bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Qualitative Study of the Contraceptive Effect on Women's Sexual Experiences
Authors: Lu Connie F. , Vargas Sara E. , Guillen Melissa , Ramirez Jaime J. , Carbone Sofia L. , Getz Melissa L. , Frimpong Yaa , Smith Kelley Alison , Shaw Julia G. , Tong Iris , Hill Melanie , Berry Robert E. , Guthrie Kate M. 
Published: June 2019

OBJECTIVE:
To elucidate the effects of the intravaginal ring, oral contraceptive pill (OCP), and spermicide plus condom on women's sexual experiences through an in-depth understanding of the physical characteristics of these contraceptive methods.

METHODS:
We conducted qualitative in-depth interviews with women (aged 18–45 years) who used up to three contraceptive methods (intravaginal ring, OCP, and spermicide plus condom). Women completed in-depth interviews after each 3-month use period. We used a summarized matrix framework and thematic content analysis to explore how each method affected participants' sexual experiences.

RESULTS:
Sixteen women completed interviews, yielding 33 transcripts. Women reported physical effects on their sexual experiences while using the intravaginal ring and spermicide plus condom. The OCP was often discussed as lacking these physical effects. Discussion themes included product administration (eg, navigating intravaginal ring removal) and physical product awareness (eg, spermicide as a lubricant). From these experiences, women often altered and individualized their use and subsequent opinions of the contraceptive method.

CONCLUSION:
The range of contraceptive effects on women's sexual experiences shape their use and opinions of the product, leading to either increased motivation and consistent use or poor adherence and discontinuation. Awareness of these individualized experiences can help providers better understand and guide their patients towards successful contraceptive use.
A Novel Porcine Stomach Tissue Model for Laparoscopic Colpotomy Simulation
Authors: Cho Maureen , Ulrich Amanda , Lam Clarissa , Lerner Veronica 
Published: June 2019

BACKGROUND:
Hysterectomies are the most common benign gynecologic surgical procedures performed in the United States. Currently, there are no tissue models that exist to teach trainees the techniques for colpotomy during laparoscopic hysterectomy. To address this educational gap, we have created a laparoscopic colpotomy model using a porcine stomach attached to a uterine manipulator.

METHODS:
A segment of a porcine stomach is secured onto a uterine manipulator to simulate the cervicovaginal junction. A uterus model created with craft materials and reused in subsequent sessions is placed above the porcine stomach onto the uterine manipulator tip. Porcine stomach was obtained from a local butcher or meat market costing less than $1.00 per model. The tissue can be refrigerated or frozen for storage, then thawed before each use. This model can be used with any energy device and any laparoscopic platform to teach and perform the colpotomy. Usability survey showed that trainees responded positively to the model and attendings thought it was a useful teaching tool.

EXPERIENCE:
Trainees and faculty responded favorably to the model and stated that the use of actual tissue enhanced the realism of a colpotomy simulation.

CONCLUSION:
The porcine stomach laparoscopic colpotomy model is an innovative, low-cost teaching tool to add to a gynecologic surgical education simulation toolkit.
Incidence of Knee Pain Beyond 1 Year: Suprapatellar Versus Infrapatellar Approach for Intramedullary Nailing of the Tibia
Authors: Isaac Marckenley , O'Toole Robert V. , Udogwu Ugo , Connelly Daniel , Baker Mitchell , Lebrun Christopher T. , Manson Theodore T. , Zomar Mauri , O'Hara Nathan N. , Slobogean Gerard P. 
Published: June 2019

Objective:
To compare the magnitude of knee pain between the suprapatellar (SP) and infrapatellar (IP) approach for tibial nailing in patients who are more than 1 year after injury.

Design:
Retrospective cohort study.

Setting:
Academic Level I trauma center.

Patients/Participants:
All tibia fracture patients 18-80 years of age treated with an intramedullary tibial nail during a 5-year period were retrospectively reviewed for inclusion. The surgical approach was determined by surgeon preference, with 3 of the 9 surgeons routinely using the SP approach. The primary outcome was knee pain during kneeling, with secondary assessments comparing knee pain during resting, walking, and the past 24 hours.

Intervention:
Intramedullary nailing of a tibia fracture with either the SP or IP approach.

Main Outcome Measurements:
Knee pain assessed with the Numeric Rating Scale between 0 and 10. A difference of >1.0 was considered to be clinically meaningful.

Results:
The study group consisted of 262 patients (SP, n = 91; IP, n = 171) with a mean age of 41.4 years (SD = 16.6). The median follow-up was 3.8 years (range: 1.5–7.0). No difference in knee pain during kneeling was detected between the surgical approaches (IP: 3.9, SP 3.8; P = 0.90; mean difference: −0.06, 95% confidence interval, −1 to 0.9). Similarly, no differences were detected in average knee pain scores at rest (IP: 2.0, SP: 2.0; P = 1.00), walking (IP: 2.7, SP 3.0; P = 0.51), or the last 24 hours (IP: 2.6, SP 2.9; P = 0.45).

Conclusions:
In contrast to a study conducted by Sun et al, in which there was a statistical difference in knee pain between the SP and IP surgical approaches, we did not detect any statistical or clinical differences in knee pain between the SP and IP surgical approaches among patients with greater than 12 months of follow-up.

Level of Evidence:
Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Risk Factors for Fistula Development Following Palatoplasty
Authors: Aldaghir Osamah Mohammed , AlQuisi Ahmed Fadhel , Aljumaily Hassanien A. 
Published: June 2019

Purpose:
The aim of this study is to assess the influence of some risks factors on the fistula development after palatoplasty to improve the outcome of the patients

Patients and Methods:
A total of 48 patients (the males were 22, The females were 26) were included in this study. All the patients were examined weekly for the first month postoperatively to assess any breakdown in the wound by inspection and by asking the parents for any nasal regurgitation during fluids feeding.

Results:
The incidence of palatal fistula development after primary palatoplasty in this study was 12.5% (6\48). Occurrence of fistula was unrelated to the gender (P >0.5), but it was directly related to the age of patients (r = 0.98) and to the size of the cleft (r = 1). Fistula had occurred most likely in cases of Baradach 2 flap palatoplasty (83.3%) this was occurred especially when it was used for isolated cleft palate, but it was not associated with the type of the cleft (P >0.4). The surgeons experience and the use of prophylactic antibiotic were associated with the development of the fistula (P = 0.01 for both).

Conclusion:
knowledge of the expected risk factors for fistula after different protocols of palatoplasty can improve the experience of the surgeon and improve the outcome on the patients.
The Familial Rhino Tooth: Two Mesiodentes
Authors: Sadeghzadeh-Araghi Ariyan , Vassiliou Leandros 
Published: June 2019

Abstract
The authors herein report on 2 cases of patients who had supernumerary teeth. The 2 cases outline how 1 was managed sub-optimally and other managed efficiently. The patients were direct relatives with a very similar clinical problem. This case report explores the genetic relevance of mesiodentes. This case report aims to outline the importance in examination, diagnosis and surgical removal of supernumerary teeth. It also describes several lessons that all members of the dental and wider surgical team can learn from, with regards to supernumerary teeth and more specifically mesiodentes.
Frequency and Implications of Paratracheal Lymph Node Metastases in Resectable Esophageal or Gastroesophageal Junction Adenocarcinoma
Authors: Harada Kazuto , Hwang Hyunsoo , Wang Xuemei , Abdelhakeem Ahmed , Iwatsuki Masaaki , Blum Murphy Mariela A. , Maru Dipen M. , Weston Brian , Lee Jeffrey H. , Rogers Jane E. , Thomas Irene , Shanbhag Namita , Zhao Meina , Bhutani Manoop S. , Nguyen Quynh-Nhu , Swisher Stephen G. , Ikoma Naruhiko , Badgwell Brian D. , Hofstetter Wayne L. , Ajani Jaffer A. 
Published: June 2019

Objective:
We aimed to evaluate the frequency of paratracheal lymph nodes (LN) metastases and their prognostic influence.

Summary Background Data:
Paratracheal LNs are considered regional nodes in the esophageal cancer classification, but their metastatic rate and influence on survival remain unclear.

Methods:
One thousand one hundred ninety-nine patients with resectable esophageal or gastroesophageal junction adenocarcinoma (EAC) (January 2002 and December 2016) in our Gastrointestinal Medical Oncology Database were analyzed. Paratracheal LNs were defined as1R, 1L, 2R, 2L, 4R, and 4L, according to the 8th American Joint Committee on Cancer classification.

Results:
Of 1199 patients, 73 (6.1%) had positive paratracheal LNs at diagnosis. The median overall survival (OS) of 73 patients with initial paratracheal LN involvement was 2.10 years (range 0.01–10.1, 5-yrs OS 24.2%). Of 1071 patients who were eligible for recurrence evaluation, 70 patients (6.5%) developed paratracheal LN metastases as the first recurrence. The median time to recurrence was 1.28 years (range 0.28–5.96 yrs) and the median OS following recurrence was only 0.95 year (range 0.03–7.88). OS in 35 patients who had only paratracheal LN recurrence was significantly longer than in patients who had other recurrences (median OS 2.26 vs 0.51 yrs, 5-yrs OS; 26.8% vs 0%, P < 0.0001). Higher T stage (T3/T4) was an independently risk factor for paratracheal LN recurrence (odds ratio 5.10, 95% confidence interval 1.46–17.89). We segregated patients in 3 groups based on the distance of tumor's proximal edge to esophagogastric junction (low; ≤2 cm, medium; 2.0–7.0 cm, and high; >7.0 cm). Paratracheal LN metastases were more frequent with the proximal tumors (low, 4.2%; medium, 12.0%; high, 30.3%; Cochran–Armitage Trend test, P < 0.001).

Conclusion:
Paratracheal LN metastases were associated with a shorter survival in resectable EAC patients. Alternate approaches to prolong survival of this group of patients are warranted.
Driver Gene Mutations and Epigenetics in Colorectal Cancer
Authors: Raskov Hans , Søby Jacob H. , Troelsen Jesper , Bojesen Rasmus D. , Gögenur Ismail 
Published: June 2019

Objective:
The majority of patients with colorectal cancer are diagnosed with locally advanced and/or disseminated disease, and treatment options include surgery in combination with cytotoxic chemotherapy regimens, biologics, and/or radiotherapy. Thus, colorectal cancer remains a heavy burden on society and health care systems.
Mounting evidence show that driver gene mutations play only part of the role in carcinogenesis. Epigenetics are strongly implicated in initiation and progression of colorectal cancer along with major players such as intestinal microbiotic dysbiosis and chronic mucosal inflammation.
To assess phenotypic changes in proteins and gene expression, multigene expression signatures based on sequencing techniques have been developed to hopefully improve predictors of the tumor profile, immune response, and therapeutic outcomes. Our objective was to review current advances in the field and to update surgeons and academics on driver gene mutations and epigenetics in colorectal cancer.

Background and methods:
This is a narrative review studying relevant research published in the PUBMED database from 2012–2018.

Results and conclusion:
Increased understanding of the molecular biology will improve options to characterize colorectal cancer with regard to mutations and molecular pathways, including microsatellite instability, epigenetics, microbiota, and microenvironment. Research will inevitably improve risk group stratification and targeted treatment approaches.
Epigenetic profiling and epigenetic modulating drugs will increase risk stratification, increase accessibility for DNA targeting chemotherapeutics and reduce cytotoxic drug resistance.
New generation antibiotics such as biofilm inhibitors and quorum sensing inhibitors are being developed to target the carcinogenetic impact of colonic dysbiosis and inflammation.
Pain in Parkinson's disease: new concepts in pathogenesis and treatment
Authors: Rukavina Katarina , Leta Valentina , Sportelli Carolina , Buhidma Yazead , Duty Susan , Malcangio Marzia , Ray Chaudhuri Kallol 
Published: June 2019

Purpose of review
In this review, we discuss the most recent evidence on mechanisms underlying pathological nociceptive processing in Parkinson's disease patients, as well as novel treatment strategies.

Recent findings
In Parkinson's disease, specific neurodegenerative changes may cause alterations in nociceptive processing at multiple levels. Optimization of dopaminergic therapies should always be the first step in the management of Parkinson's disease pain. Reportedly, rotigotine transdermal patch, a monoamine oxidase type B inhibitor safinamide (as an add-on therapy to levodopa), subcutaneous apomorphine and intrajejunal levodopa infusion therapy may have a beneficial effect on pain sensations in Parkinson's disease patients. Among the nondopaminergic pharmacological therapies, prolonged-release oxycodone/naloxone and duloxetine may be effective in the treatment of chronic pain in Parkinson's disease. Botulinum toxin (BTX) injections should be considered for the treatment of dystonic Parkinson's disease pain. Deep brain stimulation (DBS) may lead to pain relief with a long-lasting effect in Parkinson's disease patients. Physiotherapy and physical activity in general are essential for Parkinson's disease patients suffering from pain.

Summary
Pain in Parkinson's disease is not simply a consequence of motor complainants. The management of Parkinson's disease-related pain implicates maintenance of stable levels of dopaminergic drugs. Nondopaminergic pharmacological therapies (prolonged-release oxycodone/naloxone, duloxetine, BTX) and nonpharmacological interventions (DBS, physiotherapie) may also be beneficial in treatment of Parkinson's disease pain.
Dissociation of disease phenotype and allele silencing in hypertrophic cardiomyopathy
Authors: Dainis Alexandra , Zaleta-Rivera Kathia , Ribeiro Alexandre , Chia Hao Chang Andrew , Shang Ching , Lan Feng , Burridge Paul W. , Wu Joseph C. , Chia Yu Chang Alex , Pruitt Beth L. , Wheeler Matthew , Ashley Euan 
Published: June 2019

AbstractAllele-specific RNA silencing has been shown to be an effective therapeutic treatment in a number of diseases, including neurodegenerative disorders. Studies of allele-specific silencing in hypertrophic cardiomyopathy to date have focused on mouse models of disease. Here, we investigate two methods of allele-specific silencing, short hairpin RNA (shRNA) and antisense oligonucleotide (ASO) silencing, using a human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) model of disease. We used cellular micropatterning devices with traction force microscopy and automated video analysis to examine each strategy’s effects on contractile defects underlying disease. We find that shRNA silencing ameliorates contractile phenotypes of disease, reducing disease-associated increases in cardiomyocyte velocity, force, and power. We find that ASO silencing, while better able to target and knockdown a specific disease-associated allele, showed more modest improvements in contractile phenotypes. We find a dissociation between allelic-specificity and functional improvements between the two tested therapeutic strategies, suggesting a more complex method of allelic control underlying HCM-associated transcripts.Author summaryAllele-specific silencing, whereby a therapeutic molecule is used to lower the expression of just one of the two copies or alleles of a gene, may be a potential therapeutic strategy in diseases caused by a single mutation. In this paper, we examine two such strategies in hypertrophic cardiomyopathy, a disease characterized by an overgrowth of the left-ventricular heart muscle as well as contractile dysfunction. We used a human cell model of disease, creating induced pluripotent stem cell derived cardiomyocytes from a patient with HCM caused by a single base pair change in just one allele of the gene MYH7. We used two strategies to silence the disease-associated copy of MYH7, both focused on reducing RNA expression from the mutated allele, as well as state-of-the-art biophysical techniques for measuring contractility. We found that one silencing strategy, which reduced expression of both the disease-associated and the healthy alleles of MYH7, showed great improvements in contractility between treated and untreated cells. Our second strategy, which silenced only the disease-associated copy of MYH7, showed more modest improvements in contractility. This suggests that the disease mechanism underlying this type of hypertrophic cardiomyopathy may be more complex than just presence or absence of the mutated RNA.
A high-quality genome assembly from short and long reads for the non-biting midge Chironomus riparius (Diptera)
Authors: Schmidt Hanno , Waldvogel Ann-Marie , Hellmann Sören Lukas , Feldmeyer Barbara , Hankeln Thomas , Pfenninger Markus 
Published: June 2019

AbstractBackgroundChironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species.FindingsMaking use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius’ genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species and the respective recombination rate as one of the first insect recombination rates at all.ConclusionsThe genome and associated resources will be highly valuable to the broad community working with dipterans in general and chironomids in detail. The estimated recombination rate will help evolutionary biologist gain a better understanding of commonalities and differences of genomic patterns in insects.
Cell-free prototyping of AND-logic gates based on heterogeneous RNA activators
Authors: Lehr François-Xavier , Hanst Maleen , Vogel Marc , Kremer Jennifer , Göringer H. Ulrich , Suess Beatrix , Koeppl Heinz 
Published: June 2019

AbstractRNA-based devices controlling gene expression bear great promise for synthetic biology, as they offer many advantages like short response times and light metabolic burden compared to protein-circuits. However, little work has been done regarding their integration to multi-level regulated circuits. In this work, we combined a variety of small transcriptional activator RNAs (STARs) and toehold switches to build highly effective AND-gates. To characterise the components and their dynamic range, we used an Escherichia coli (E. coli) cell-free transcription-translation (TX-TL) system dispensed via nanoliter droplets. We analysed a prototype gate in vitro as well as in silico, employing parameterised ordinary differential equations (ODEs), where parameters were inferred via parallel tempering, a Markov chain Monte Carlo (MCMC) method. Based on this analysis, we created nine additional AND-gates and tested them in vitro. The functionality of the gates was found to be highly dependent on the concentration of the activating RNA for either the STAR or the toehold switch. All gates were successfully implemented in vivo, offering a dynamic range comparable to the level of protein circuits. This study shows the potential of a rapid prototyping approach for RNA circuit design, using cell-free systems in combination with a model prediction.AbbreviationsTX-TL (transcription-translation), ODEs (ordinary differential equations), STARs (small transcriptional activator RNAs), MCMC (Markov chain Monte Carlo).
Staphylococcus epidermidismetabolic adaptation and biofilm formation in response to varying oxygen
Authors: Pedroza-Dávila Ulrik H. , Uribe-Alvarez Cristina , Morales-García Lilia , Espinoza-Simón Emilio , Muhlia-Almazán Adriana , Chiquete-Félix Natalia , Uribe-Carvajal Salvador 
Published: June 2019

ABSTRACTStaphylococcus epidermidisis a Gram-positive saprophytic bacterium found in the microaerobic/anaerobic layers of the skin. It becomes a health hazard when introduced across the skin by punctures or wounds.S. epidermidisforms biofilms in low O2environments. As oxygen concentrations ([O2]) decreased, the metabolism ofS. epidermidiswas modified ranging from fully aerobic to anaerobic. Respiratory activity increased at high [O2], while anaerobically grown cells exhibited the highest rate of fermentation. High aerobic metabolism coincided with high hydrogen peroxide-mediated damage. Remarkably, the rate of growth decreased at low [O2] even though the concentration of ATP was high. Under these conditions bacteria associated into biofilms. Then, in the presence of metabolic inhibitors, biofilm formation decreased. It is suggested that when [O2] is lowS. epidermidisaccumulates ATP in order to synthesize the proteins and polysaccharides needed to attach to surfaces and form biofilms.ImportanceBacteria and humans coexist, establishing all kinds of relationships that may change from saprophytic to infectious as environmental conditions vary. S. epidermidis is saprophytic when living in the skin. Inside the organism it evokes a pathologic reaction and is thus rejected by the organism. Additionally it is forced to adapt to high oxygen concentrations, becoming vulnerable to reactive oxygen species, which may come from leukocyte attack. Avoiding both, high oxygen and leukocytes is a must for bacteria. Escaping from oxygen involves a clever response: whenever it finds a low oxygen environment it attaches to surfaces, associating into biofilms. Biofilms protectS. epidermidisagainst host cells. Understanding these responses is a must in order to develop treatments and prevent infection success.