and 29 females; age range, 7–77 years; mean age, 43 years). Four patients experienced major complications related to surgery: total flap loss in one patient, partial flap necrosis requiring reoperation in one patient, hematoma requiring operative evacuation in 1 patient, and diplopia requiring reoperation in 1 patient. Two patients experienced minor complications: partial flap loss healed by secondary intention with local wound care, and donor site suture rupture in 1 patient healed by secondary intention. Six patients died because of cancer-related death (after local recurrence or metastatic disease). The defects in 5 patients involved the facial skin for which the ALT was segmented into three parts to reconstruct the facial skin, nasal lining, and oral lining. The defects in 4 patients involved the orbital floor for which a segment of tensor fascia lata was included with the flap on the same pedicle and used to repair the orbital floor. In the remaining patients, the free ALT flap, including a segment of vastus lateralis, was used to repair the maxillary defect and fill the dead space. All but one of the surviving patients were satisfied with their final appearance postoperatively.Conclusion:The free ALT flap with or without fascia lata to repair the orbital floor is safe, reliable, and acceptable for reconstructing total maxillectomy defects.
Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent
Authors: Uyenoyama Marcy K. , Takebayashi Naoki , Kumagai Seiji 
Published: December 2019

ABSTRACTWe address the effect of population structure on key properties of the Ewens sampling formula. We use our previously-introduced inductive method for determining exact allele frequency spectrum (AFS) probabilities under the infinite-allele model of mutation and population structure for samples of arbitrary size. Fundamental to the sampling distribution is the novel-allele probability, the probability that given the pattern of variation in the present sample, the next gene sampled belongs to an as-yet-unobserved allelic class. Unlike the case for panmictic populations, the novel-allele probability depends on the AFS of the present sample. We derive a recursion that directly provides the marginal novel-allele probability across AFSs, obviating the need first to determine the probability of each AFS. Our explorations suggest that the marginal novel-allele probability tends to be greater for initial samples comprising fewer alleles and for sampling configurations in which the next-observed gene derives from a deme different from that of the majority of the present sample. Comparison to the efficient importance sampling proposals developed by De Iorio and Griffiths and colleagues indicates that their approximation for the novel-allele probability generally agrees with the true marginal, although it may tend to overestimate the marginal in cases in which the novel-allele probability is high and migration rates are low.
Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements
Authors: Hosseini Morteza , Pratas Diogo , Morgenstern Burkhard , Pinho Armando J. 
Published: December 2019

AbstractBackgroundThe development of high-throughput sequencing technologies and, as its result, the production of huge volumes of genomic data, has accelerated biological and medical research and discovery. Study on genomic rearrangements is crucial due to their role in chromosomal evolution, genetic disorders and cancer;ResultsWe present Smash++, an alignment-free and memory-efficient tool to find and visualize small- and large-scale genomic rearrangements between two DNA sequences. This computational solution extracts information contents of the two sequences, exploiting a data compression technique, in order for finding rearrangements. We also present Smash++ visualizer, a tool that allows the visualization of the detected rearrangements along with their self- and relative complexity, by generating an SVG (Scalable Vector Graphics) image;ConclusionsTested on several synthetic and real DNA sequences from bacteria, fungi, Aves and mammalia, the proposed tool was able to accurately find genomic rearrangements. The detected regions complied with previous studies which took alignment-based approaches or performed FISH (Fluorescence in situ hybridization) analysis. The maximum peak memory usage among all experiments was ~1 GB, which makes Smash++ feasible to run on present-day standard computers.