bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pervasive and non-random recombination in near full-length HIV genomes from Uganda
Authors: Grant Heather E , Hodcroft Emma B , Ssemwanga Deogratius , Kitayimbwa John M , Yebra Gonzalo , Esquivel Gomez Luis Roger , Frampton Dan , Gall Astrid , Kellam Paul , de Oliveira Tulio , Bbosa Nicholas , Nsubuga Rebecca N , Kibengo Freddie , Kwan Tsz Ho , Lycett Samantha , Kao Rowland , Robertson David L , Ratmann Oliver , Fraser Christophe , Pillay Deenan , Kaleebu Pontiano , Leigh Brown Andrew J 
Published: January 2020

AbstractRecombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50 years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants in this population and the location of breakpoints along the genome. As part of the PANGEA-HIV consortium, 1,472 consensus genome sequences over 5 kb have been obtained from 1,857 samples collected by the MRC/UVRI & LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (&gt;8 kb). Using the subtyping tool SCUEAL, we find that of the near full-length dataset, 233 (50.1 per cent) genomes contained only one subtype, 30.8 per cent A1 (n = 143), 17.6 per cent D (n = 82), and 1.7 per cent C (n = 8), while 49.9 per cent (n = 232) contained more than one subtype (including A1/D (n = 164), A1/C (n = 13), C/D (n = 9); A1/C/D (n = 13), and 33 complex types). K-means clustering of the recombinant A1/D genomes revealed a section of envelope (C2gp120-TMgp41) is often inherited intact, whilst a generalized linear model was used to demonstrate significantly fewer breakpoints in the gag–pol and envelope C2-TM regions compared with accessory gene regions. Despite similar recombination patterns in many recombinants, no clearly supported circulating recombinant form (CRF) was found, there was limited evidence of the transmission of breakpoints, and the vast majority (153/164; 93 per cent) of the A1/D recombinants appear to be unique recombinant forms. Thus, recombination is pervasive with clear biases in breakpoint location, but CRFs are not a significant feature, characteristic of a complex, and diverse epidemic.
Assessment of prophylactic antibiotics administration for acute pancreatitis: a meta-analysis of randomized controlled trials
Authors: Ding Nan , Sun Yong-Hui , Wen Li-Mei , Wang Jian-Hua , Yang Jian-Hua , Cheng Kun , Lin Hai , Chen Qi-Long 
Published: January 2020

Abstract

Background:
Recent evidence has shown that prophylactic antibiotic treatment in patients with acute pancreatitis is not associated with a significant decrease in mortality or morbidity. The use and efficacy of prophylactic antibiotic treatment in acute pancreatitis remain controversial. This meta-analysis was conducted to assess whether antibiotic prophylaxis is beneficial in patients with acute pancreatitis.

Methods:
We searched randomized controlled trials (RCTs) of prophylactic use of antibiotics using Medline (PubMed), Embase, the Cochrane Library, and Web of Science. The data were analyzed using Review Manager 5.3 software. We performed pooled analyses for infected pancreatic necrosis, mortality, surgical intervention, and non-pancreatic infection. Odds ratios (ORs) from each trial were pooled using a random or fixed effects model, depending on the heterogeneity of the included studies. Sub-group analysis or sensitivity analysis was conducted to explore potential sources of heterogeneity, when necessary.

Results:
Totally, 11 RCTs involving 747 participants were included, with an intervention group (prophylactic use of antibiotics, n = 376) and control group (n = 371). No significant differences were found regarding antibiotic prophylaxis with respect to incidence of infected pancreatic necrosis (OR, 0.74; 95% confidence interval [CI], 0.50–1.09; P
= 0.13), surgical intervention (OR, 0.92; 95% CI, 0.62–1.38; P
= 0.70), and morality (OR, 0.71; 95% CI, 0.44–1.15; P
= 0.16). However, antibiotic prophylaxis was associated with a statistically significant reduction in the incidence of non-pancreatic infection (OR, 0.59; 95% CI, 0.42–0.84; P
= 0.004).

Conclusions:
Prophylactic antibiotics can reduce the incidence of non-pancreatic infection in patients with AP.
Pulsed radiofrequency alleviated neuropathic pain by down-regulating the expression of substance P in chronic constriction injury rat model
Authors: Wang Jing-Ai , Niu Shao-Ning , Luo Fang 
Published: January 2020

Abstract

Background
Pulsed radiofrequency (PRF), as a non-invasive treatment of neuropathic pain (NP), has been widely administered clinically. Previous studies have shown that PRF has the potential to improve hyperalgesia in animal models of NP. However, there have been few reports to clarify whether the mechanism of PRF treatment of NP involves intervention in the expression of substance P (SP). Therefore, this study administered PRF treatment to chronic constriction injury (CCI) model rats and observed the sciatic nerve mechanical pain threshold and SP expression in the spinal cord to explore the mechanism of PRF treatment.

Methods
A total of 96 Sprague-Dawley rats were randomly divided into the sham-surgery-sham-treatment group (S-S group), the sham-surgery-PRF group (S-P group), the CCI-sham-treatment group (C-S group), and the CCI-PRF group (C-P group). The C-S group and the C-P group underwent sciatic nerve CCI, while the other groups received a sham operation. At 14 days after the operation, the C-P group and the S-P group were treated with PRF for 300 s. We recorded the hindpaw withdrawal threshold (HWT) and the thermal withdrawal latency (TWL) of rats in the various groups at baseline, before treatment (0 days), and at 1, 7, 14, and 28 days after treatment. L4 to L6 spinal cord tissues were taken before treatment (0 days) and 1, 7, 14, and 28 days after treatment. The transcription and translation of SP were measured by quantitative polymerase chain reaction and Western blotting, respectively.

Results
The HWT and the TWL in the C-P group 28 days after PRF treatment were significantly higher than those in the C-S group (95% confidence interval [CI]: 5.84–19.50, P < 0.01; 95% CI: 2.58–8.69, P = 0.01). The expression of SP in the C-P group 28 days after PRF treatment was significantly lower than that in the C-S group (95% CI: 1.17–2.48, P < 0.01).

Conclusions
PRF may alleviate CCI-induced NP by down-regulating the expression of SP in the spinal cord of CCI model rats.
Management of Optic Disk Pit-associated Macular Detachment with Human Amniotic Membrane Patch
Authors: Rizzo Stanislao , Caporossi Tomaso , Pacini Bianca , De Angelis Lorenzo , De Vitto Maria Luce , Gainsanti Fabrizio 
Published: January 2020

Purpose:
To report a new surgical technique involving a human amniotic membrane patch (hAM) to solve a serous macular detachment associated with optic nerve head pit.

Methods:
Three eyes of three patients affected by macular detachment associated with optic nerve head pit were enrolled. A 23-gauge pars plana vitrectomy were performed. hAM patch was implanted inside the optic nerve pit; air was used as endotamponade. The patients were instructed to maintain face-down position for the first days after surgery.

Results:
The subretinal fluid gradually resolved during 6 months of follow-up, and visual acuity improved to 20/25 at the sixth month after surgery. We did not observe a recurrence of subretinal fluid during the 6 months of follow-up. No postoperative complications were reported during the follow-up.

Conclusion:
Implant of the hAM may be effective to repair optic disk pit maculopathy. All the cases were successful with encouraging visual acuity recovery.
Effectiveness of Enhanced External Counterpulsation Treatment on Symptom Burden, Medication Profile, Physical Capacity, Cardiac Anxiety, and Health-Related Quality of Life in Patients With Refractory Angina Pectoris
Authors: Wu Eline , Desta Liyew , Broström Anders , Mårtensson Jan 
Published: January 2020

Background
Patients with refractory angina pectoris experience recurrent symptoms that limit their functional capacity, including psychological distress and impaired health-related quality of life (HRQoL), despite optimized medical therapy. Enhanced external counterpulsation (EECP) is an evidence-based alternative noninvasive treatment. Although physical well-being and mental well-being are equally important components of health, few studies have investigated the psychological effects of EECP in patients with refractory angina pectoris.

Objective
The aim of this study was to evaluate the effects of EECP treatment in patients with refractory angina pectoris regarding medication profile, physical capacity, cardiac anxiety, and HRQoL.

Methods
This quasi-experimental study with 1-group pretest-posttest design includes a 6-month follow-up of 50 patients (men, n = 37; mean age, 65.8 years) who had undergone 1 EECP course. The following pretreatment and posttreatment data were collected: medication use, 6-minute walk test results, functional class according to the Canadian Cardiovascular Society, and self-reported (ie, questionnaire data) cardiac anxiety and HRQoL. In addition, the questionnaires were also completed at a 6-month follow-up.

Results
After EECP treatment, patients used significantly less nitrates (P < .001), walking distance increased on average by 46 m (P < .001), and Canadian Cardiovascular Society class improved (P < .001). In addition, all but 1 subscale of cardiac anxiety and all HRQoL components improved significantly (P < .05). The positive effects for cardiac anxiety and HRQoL were maintained at the 6-month follow-up.

Conclusions
Enhanced external counterpulsation treatment resulted in reduced symptom burden, improved physical capacity, and less cardiac anxiety, leading to increased physical activity and enhanced life satisfaction for patients with refractory angina pectoris. Enhanced external counterpulsation treatment should be considered to improve the life situation for these patients.
Sociodemographic Characteristics Associated With Speech and Language Delay and Disorders
Authors: Uzun Çiçek Ayla , Akdag Emrah , Celebi Erdivanli Ozlem 
Published: January 2020

Abstract
The aim of this study was to identify major risk factors and sociodemographic characteristics responsible for speech and language delay/disorders. Two hundred twenty-eight children (aged 24–72 months) with speech and language delay/disorders participated in this study. The Ankara Developmental Screening Inventory and The Peabody Picture Vocabulary Test were used to assess language profiles and developmental stages of children. Low income, nonattendance in preschool education, low maternal education, having two or more siblings, later birth order (order of siblings), family history of speech and language delay/disorders, preterm birth, low birth weight, and birth complications or the need for intensive care support during neonatal period were identified as risk factors (all p < 0.005). Both sociodemographic and biologic factors were associated with speech and language delay/disorders. Awareness of these factors may provide a chance for earlier diagnosis and intervention. Identification of risk factors of these children would contribute to our knowledge in this field.
Reversible Cortical Blindness in Pediatric Native Valve Endocarditis
Authors: Sahai Archit , Suarez William A. 
Published: January 2020

Abstract
Native valve endocarditis, a rare phenomenon in children, can present with septic embolization and devastating consequences. We present a healthy child with bilateral cortical blindness due to native mitral valve endocarditis. After prompt medical and surgical therapy, he regained complete vision. Early surgical intervention resulted in the best outcome.
Underdiagnosis of Nasoorbitoethmoid Fractures in Patients with Zygoma Injury
Authors: Nissen Nicholas J. , Okhah Zachary I. , Basta Marten N. , Hsieh Sun , Crozier Joseph W. , Jehle Charles C. , Rao Vinay , Woo Albert S. 
Published: January 2020

Background:
Nasoorbitoethmoid fractures commonly accompany midface fractures and may be underdiagnosed, resulting in incomplete reconstruction or inadequate treatment following facial trauma. To better understand the nasoorbitoethmoid fracture diagnosis and treatment tendencies, the authors analyzed concomitant nasoorbitoethmoid injuries in the setting of zygoma fractures.

Methods:
The facial trauma database at a level I trauma center was evaluated. All patients with diagnosed zygoma fractures from June of 2011 to March of 2016 were assessed for a concomitant nasoorbitoethmoid injury. Documentation of these fractures in radiology, plastic surgery, and operative notes was recorded, as was the rate of nasoorbitoethmoid fracture surgical repair.

Results:
The authors identified 339 eligible patients and completed retrospective analysis of computed tomographic images for their 356 zygoma fractures. The incidence of concomitant nasoorbitoethmoid fractures was 30.6 percent (109 of 356). Documentation rates of nasoorbitoethmoid fractures were 0 percent, 3.7 percent, and 8.3 percent in radiology, plastic surgery, and operative notes, respectively. The rate of surgical correction of nasoorbitoethmoid injuries was 22.9 percent (25 of 109). Of those fractures identified, 44.9 percent (49 of 109) were minimally displaced or nondisplaced. Subset analysis of only significantly displaced fractures yielded an incidence of 16.8 percent (60 of 356). Of significantly displaced fractures, documentation rates were 0 percent, 6.7 percent, and 16.8 percent in radiology, plastic surgery, and operative notes, respectively. The surgical repair rate of significantly displaced fractures was 31.7 percent (19 of 60).

Conclusions:
These findings suggest a high concomitance rate of nasoorbitoethmoid fractures with zygoma fractures and identify a tendency to underdocument and undertreat this injury pattern. Clinicians managing patients with midface trauma should have a high suspicion for nasoorbitoethmoid trauma. Plastic surgeons and radiologists should be better trained in identifying the nasoorbitoethmoid fracture pattern.
Neurotized Free Platysma Flap for Functional Eyelid Reconstruction: A Cadaveric Study of Anatomical Feasibility
Authors: Vaca Elbert E. , Surek Christopher , Klosowiak Julian , Dumanian Gregory A. , Alghoul Mohammed S. 
Published: January 2020

Background:
Conventional reconstructive options for large full-thickness eyelid defects are limited to static local flaps without replacing the missing orbicularis. The authors’ aim is to delineate the platysma neurovascular anatomy for innervated functional eyelid reconstruction.

Methods:
Fourteen fresh latex-injected heminecks were dissected. The locations where neurovascular structures entered the platysma muscles were expressed as the percentage distance ± SD from the sternocleidomastoid muscle mastoid insertion to manubrium origin.

Results:
The superior thyroid, facial, and lingual vessels were the major pedicles in eight of 14 (57.1 percent), four of 14 (28.6 percent), and one of 14 specimens (7.1 percent), respectively. In one specimen (7.1 percent), both the superior thyroid and facial vessels supplied a major pedicle. Venous drainage generally mirrored arterial inflow but was redundant, with 43 percent and 14 percent of flaps also with major contributions from the external jugular and anterior jugular veins, respectively. Neurovascular pedicles entered the platysma 28 to 57 percent caudal to the sternocleidomastoid muscle mastoid insertion, between 0.5 and 4.8 cm anterior to the medial sternocleidomastoid muscle border.

Conclusion:
Although variability exists, platysma neurovascular pedicles enter at predictable locations between 28 and 57 percent of the distance from the mastoid insertion of the sternocleidomastoid muscle, therefore making free platysma transfer a feasible option for eyelid reconstruction.
Brief Report: Sexual Mixing Patterns by HIV Status and PrEP Use Among Men Who Have Sex With Men Partnerships in Melbourne, 2011–2018
Authors: Chow Eric P. F. , Phillips Tiffany R. , Bradshaw Catriona S. , Chen Marcus Y. , Fairley Christopher K. 
Published: January 2020

Background:
Sexual mixing between HIV-positive, HIV-negative, and pre-exposure prophylaxis (PrEP) users among men who have sex with men (MSM) is an important determinant of the incidence of infection. There have been very limited studies examining the patterns of sexual mixing in relation to HIV status and PrEP use in the era of PrEP.

Setting:
Melbourne Sexual Health Centre (MSHC), Australia.

Methods:
We included all MSM partnerships attending MSHC on the same day between 2011 and 2018. A chi-square trend test was used to examine the changes in the annual proportion of partnerships by HIV serostatus in 2011–2018 and by PrEP use in 2016–2018.

Results:
Of the 1765 MSM partnerships who attended MSHC between 2011 and 2018, 1.3% of the partnerships were concordant HIV-positive, 91.0% were concordant HIV-negative, and 7.6% were HIV-discordant. The proportion of HIV-discordant partnerships increased from 0% in 2011 to 12.5% in 2018 (p
trend < 0.001). In 2016–2018, only a small proportion (1.2%) of concordant HIV-negative partnerships involved both men taking PrEP, whereas 6.0% involved at least one man taking PrEP. Overall, 79.1% of concordant HIV-negative partnerships were not protected against HIV (ie, neither man taking PrEP), and this proportion declined significantly from 84.3% in 2016 to 74.0% in 2018 (p
trend = 0.001).

Conclusions:
The pattern of sexual mixing by HIV status and PrEP use among MSM partnerships has changed over time. PrEP use in both men within MSM partnerships is not common. About 79% of concordant HIV-negative partnerships were not protected against HIV as neither man taking PrEP.
Brief Report: Phase IIa Safety Study of a Vaginal Ring Containing Dapivirine in Adolescent Young Women
Authors: Bunge Katherine E. , Levy Lisa , Szydlo Daniel W. , Zhang Jingyang , Gaur Aditya H. , Reirden Daniel , Mayer Kenneth H. , Futterman Donna , Hoesley Craig , Hillier Sharon L. , Marzinke Mark A. , Hendrix Craig W. , Gorbach Pamina M. , Wilson Craig M. , Soto-Torres Lydia , Kapogiannis Bill , Nel Annalene , Squires Kathleen E. ,   for the MTN-023/IPM 030 Study Team
Published: January 2020

Background:
Young women aged 15–24 years are disproportionately affected by the HIV epidemic. Two phase III trials of a vaginal ring containing 25-mg dapivirine demonstrated HIV-1 risk reduction in adult women older than 21 years but not in those aged 18–21 years. Lack of protection was correlated with low adherence.

Methods:
In this phase-IIa, randomized, double-blind, placebo-controlled, US, multicenter trial of the dapivirine ring in sexually active females, aged 15–17 years, participants were randomized 3:1 to a dapivirine or placebo ring to be inserted monthly for 6 months (NCT02028338). Primary safety end points included grade 2 product related adverse events and any grade 3 and higher adverse events. Adherence to ring use was assessed by plasma dapivirine concentrations, residual levels in used rings, and self-report. A plasma dapivirine concentration of >95 pg/mL was used to define short-term adherence; a residual ring level of <23.5 mg was used to define long-term adherence. Acceptability was assessed through computer-assisted self-interviews.

Results:
Ninety-six participants were enrolled across 6 US sites. The median age was 16.0 years. There were no differences in safety outcomes between treatment arms. Adherence to the dapivirine ring was demonstrated by both plasma measurements (87%) and residual drug levels in rings (95%). Forty-two percent (95% confidence interval: 32 to 52) of participants reported that they never removed the ring. Participants noted no discomfort due to the ring at 87% of visits and “liking” the ring at 93% of visits.

Conclusion:
The dapivirine vaginal ring, a promising topical microbicide, was well tolerated and acceptable in young US adolescents.
Carbon Dioxide Cryotherapy for Treatment of Nasal and Perinasal Congenital Melanocytic Nevi
Authors: Elmelegy Nader , Elghamry Sameh 
Published: January 2020

Abstract
Congenital melanocytic nevi, reported in 1% to 6% of newborns. There are many complications the most dangerous is the malignant transformation, but the most depressive is the cosmetic one specially for facial lesions. There is a wide range of treatment modalities none of them provide an acceptable solution for facial lesions. In this study we provide a simple, cheap and effective treatment modality for nasal and perinasal congenital melanocytic nevi. In our study, significant improvement was observed with no repigmentation throughout the follow-up period. We conclude that carbon dioxide cryotherapy is an effective treatment modality for nasal and perinasal congenital melanocytic nevi that should be used by others to stand on its long-term persistence and possible complications.
Improvement of Constipation Symptoms in an Older Adult Patient by Defecation Care Based on Using a Handheld Ultrasound Device in Home Care Settings
Authors: Matsumoto Masaru , Yabunaka Koichi , Yoshida Mikako , Nakagami Gojiro , Miura Yuka , Okawa Yohei , Sugama Junko , Okada Shingo , Ohta Hideki , Sanada Hiromi 
Published: January 2020

BACKGROUND:
Although previous studies have demonstrated the ability of ultrasound to detect stool in the colon and rectum, the clinical utility of evaluating constipation via ultrasonic imaging by nurses has not been determined. In this case report, we observed fecal retention, assessed the presence of constipation, and performed defecation care in an older adult patient in a home care setting in a city near the metropolitan area in Japan.

CASE:
An 85-year-old male with advanced stage prostate cancer and multiple metastases was diagnosed with fecal impaction via digital rectal examination and evaluation of stool consistency. He was managed by regular digital evacuation of stool, but ultrasonic imaging indicated constipation with fecal retention in both the rectum and the colon despite this bowel evacuation program. When faced with this situation, we advocate a bowel management program that considers both intestinal elimination dysfunction and fecal transport dysfunction. Based on ultrasonic imaging, stool consistency was altered by promoting water intake, and we promoted self-defecation by asking the patient to attempt to move his bowels (regardless of cues to defecation) by sitting on the toilet every morning. As a result, the number of weekly enemas and digital dis-impaction episodes decreased while the number of spontaneous defecations increased.

CONCLUSION:
This case report demonstrated that ultrasonography improved bowel management in this patient with clinically severe chronic constipation.
Management of Complicated Ostomy Dehiscence
Authors: Bilgin Ismail Ahmet , Bas Mustafa , Demir Sehri , Esen Eren , Kirbiyik Ebru , Aghayeva Afag , Ozben Volkan , Aytac Erman , Baca Bilgi , Hamzaoglu Ismail , Karahasanoglu Tayfun 
Published: January 2020

BACKGROUND:
Stoma creation is a common procedure in colorectal surgery. Despite improved surgical techniques, ostomy-related wound complications may prolong the recovery period and impair health-related quality of life. Negative pressure wound therapy (NPWT), autolytic debridement agents, and silver dressings are often used for managing complex wound infection and dehiscence. These applications have the potential to increase patient comfort and accelerate recovery.

CASE:
We report our experience in a 66 year old female who had a wound dehiscence involving the ostomy after robotic abdominoperineal resection. Her medical history was significant for a rectovaginal fistula which occurred after a low anterior resection for rectal cancer 5 years ago. Interventions for treatment of the dehiscence were use of NPWT, autolytic debriding agent, and silver dressing.

CONCLUSION:
Combined use of these interventions for dehiscence of an ostomy can minimize patient discomfort and accelerate wound healing.