bluuebunny/crossref_metadata_2025 huggingface dataset:
Subpectoral Implantation of Internal Pulse Generators for Deep Brain Stimulation: Technical Note for Improved Cosmetic Outcomes
Authors: White-Dzuro Gabrielle A. , Lake Wendell , Neimat Joseph S.
Published: March 2017

BACKGROUND: Deep brain stimulation is increasingly used to treat a variety of disorders. As the prevalence of this technology increases, greater demands are placed on neurosurgical practitioners to improve cosmetic results, maximize patient comfort, and minimize complication rates. We have increasingly employed subpectoral implantation of internal pulse generators (IPGs) to improve patient satisfaction.

OBJECTIVE: To determine the complication rates of subpectorally placed IPGs as compared to those placed in a subcutaneous location.

METHODS: We reviewed a series of 301 patients from a single institution. Complication rates including infection, hematoma, and lead fracture were recorded. Rates were compared for subcutaneously and subpectorally located devices.

RESULTS: Of the records reviewed, we found 301 patients who underwent 308 procedures for initial IPG implantation. Of these, 275 were subpectoral IPG implantation, 19 were infraclavicular subcutaneous implantation, and 14 were subcutaneous implantation in the abdomen. A total of 6 IPG pocket infections occurred, 2 subpectoral and 4 infraclavicular subcutaneous. Of the IPG infections, 2 of the infraclavicular subcutaneous devices had associated erosions. Two patients had their devices relocated from a subpectoral pocket to a subcutaneous pocket in the abdomen due to discomfort. Two patients in the subpectoral group suffered from hematoma requiring evacuation. Two patients in the infraclavicular subcutaneous group had lead fracture occur.

CONCLUSIONS: Subpectoral implantation of deep brain stimulation IPGs is a viable alternative with a low complication rate. This technique may offer a lower rate of infection and wound erosion.
One-hit Models of Ventilator-induced Lung Injury
Authors: Lex Dennis , Uhlig Stefan
Published: March 2017

Background

One important explanation for the detrimental effects of conventional mechanical ventilation is the biotrauma hypothesis that ventilation may trigger proinflammatory responses that subsequently cause lung injury. This hypothesis has frequently been studied in so-called one-hit models (overventilation of healthy lungs) that so far have failed to establish an unequivocal link between inflammation and hypoxemic lung failure. This study was designed to develop a one-hit biotrauma model.

Methods

Mice (six per group) were ventilated for up to 7 h (positive end-expiratory pressure 2 cm H2O) and received 300 μl/h fluid support. Series_1: initial plateau pressures of 10, 24, 27, or 30 cm H2O. Series_2: ventilation with pressure release at 34 cm H2O and initial plateau pressure of 10, 24, 27, or 30 cm H2O. To study the significance of inflammation, the latter groups were also pretreated with the steroid dexamethasone.

Results

Within 7 h, 20 of 24 mice ventilated with plateau pressure of 27 cm H2O or more died of a catastrophic lung failure characterized by strongly increased proinflammatory markers and a precipitous decrease in pulmonary compliance, blood pressure, and oxygenation. Pretreatment with dexamethasone reduced inflammation, but prolonged median survival time by 30 min.

Conclusions

Our findings demonstrate a sharp distinction between ventilation with 24 cm H2O that was well tolerated and ventilation with 27 cm H2O that was lethal for most animals due to catastrophic lung failure. In the former case, inflammation was benign and in the latter, a by-product that only accelerated lung failure. The authors suggest that biotrauma—when defined as a ventilation-induced and inflammation-dependent hypoxemia—is difficult to study in murine one-hit models of ventilation, at least not within 7 h. (Anesthesiology 2017; 126:909-22)
Risk of Adverse Pregnancy Outcome After Paternal Exposure to Methotrexate Within 90 Days Before Pregnancy
Authors: Eck Lasse Karlsen , Jensen Thomas Bo , Mastrogiannis Dimitrios , Torp-Pedersen Arendse , Askaa Bjarke , Nielsen Torben Kjær , Poulsen Henrik Enghusen , Jimenez-Solem Espen , Andersen Jon Trærup
Published: March 2017

OBJECTIVE:

To study the association between paternal exposure to methotrexate within the 90-day period before pregnancy and congenital malformations and stillbirth in the offspring.

METHODS:

We conducted a nationwide register study. Our cohort consisted of all live births in Denmark between 1997 and 2011 identified from the Medical Birth Registry. Methotrexate-exposed fathers were identified from the National Prescription Registry. From the national Hospital Registry we identified paternity, live births, and stillbirths as well as discharge diagnoses on congenital malformations.

RESULTS:

We identified 849,676 live births with known paternity. There were 127 live births of methotrexate-exposed fathers. Of these, four (3.2%) had major malformations compared with 28,814 (3.4%) of the unexposed. The odds ratio (OR) for major congenital malformation among exposed fathers compared with unexposed was 0.93 (95% confidence interval [CI] 0.34–2.51) and when adjusted for year of birth, maternal age, educational length, household income, and parity, the adjusted OR was 1.01 (95% CI 0.37–2.74). There were no stillbirths in the methotrexate-exposed group compared with 2,541 (0.3%) in the unexposed group and no increased risk of preterm birth (adjusted OR 1.31, 95% CI 0.66–2.59) among the children from exposed fathers.

CONCLUSION:

We found no association between paternal exposure to methotrexate within 90 days before pregnancy and congenital malformations, stillbirths, or preterm birth. Available data suggest that prepregnancy paternal methotrexate exposure should not be of major concern. Multinational recommendations should be changed accordingly.
Executive Summary of the reVITALize Initiative
Authors: Sharp Howard T. , Johnson Julia V. , Lemieux Lauren A. , Currigan Sean M.
Published: March 2017

Effective care coordination across the women's health continuum is critically important. Unlike obstetric care, which tends to be more episodic and limited to pregnant and postpartum women, women receive health care, whether around pregnancy or for nonobstetric issues, in a variety of care settings by members of multiple health disciplines. Having access to standardized clinical data is imperative to providing optimal patient care. The reVITALize Gynecology Data Definitions Initiative leads a national multidisciplinary movement to offer standard gynecologic data definitions for use in written and verbal clinical communication, electronic health record data capture, quality improvement, and clinical research.
Association of Group Prenatal Care With Gestational Weight Gain
Authors: Kominiarek Michelle A. , Crockett Amy , Covington-Kolb Sarah , Simon Melissa , Grobman William A.
Published: March 2017

OBJECTIVE:

To compare gestational weight gain among women in group prenatal care with that of women in individual prenatal care.

METHODS:

In this retrospective cohort study, women who participated in group prenatal care from 2009 to 2015 and whose body mass indexes (BMIs) and gestational weight gain were recorded were matched with the next two women who had the same payer type, were within 2-kg/m2 prepregnancy BMI and 2-week gestational age at delivery, and had received individual prenatal care. Bivariate comparisons of demographics and antenatal complications were performed for women in group and individual prenatal care, and weight gain was categorized as “below,” “met,” or “exceeded” goals according to the 2009 Institute of Medicine guidelines. Logistic regression analysis estimated the association between excessive weight gain and model of care, with adjustment for confounders, stratified by BMI.

RESULTS:

Women in group prenatal care (n=2,117) were younger and more commonly non-Hispanic black, nulliparous, and without gestational diabetes (P≤.005 for all). Women in group prenatal care more commonly exceeded the weight gain goals (55% compared with 48%, P<.001). The differences in gestational weight gain were concentrated among normal-weight (mean 34.2 compared with 32.1 pounds, P<.001; 47% compared with 41% exceeded, P=.008) and overweight women (mean 31.5 compared with 27.1 pounds, P<.001; 69% compared with 54% exceeded, P<.001). When adjusted for age, race–ethnicity, parity, education, and tobacco use, the increased odds for excessive gestational weight gain persisted among normal-weight (odds ratio [OR] 1.28, 95% confidence interval [CI] 1.09–1.51) and overweight (OR 1.84, 95% CI 1.50–2.27) women. Nulliparity was associated with increased excessive gestational weight gain (OR 1.49, 95% CI 1.33–1.68), whereas Hispanic ethnicity was associated with decreased excessive gestational weight gain (OR 0.68, 95% CI 0.59–0.78).

CONCLUSION:

Among normal-weight or overweight women, group prenatal care, compared with individual prenatal care, is associated with excessive gestational weight gain.
Incidence and risk factors of hardware-related complications after proximal femoral osteotomy in children and adolescents
Authors: Chung Myung Ki , Kwon Soon-Sun , Cho Byung Chae , Lee Gye Wang , Kim Jaeyoung , Moon Seung Jun , Lee Jae Woo , Chung Chin Youb , Sung Ki Hyuk , Lee Kyoung Min , Park Moon Seok
Published: March 2017

Proximal femoral osteotomy has been used in cerebral palsy, Perthes disease, hip dysplasia, idiopathic femoral anteversion, and various hip diseases in children and adolescents. Conventionally, a blade plate (BP) has been used. However, the pediatric locking compression plate (LCP) has recently been applied widely. We compared the hardware-related complications of the BP and the LCP as well as the factors influencing these complications in patients who have undergone a proximal femoral osteotomy in children and adolescents. We enrolled consecutive patients aged less than or equal to 20 years who had undergone proximal femoral osteotomy with BP or LCP between May 2003 and December 2014, and who were followed up until 6 months after hardware removal. Following consensus building, hardware-related complications were identified from the patients’ medical records and hip radiographs. Patient age, sex, type of plate, and Gross Motor Function Classification System (GMFCS) level in cerebral palsy patients were evaluated as possible risk factors, and a generalized estimating equation was used to assess the risk factors for hardware-related complications. A total of 417 hips from 251 patients were finally included in this study. Seven losses of fixation around the plate (five patients, 3.0%) occurred in the BP, three implant-related fractures (three patients, 3.6%) occurred in the LCP, and there was no significant difference (P=0.74). All hardware-related complications occurred in cerebral palsy patients, and the implant-related fractures occurred in patients with GMFCS IV/V. The risk of complications increased with age (P=0.002). The risk of loss of fixation around the BP is a well-known complication. However, LCP is not without hardware-related complications. The LCP provides strong stability of fixation. However, it is speculated that the LCP is related to implant-related fractures because of the stress shielding effect. Therefore, care should be exercised when using a locking plate in patients with osteoporosis, such as cerebral palsy with GMFCS IV/V. Level of Evidence: Therapeutic Level III.
The Outcomes of Nonelongating Intramedullary Fixation of the Lower Extremity for Pediatric Osteogenesis Imperfecta Patients: A Meta-analysis
Authors: Scollan Joseph P. , Jauregui Julio J. , Jacobsen Christina M. , Abzug Joshua M.
Published: March 2017

Background:

Osteogenesis imperfecta is usually due to autosomal dominant mutations in type I collagen, leading to an increase in fractures and bone deformities, especially in the long bones of the lower extremities. The use of nonelongating intramedullary rods is an established surgical intervention to address such deformities. The rate of surgical complications has been reported to be as high as 187%, with revision rates as high as 90%, although exact global rates are unknown. As such, we sought to determine the published rates of (1) bone-related complications (including both fracture and deformity), (2) rod migration, and (3) complications that require reoperation.

Methods:

Following the Preferred Reporting Items for Systematic reviews and Meta-analyses (PRISMA) guidelines, 1295 studies were evaluated. After cross-referencing, and applying specific inclusion and exclusion criteria, a total of 7 studies were included in the final cohort. Data were extracted from the studies and analyzed. Random effect models determined the complication rates of intramedullary nonelongating rod procedures.

Results:

A total of 359 primary nonelongating intramedullary rod procedures of tibiae and femurs, in patients with a mean age of 6 years (5.2 to 7.3 y), at a mean follow-up of 63 months (24 to 118 mo), were evaluated. 60% of the surgical procedures were on femurs, and 40% were on tibiae. The reoperation rate was 39.4%. The most common complication was rod migration, with a rate of 25.7%. The rate of bone-related complications was 19.5% including fractures (15.0%) and worsening bone deformity (4.3%).

Conclusions:

This is the first meta-analysis to identify the rates of complication and reoperation in lower limb intramedullary fixation for pediatric osteogenesis imperfecta patients. This study has shown that rod migration is the most common complication, followed by bone-related complications including fractures and deformity. Reoperations occur after nearly 40% of all procedures due to rod migration or bone-related complications.

Level of Evidence:

Level IV—retrospective meta-analysis.
A Comparative Analysis of the Most Common Complications for Patients Undergoing Traumatic Foot and Ankle Surgery
Authors: Hunter Joshua G. , Baumhauer Judith F.
Published: March 2017

Patient safety is protection from adverse outcome through reduction of complications. The purpose of this study is to accurately identify the most common complications after foot and ankle (FA) and traumatic FA surgery and characterize their incidence compared with all other orthopedic procedures. The American Board of Orthopaedic Surgeons (ABOS) database was searched from 2006 to 2010 for all reported orthopedic and FA procedures. The incidence of complications was identified for the following groups: the 10 most common trauma FA procedures, and all FA procedures cumulatively. The incidence of complications for each group were then compared with all other orthopedic procedures reported during that same period. Statistical analysis was performed using a 2-tailed Student t test and χ2 with Yates. A total of 56,786 FA codes and their associated complication(s) were compared with 429,358 orthopedic codes and their complication(s). The 10 most commonly reported trauma FA procedures accounted for 51% of all FA CPT codes and 46.3% of FA complications. Procedures reporting at least 1 complication were significantly higher for all FA codes when compared with all orthopedic procedures, 13.7% versus 9.2% (P=0.001). The most commonly performed trauma FA procedures had a higher complication rate of 13.5% versus 9.2% (P=0.001). Overall, soft tissue complications (infection, wound dehiscence, and skin ulcer/blister) were each reported significantly more in all FA and trauma FA when compared with other orthopedic procedures (P<0.001). Comprehensive databases, such as the ABOS oral examination case list, can be a valuable tool to direct current practice improvement initiatives and improving patient care. All FA and trauma FA procedures are associated with a higher incidence of complications when compared with all orthopedic surgeries, particularly infection, wound dehiscence, and blistering.

Levels of Evidence: Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.
New developments in the management of nonmuscle invasive bladder cancer
Authors: Tyson Mark D. , Lee Daniel , Clark Peter
Published: March 2017

Purpose of review

In this review, we summarize the core principles in the management of nonmuscle invasive bladder cancer (NMIBC) with an emphasis on new developments that have emerged over the last year.

Recent findings

NMIBC has a propensity to recur and progress. Risk stratification has facilitated appropriate patient selection for treatment but improved tools, including biomarkers, are still needed. Enhanced cystoscopy with photodynamic imaging and narrow band imaging show promise for diagnosis, risk stratification, and disease monitoring and has been formally recommended this year by the American Urological Association. Attempts at better treatment, especially in refractory high-risk cases, include the addition of intravesical hyperthermia, combination and sequential therapy with existing agents, and the use of novel agents such as mycobacterial cell wall extract. New data are emerging regarding the potential role of early cystectomy in bacillus Calmette–Guerin-refractory NMIBC patients.

NMIBC represents an assortment of disease states and continues to pose management challenges. Continued research is needed to bolster the evidence needed for patients and providers to make data-driven treatment decisions.
New developments in the biology and the treatment of metastatic Merkel cell carcinoma
Authors: Terheyden Patrick , Becker Jürgen C.
Published: March 2017

Purpose of review

Patients with stage IIIB und IV metastatic Merkel cell carcinoma (mMCC), who are not suitable candidates for surgery or radiotherapy, are unlikely to achieve lasting remission or tumor control by chemo or targeted therapy. In the majority of cases, the tumor arises from viral carcinogenesis associated with the Merkel cell polyomavirus (MCPyV). In MCPyV-negative tumors with a presumable ultraviolet carcinogenesis, a high mutational burden resulting in neoantigens was discovered. In two phase II clinical trials in either the first or second-line setting, a high response rate was observed for immunotherapies with antibodies blocking the programmed death-1 (PD-1) and programmed death ligand-1 (PD-L1) immune checkpoints.

Recent findings

The response rate was 56% with the anti-PD-1 inhibitor pembrolizumab as a first-line and 32% with the anti-PD-L1 antibody avelumab used as second-line therapy. Both treatments were well tolerated. Treatment response was rapid and in most cases maintained during follow-up, which, however, is still rather short. Whether the MCPyV or the PD-L1 status is predictive for treatment response and progression-free survival is still ambiguous. Additionally, clinical criteria for patient selection for immunotherapy of mMCC have not yet been defined.

PD-1/PD-L1 inhibition can be regarded as new first-line therapy for patients with mMCC not amendable by surgery and/or radiation.
BRCA1/2 germline missense mutations: a systematic review
Authors: Corso Giovanni , Feroce Irene , Intra Mattia , Toesca Antonio , Magnoni Francesca , Sargenti Manuela , Naninato Paola , Caldarella Pietro , Pagani Gianmatteo , Vento Annarita , Veronesi Paolo , Bonanni Bernardo , Galimberti Viviana
Published: March 2017

Hereditary breast and ovarian cancer is an inherited syndrome associated with BRCA1/2 germline defects. The identified mutations are classified as missense, large deletion, insertion, nonsense and splice-site variants with a deleterious impact on BRCA1/2 function. Part of these forms the well-documented truncating mutations, and missense variants represent a clinical dilemma as the pathogenic role is yet to be clearly shown. In this systematic review, we collected these missense variations with a documented deleterious function. We focused on English language articles from MEDLINE. This study included all BRCA1/2 germline missense mutations identified in breast and ovarian cancer patients. The method of this study followed the ‘PRISMA statement for reporting systematic reviews and meta-analyses’. A total of 61 BRCA1/2 germline and pathogenic missense mutations were identified: 70.5% affected BRCA1 and 29.5% BRCA2, respectively. In BRCA1, the majority of mutations were located in the BRCA C-terminus (48.8%), leading to a disruption of function. Conversely, no specific associations were verified between mutations and the BRCA2 gene. The European population was the most affected by BRCA1 and the Asian population by BRCA2 mutant patterns. The identification of novel BRCA1/2 missense mutations requires specific genetic tests to assess pathogenicity. With this systematic review, we are, to the best of our knowledge, the first to collect the overall amount of data on these pathogenic mutants with the aim of improving the management of carriers and their kindred.
Gene-to-gene interactions regulate endogenous pain modulation in fibromyalgia patients and healthy controls—antagonistic effects between opioid and serotonin-related genes
Authors: Tour Jeanette , Löfgren Monika , Mannerkorpi Kaisa , Gerdle Björn , Larsson Anette , Palstam Annie , Bileviciute-Ljungar Indre , Bjersing Jan , Martin Ingvar , Ernberg Malin , Schalling Martin , Kosek Eva
Published: March 2017

Chronic pain is associated with dysfunctional endogenous pain modulation, involving both central opioid and serotonergic (5-HT) signaling. Fibromyalgia (FM) is a chronic pain syndrome, characterized by widespread musculoskeletal pain and reduced exercise-induced hypoalgesia (EIH). In this study, we assessed the effects of 3 functional genetic polymorphisms on EIH in 130 patients with FM and 132 healthy controls. Subjects were genotyped regarding the mu-opioid receptor (OPRM1) gene (rs1799971), the serotonin transporter (5-HTT) gene (5-HTTLPR/rs25531), and the serotonin-1a receptor (5-HT1a) gene (rs6296). The patients with FM had increased pain sensitivity and reduced EIH compared with healthy controls. None of the polymorphisms had an effect on EIH on their own. We found significant gene-to-gene interactions between OPRM1 x 5-HTT and OPRM1 x 5-HT1a regarding activation of EIH, with no statistically significant difference between groups. Better EIH was found in individuals with genetically inferred strong endogenous opioid signaling (OPRM1 G) in combination with weak 5-HT tone (5-HTT low/5-HT1a G), compared with strong 5-HT tone (5-HTT high/5-HT1a CC). Based on the proposed mechanisms of these genetic variants, the findings indicate antagonistic interactions between opioid and serotonergic mechanisms during EIH. Moreover, despite different baseline pain level, similar results were detected in FM and controls, not supporting an altered interaction between opioid and 5-HT mechanisms as the basis for dysfunction of EIH in patients with FM. In summary, our results suggest that, by genetic association, the mu-opioid receptor interacts with 2 major serotonergic structures involved in 5-HT reuptake and release, to modulate EIH.
Exploring the Strengths of Patients With Psychiatric Disorders: A Qualitative Study
Authors: Maghsoudi Jahangir , Oreyzi HamidReza , Zargham-Boroujeni Ali
Published: March 2017

Background:

Professional nurses typically pay significantly more attention to the weaknesses rather than strengths of their psychiatric patients. Thus, new approaches to care are needed to discover the strengths of these patients and to provide effective encouragement during the caring process. However, little is currently known regarding the strengths that psychiatric patients possess during their illness and healing.

Purpose:

The current study aimed to explore the self-perceptions and experiences of psychiatric patients regarding their strengths.

Methods:

Psychiatric patients were recruited through purposive sampling in Isfahan, Iran, from July to December 2012. Variables such as age, gender, and diagnosis were used to vet potential participants to ensure adequate sample diversity. All of the qualified individuals were informed verbally and in writing regarding the information that they would be asked to provide during the interview process, and the researchers obtained written and oral informed consent from each before enrolment. Twenty-one semistructured, qualitative interviews were conducted, and content analysis was performed to identify the themes.

Results:

Four major themes emerged from the interviews, including (a) life with spiritual factors, (b) responsibility, (c) love of learning, and (d) sources of support.

Conclusions:

A repertoire of strengths was identified among the participants. Furthermore, all of the participants voiced the opinion that healthcare providers rarely focused on their strengths. Therefore, mental health professionals, particularly nurses, should pay closer attention to the strengths of their psychiatric patients to use these strengths in advancing their care.
Clinical dilemmas in the management of transgender men
Authors: Irwig Michael S.
Published: March 2017

Purpose of review

To explore the medical and surgical clinical dilemmas in the management of trans (transgender) men, a growing population receiving more attention than in the past.

Recent findings

Testosterone therapy is commonly prescribed to trans men for masculinization. Nonetheless, the optimal formulations and doses of testosterone therapy for trans men have not been well established. Testosterone therapy has been associated with increased levels of hemoglobin and triglycerides, as well as diabetes. Periodic monitoring of hemoglobin, cholesterol, and fasting glucose is therefore recommended. As compared to non-transgender women, trans men have lower age-specific rates of breast cancer and cervical cancer which can be attributed, in part, to surgeries such as bilateral mastectomies and hysterectomies. The frequency in which to recommend mammograms and Pap smears (in patients with intact cervices) is uncertain in this population because of a lack of evidence-based data. Many trans men desire and undergo bilateral mastectomies with much fewer undergoing metoidioplasty or phalloplasty.

For trans men, most clinicians target serum testosterone concentrations in the normal male reference range. The frequency of screening for breast and cervical cancer should be individualized based upon anatomy, patient age, age of initiation of testosterone therapy, and other factors.
Voice and swallowing outcomes for adults undergoing reconstructive surgery for laryngotracheal stenosis
Authors: Clunie Gemma M. , Kinshuck Andrew J. , Sandhu Gurpreet S. , Roe Justin W.G.
Published: March 2017

Purpose of review

Adult laryngotracheal stenosis is a rare, multifactorial condition which carries a significant physical and psychosocial burden. Surgical approaches have developed in recent years, however, voice and swallowing function can be affected prior to treatment, in the immediate postoperative phase, and as an ongoing consequence of the condition and surgical intervention. In this study we discuss: the nature of the problem; surgical interventions to address airway disorders; optimal patterns of care to maximize voice and swallowing outcomes.

Recent findings

Studies in this field are limited and focused on surgical outcomes and airway status with voice and swallowing a secondary consideration. Retrospective studies of swallowing have focused on factors such as the duration of dysphagia symptoms following airway surgery and made comparisons between type of surgery, use of stent, and length of swallowing problems. The literature suggests that patients are likely to return to their preoperative diet. There has been a focus on voice outcomes following cricotracheal resection which results in a postoperative decrease in the fundamental frequency. However, study comparisons are limited by the use of inconsistent outcome measures (for both voice and swallowing) which are often not validated, with heterogeneous groups and varying surgical techniques.

The limited literature suggests that swallowing function is more likely to recover to presurgical status than voice function. Further prospective studies incorporating consistent instrumental, clinician, and patient-reported outcome measurement are required to understand the nature and extent of dysphagia and dysphonia resulting from this condition and its treatment.
Voice outcomes for early laryngeal cancer
Authors: Kinshuck Andrew J. , Shenoy Aditya , Jones Terry M.
Published: March 2017

Purpose of review

Treatment options for early laryngeal cancer are well established with good local control and 5-year survival. The commonest treatments are radiotherapy or transoral laser microsurgery (TLM). There are advantages and disadvantages of the different modalities, but debate continues regarding the voice outcomes posttreatment. This review will focus on early glottic carcinoma and voice outcomes following the different treatments.

Recent findings

TLM and radiotherapy are both likely to affect voice quality, but the extent of voice change depends on different factors. These factors can be divided into patient, tumour and treatment factors. Recent meta-analyses data show similar voice outcomes for either modality in the treatment of early glottic carcinoma. However, larger tumours and those involving the anterior commissure are associated with worse voice outcomes.

There are various considerations for the patient and clinician before deciding on the preferred treatment for early glottic carcinoma. Although both TLM and radiotherapy will affect voice outcomes, the recent meta-analyses show similar voice outcomes for either modality in the treatment of early glottic carcinoma. There are numerous variables in the published studies hindering direct comparisons. These include heterogeneous patient groups, different treatment standardization and methods of voice analysis.
HPV L1 and P16 Expression in CIN1 to Predict Future CIN2+
Authors: Liu Chong , Du Hui , Wang Chun , Belinson Jerome L. , Yang Bin , Zhang Wei , Tang Jinlong , Wu Ruifang
Published: March 2017

The goal of this study was to use the biomarkers human papillomavirus (HPV) L1 and p16 to develop an algorithm that could triage the individual patient with CIN1 at risk for progression. A total of 82 patients initially diagnosed with CIN1 at Peking University Shenzhen Hospital in China had their initial and follow-up paraffin-embedded tissue blocks immune-stained for HPV L1 capsid protein and p16. For CIN1, any staining of abnormal epithelium was considered positive. All patients were followed until they developed CIN2+ or for ≥3 years. About 38 patients regressed (HPV−, Cytology−), 17 persisted (CIN1), and 27 progressed (≥CIN2+). At initial diagnosis, HPV L1 capsid protein was expressed in 42.7% of the CIN1 cases. There was no difference in L1 expression among the 3 groups. However, p16-positive staining in the progression group was significantly higher than in the regression group (P<0.05). In the regression group, the proportion of HPV L1−/p16− category was significantly higher than that in the progression group. In the progression group, when CIN1 lesions progressed to CIN2+, the L1-positive rate was significantly decreased from 51.9% to 18.5%, the p16+/HPV L1+ rate decreased from the initial (44.4%) to the final diagnosis (14.8%), and the p16+/HPV L1− rate increased from the initial (25.9%) to the final diagnosis (66.7%). P16 expression is a clear risk factor for the progression of CIN1. The p16−/HPV L1− pattern was significantly associated with the regression of CIN1. Moving from CIN1 to CIN2+ over time, p16+/HPV L1+ decreased, and p16+/HPV L1− increased. Unfortunately, our objective of finding a sensitive and specific triage algorithm for the individual patient with CIN1 was not achieved.
Randomized Controlled Trial of an Intervention to Maintain Suppression of HIV Viremia After Prison Release: The imPACT Trial
Authors: Wohl David A. , Golin Carol E. , Knight Kevin , Gould Michele , Carda-Auten Jessica , Groves Jennifer S. , Napravnik Sonia , Cole Stephen R. , White Becky L. , Fogel Cathie , Rosen David L. , Mugavaro Michael J. , Pence Brian W. , Flynn Patrick M.
Published: March 2017

Background:

HIV-infected individuals transitioning from incarceration to the community are at risk for loss of viral suppression. We compared the effects of imPACT, a multidimensional intervention to promote care engagement after release, to standard care on sustaining viral suppression after community re-entry.

Methods:

This trial randomized 405 HIV-infected inmates being released from prisons in Texas and North Carolina with HIV-1 RNA levels <400 copies/mL to imPACT versus standard care. The imPACT arm received motivational interviewing prerelease and postrelease, referral to care within 5 days of release, and a cellphone for medication text reminders. The standard care arm received routine discharge planning and a cellphone for study staff contact. The primary outcome was the difference between arms in week 24 postrelease viral suppression (HIV-1 RNA <50 copies/mL) using intention-to-treat analysis with multiple imputation of missing data.

Results:

The proportion with 24-week HIV-1 RNA <50 copies/mL was 60% and 61% in the imPACT and standard care arms, respectively [odds ratio for suppression 0.95 (95% confidence interval: 0.59 to 1.53)]. By week 6 postrelease, 86% in the imPACT arm versus 75% in the standard care arm attended at least 1 nonemergency clinic visit (P = 0.02). At week 24, 62% in both arms reported not missing any antiretroviral doses in the past 30 days (P > 0.99).

Conclusions:

Higher rates of HIV suppression and medical care engagement than expected based on previous literature were observed among HIV-infected patients with suppressed viremia released from prison. Randomization to a comprehensive intervention to motivate and facilitate HIV care access after prison release did not prevent loss of viral suppression. A better understanding of the factors influencing prison releasees' linkage to community care, medication adherence, and maintenance of viral suppression is needed to inform policy and other strategic approaches to HIV prevention and treatment.
Endoscopic Sphincterotomy for Gallbladder Muddy Stones or Sludge in Patients With Papillary Disease: A Retrospective Study
Authors: Zhang Cheng , Yang Yu-long , Ma Yue-feng , Zhang Hong-wei , Shi Li-jun , Li Jing-yi , Lin Mei-ju , Qi Chun-chun
Published: March 2017

Background:

The formation of gallbladder stones is associated with dysfunctional contraction and duodenal papilla diseases. However, endoscopic sphincterotomy can improve the contraction of the gallbladder and resolve duodenal papilla disease.

Aim:

The aim of the study was to assess the feasibility and effectiveness of endoscopic sphincterotomy in the treatment of muddy stones or sludge in the gallbladder during papillary disease.

Methods:

The clinical data of 53 patients with gallbladder muddy stones or sludge undergoing endoscopic sphincterotomy were retrospectively analyzed.

Results:

A total of 53 patients received successful endoscopic sphincterotomy with no serious complications. Sphincterotomy did not significantly lower resting gallbladder volume from 63.2±10.8 to 50.1±5.9 mL (P>0.05), but significantly increased gallbladder ejection fraction from 0.41±0.13 to 0.63±0.16 (P<0.01), as measured by the lipoid food test. The static liver and gallbladder imaging examination also showed an increase in gallbladder ejection fraction from 0.45±0.08 to 0.68±0.11 (P<0.01). In addition, the choledochus pressure reduced from 21.9±4.0 to 15.6±2.5 mm Hg, and the gallbladder muddy stones or sludge disappeared after endoscopic sphincterotomy. At the end of the follow-up period, there was no relapse of sludge or muddy stones in the gallbladder.

Conclusions:

The formation of gallbladder muddy stones or sludge is associated with papilla disease. Endoscopic sphincterotomy can resolve papilla disease, decrease gallbladder bile stasis, improve gallbladder evacuation, and prevent the formation of gallbladder stones.
Patient-Reported Impact of Pelvic Organ Prolapse on Continence and Sexual Function in Women With Exstrophy-Epispadias Complex
Authors: Everett Ross G. , Lue Kathy M. , Reddy Sunil S. , Friedlander Daniel A. , Alexander Cameron E. , Young Ezekiel E. , Abdelwahab Mahmoud , Gandhi Nilay M. , Wright Edward J. , Gearhart John P.
Published: March 2017

Objective

This study aimed to characterize long-term urogynecologic issues of women with a history of bladder exstrophy and pelvic organ prolapse (POP) and to assess the impact of POP repair on continence and sexual function.

Design

Patient demographics and surgical history related to exstrophy and POP were collected through chart review. Patient perceptions regarding sexual function, urinary continence, and quality of life were assessed through Web-based administration of validated questionnaires: International Consultation on Incontinence Questionnaire-Urinary Incontinence Short Form and POP-Urinary Incontinence Sexual Questionnaire.

Setting

Maryland, United States.

Participants

Review of a single-institution exstrophy-epispadias complex database resulted in 25 adult female patients with a history of POP treated at the authors' institution. Eleven patients participated and were included in the analysis.

Main Outcome Measures

Urinary continence and sexual function.

Results

All participants underwent surgical repair for prolapse, with 7 (63.6%) experiencing unsuccessful initial repair and subsequent recurrence. Median total number of POP repairs was 2.5 (1–4). After correction of POP, patients reported a median improvement in International Consultation on Incontinence Questionnaire-Urinary Incontinence Short Form scores of 11 (21 to −1) of 21 and in POP-Urinary Incontinence Sexual Questionnaire scores of 9.5 (6.5–33.0) of 48.0. With regard to urinary continence, 6 (54.5%) patients presently reported no incontinence, 3 (27.3%) reported mild incontinence, and 2 (18.2%) reported continuous incontinence.

Conclusions

Pelvic organ prolapse poses significant reductions in quality of life for women born with exstrophy, with effects on urinary continence and sexual function. Identification and correction of prolapse seems to result in notable improvements in the lives of these patients.
Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes
Authors: Kothari Ankita , Wu Yu-Wei , Charrier Marimikel , Rajeev Lara , Rocha Andrea M. , Paradis Charles J. , Hazen Terry C. , Singer Steven W. , Mukhopadhyay Aindrila
Published: March 2017

Native plasmids constitute a major category of extrachromosomal DNA elements responsible for harboring and transferring genes important in survival and fitness. A focused evaluation of plasmidomes can reveal unique adaptations required by microbial communities. We examined the plasmid DNA from two pristine wells at the Oak Ridge Field Research Center. Using a cultivation-free method that targets plasmid DNA, a total of 42,440 and 32,232 (including 67 and 548 complete circular units) scaffolds > 2 kb were obtained from the two wells. The taxonomic distribution of bacteria in the two wells showed greater similarity based on their plasmidome sequence, relative to 16S rRNA sequence comparison. This similarity is also evident in the plasmid encoded functional genes. Among functionally annotated genes, candidates providing resistance to copper, zinc, cadmium, arsenic, and mercury were particularly abundant and common to the plasmidome of both wells. The primary function encoded by the most abundant circularized plasmid, common to both wells, was mercury resistance, even though the current ground water does not contain detectable levels of mercury. This study reveals that the plasmidome can have a unique ecological role in maintaining the latent capacity of a microbiome enabling rapid adaptation to environmental stresses.
Affinity-mass spectrometric technologies for quantitative proteomics in biological fluids
Authors: Li Huiyan , Popp Robert , Borchers Christoph H.
Published: March 2017

Proteins are the functional molecules in organisms and are therefore excellent biomarker candidates for a diversity of diseases. Immunoassays and mass spectrometry (MS) are two major technologies being used in proteomics; however, they either lack specificity or sensitivity. An emerging trend is to combine immunoassays with MS (which we call “affinity-MS”). This is an important milestone in quantitative proteomics, making it possible to measure low-abundance proteins with high specificity. The targeted enrichment and the assignment of mass-to-charge ratios to different molecules provide two selection criteria, making affinity-MS highly specific. Picogram-per-milliliter limits of detection have been obtained for many proteins. Furthermore, multiplexing capacity of >150 proteins has been achieved. This article reviews different formats of affinity-enrichment methods, and demonstrates how they are interfaced with both electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) MS. The pros and cons of these techniques are compared, and future prospectives are discussed.
Application of t-SNE to Human Genetic Data
Authors: Li Wentian , Cerise Jane E , Yang Yaning , Han Henry
Published: March 2017

The t-SNE (t-distributed stochastic neighbor embedding) is a new dimension reduction and visualization technique for high-dimensional data. t-SNE is rarely applied to human genetic data, even though it is commonly used in other data-intensive biological fields, such as single-cell genomics. We explore the applicability of t-SNE to human genetic data and make these observations: (i) similar to previously used dimension reduction techniques such as principal component analysis (PCA), t-SNE is able to separate samples from different continents; (ii) unlike PCA, t-SNE is more robust with respect to the presence of outliers; (iii) t-SNE is able to display both continental and sub-continental patterns in a single plot. We conclude that the ability for t-SNE to reveal population stratification at different scales could be useful for human genetic association studies.
Extensive hidden genetic variation shapes the structure of functional elements in Drosophila
Authors: Chakraborty Mahul , Zhao Roy , Zhang Xinwen , Kalsow Shannon , Emerson J.J.
Published: March 2017

Mutations that add, subtract, rearrange, or otherwise refashion genome structure often affect phenotypes, though the fragmented nature of most contemporary assemblies obscure them. To discover such mutations, we assembled the first reference quality genome of Drosophila melanogaster since its initial sequencing. By comparing this genome to the existing D. melanogaster assembly, we create a structural variant map of unprecedented resolution, revealing extensive genetic variation that has remained hidden until now. Many of these variants constitute strong candidates underlying phenotypic variation, including tandem duplications and a transposable element insertion that dramatically amplifies the expression of detoxification genes associated with nicotine resistance. The abundance of important genetic variation that still evades discovery highlights how crucial high quality references are to deciphering phenotypes.
So many genes, so little time: a practical approach to divergence-time estimation in the genomic era
Authors: Smith Stephen A. , Brown Joseph W. , Walker Joseph F.
Published: March 2017

Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. “Gene shopping”, wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available inSortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-specification are minimized, therefore reducing error in divergence-time estimation. We demonstrated the efficacy of this approach through simulation and applied it to published animal (Aves, Diplopoda, and Hymenoptera) and plant (carnivorous Caryophyllales, broad Caryophyllales, and Vitales) phylogenomic datasets. By quantifying rate heterogeneity across both genes and lineages we found that every empirical dataset examined included genes with clock-like, or nearly clock-like, behavior. Moreover, many datasets had genes that were clock-like, exhibited reasonable evolutionary rates, and were mostly compatible with the species tree. We identified overlap in age estimates when analyzing these filtered genes under strict clock and uncorrelated lognormal (UCLN) models. However, this overlap was often due to imprecise estimates from the UCLN model. We find that “gene shopping” can be an efficient approach to divergence-time inference for phylogenomic datasets that may otherwise be characterized by extensive gene tree heterogeneity.
Tagger: BeCalm API for rapid named entity recognition
Authors: Jensen Lars Juhl
Published: March 2017

Most BioCreative tasks to date have focused on assessing the quality of text-mining annotations in terms of precision of recall. Interoperability, speed, and stability are, however, other important factors to consider for practical applications of text mining. The new BioCreative/BeCalm TIPS task focuses purely on these. To participate in this task, I implemented a BeCalm API within the real-time tagging server also used by the Reflect and EXTRACT tools. In addition to retrieval of patent abstracts, PubMed abstracts, and Pub-Med Central open-access articles as required in the TIPS task, the BeCalm API implementation facilitates retrieval of documents from other sources specified as custom request parameters. As in earlier tests, the tagger proved to be both highly efficient and stable, being able to consistently process requests of 5000 abstracts in less than half a minute including retrieval of the document text.
How ecosystems recover from pulse perturbations: A theory of short- to long-term responses
Authors: Arnoldi J.-F. , Bideault A. , Loreau M. , Haegeman B.
Published: March 2017

Quantifying stability properties of ecosystems is an important problem in ecology. A common approach is based on the recovery from pulse perturbations, and posits that the faster ecosystems return to their pre-perturbation state, the more stable they are. In theoretical studies the recovery dynamics are often collapsed into a single quantity: the long-term rate of return, called asymptotic resilience. However, empirical studies typically measure the recovery dynamics at much shorter time scales. In this paper we explain why asymptotic resilience is rarely representative of the short-term recovery. First, we show that, in contrast to asymptotic resilience, short-term return rates depend on features of the perturbation, in particular on the way its intensity is distributed over species. We argue that empirically relevant predictions can be obtained by considering the median response over a set of perturbations, for which we provide explicit formulas. Next, we show that the recovery dynamics are controlled through time by different species: abundant species tend to govern the short-term recovery, while rare species often dominate the long-term recovery. This shift from abundant to rare species typically causes short-term return rates to be unrelated to asymptotic resilience. Finally, we discuss how these findings might help to better connect empirical observations and theoretical predictions.