bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gynecologic Screening for Men in an OBGYN Resident Community Outreach Clinic: The Transgender Care Experience
Authors: Woodland Mark B. , Callanan Laura , Schnatz Peter F. , Jiang Xuezhi 
Published: September 2018

Objective
The aim of the study was to promote the importance of providing gynecologic screening for transgender men (TGM) who desire to keep their female organs.

Materials and Methods
In June 2015, the Women's Health Center (WHC) at Reading Hospital was approached to become a resource for transgender (TG) patients in our community. This also presented the opportunity to develop an educational program for OBGYN residents/providers in TG healthcare. From June 2015 to August 2016, we educated ourselves, established standards of care, collaborated with other services, and reached out to the community we represent. We present our experience in creating this specialty clinic as well as our first 16 months of experiential data to help other facilities meet the needs of this community.

Results
The primary outcome was the establishment of a comprehensive service for TG patients in our community. From August 2016 to December 2017, a total of 27,516 patient visits were conducted in WHC, 67 (0.2%) were TG patient visits with an average age of 33 years. Of 67, 16 (23.9%) were TGM and 51 (76.1%) were transgender women (TGW) visits, representing a total of 20 new TG patients including 9 (45%) TGM and 11 (55%) TG women. A total of 5 (55.6%) of 9 TGM received vaginal/cervical cytology screening. Sexually transmitted infection screenings were performed in 14 (70%) TG patients versus 6,689 (40.7%) in a non-TG WHC population.

Conclusions
Servicing the transgender community is an important aspect of care for OBGYN providers. Our data suggest that TGM have similar gynecologic needs to the rest of our clinic population.
Effect of Antiretroviral Therapy on Treatment Outcomes in a Prospective Study of Extensively Drug-Resistant Tuberculosis (XDR-TB) HIV Coinfection Treatment in KwaZulu-Natal, South Africa
Authors: Yuengling Katharine A. , Padayatchi Nesri , Wolf Allison , Mathema Barun , Brown Tyler , Horsburgh C. Robert , O'Donnell Max R. 
Published: September 2018

Background:
Extensively drug-resistant tuberculosis (XDR-TB)/HIV coinfection has been associated with high mortality and poor TB outcomes. We performed a prospective study to comprehensively characterize a cohort of patients with XDR-TB.

Methods:
Adult patients with XDR-TB were enrolled at treatment initiation at a TB referral hospital in KwaZulu-Natal Province, South Africa, and followed through the end of treatment. Clinical data, questionnaires, adherence data, and sputum were collected monthly. Whole genome sequencing was performed on baseline Mycobacterium tuberculosis (MTB) isolates. Treatment outcomes were defined using standard definitions.

Results:
One hundred five patients with XDR-TB (76.1% HIV-infected) were enrolled from August 2009 to July 2011. Among HIV-coinfected patients, 82.5% were on antiretroviral therapy initially and 93.8% cumulatively over the study period. At 24 months, 31.4% had a successful outcome and 68.6% had an unsuccessful outcome with 41% mortality. Antiretroviral therapy was associated with improved mortality in HIV-coinfected patients (P = 0.05), as was TB culture conversion (P < 0.0001). On whole genome sequencing, most strains were LAM4/KZN lineage (68%), with few single nucleotide polymorphism differences.

Conclusions:
Despite improved HIV care, treatment outcomes and mortality were only modestly improved compared with previous South African XDR-TB/HIV treatment cohorts. Of note, this study was completed before the introduction of new antimycobacterial agents (eg, bedaquiline and delamanid). As new TB drugs and regimens become available, it is important to monitor treatment to ensure that benefits seen in clinical trials are reproduced in high-burden, low-resource settings.
Identification of a Syndemic of Blood-Borne Disease Transmission and Injection Drug Use Initiation at the US–Mexico Border
Authors: Rafful Claudia , Jain Sonia , Sun Xiaoying , Strathdee Steffanie A. , Garfein Richard S. , Cuevas-Mota Jazmine , Magis-Rodríguez Carlos , Smith Laramie R. , Werb Dan 
Published: September 2018

Background:
Efforts to prevent injection drug use (IDU) are increasingly focused on the role that people who inject drugs (PWID) play in the assistance with injection initiation. We studied the association between recent (ie, past 6 months) injection-related HIV risk behaviors and injection initiation assistance into IDU among PWID in the US–Mexico border region.

Setting:

Preventing Injecting by Modifying Existing Responses (PRIMER) is a multicohort study assessing social and structural factors related to injection initiation assistance. This analysis included data collected since 2014 from 2 participating cohorts in San Diego and Tijuana.

Methods:
Participants were 18 years and older and reported IDU within the month before study enrollment. Logistic regression analyses were conducted to assess the association between recent injection-related HIV risk behaviors (eg, distributive/receptive syringe sharing, dividing drugs in a syringe, and paraphernalia sharing) and recent injection initiation assistance.

Results:
Among 892 participants, 41 (4.6%) reported recently providing injection initiation assistance. In multivariable analysis adjusting for potential confounders, reporting a higher number of injection-related risk behaviors was associated with an increased odds of recently assisting others with injection initiation (adjusted odds ratio per risk behavior: 1.3; 95% confidence interval: 1.0 to 1.6, P = 0.04).

Conclusions:
PWID who recently engaged in one or more injection-related HIV risk behavior were more likely to assist others in injection initiation. These results stress the syndemic of injection initiation and risk behaviors, which indicates that prevention of injection-related HIV risk behaviors might also reduce the incidence of injection initiation.
Nerve Ultrasound, Electrophysiological, and Clinical Changes in Treatment-Naive Chronic Inflammatory Demyelinating Polyneuropathy: A Case Report
Authors: Sato Takeo , Terasawa Yuka , Higa Hitomi , Matsuno Hiromasa , Arai Ayumi , Omoto Shusaku , Mitsumura Hidetaka , Toyoda Chizuko , Koike Haruki , Iguchi Yasuyuki 
Published: September 2018

Summary:
We report the case of a 74-year-old woman with treatment-naive chronic inflammatory demyelinating polyneuropathy evaluated by both nerve conduction studies and nerve ultrasound (NUS) before and after initial treatment. Performing both nerve conduction study and NUS before and after initial treatment seems rare for treatment-naive chronic inflammatory demyelinating polyneuropathy. This case yielded two major findings. First, improvement of nerve swelling as evaluated by NUS correlated well with the improvement of neurological symptoms. Second, NUS improvements were seen right after treatment, whereas electrophysiological improvements were not. Nerve ultrasound might thus allow for judgment of curative effects much more immediately and sensitively than nerve conduction study in treatment-naive chronic inflammatory demyelinating polyneuropathy.
YAP activity is necessary and sufficient for basal progenitor abundance and proliferation in the developing neocortex
Authors: Kostic Milos , Paridaen Judith T.M.L. , Long Katherine , Kalebic Nereo , Langen Barbara , Wimberger Pauline , Kawasaki Hiroshi , Namba Takashi , Huttner Wieland B. 
Published: September 2018

SummaryThe expansion of the neocortex during mammalian evolution has been linked to an enlargement of the subventricular zone during cortical development and an increase in the proliferation of the basal progenitors residing therein. Here, we explored a potential role of YAP, the major downstream effector of the Hippo signaling pathway, in proliferation of basal progenitors. We show that YAP expression and activity are high in ferret and human basal progenitors, which are known to exhibit high proliferative capacity, but low in mouse basal progenitors, which lack such capacity. To induce YAP activity in mouse basal progenitors, we expressed a constitutively active YAP (CA-YAP). This resulted in an increase in proliferation of basal progenitor. In addition, CA-YAP expressing mouse basal progenitors promoted the production of upper-layer neurons. To investigate if YAP is required for the proliferation of basal progenitors, we pharmacologically interfered with the function of YAP in the developing ferret and human neocortex. This resulted in a decrease of cycling basal progenitors. In concert, genetical interference with the function of YAP in ferret developing neocortex resulted in decreased abundance of basal progenitors. Together, our data indicate that YAP promotes the proliferation of basal progenitors and suggest that changes in YAP activity levels contributed to the evolutionary expansion of the neocortex.
Discovery of novel thrips vector proteins that bind to the viral attachment protein of the plant bunyavirus, tomato spotted wilt virus
Authors: Badillo-Vargas Ismael E. , Chen Yuting , Martin Kathleen M. , Rotenberg Dorith , Whitfield Anna E. 
Published: September 2018

AbstractThe plant-pathogenic virus, tomato spotted wilt virus (TSWV), encodes a structural glycoprotein (GN) that, like with other bunyavirus/vector interactions, serves a role in viral attachment and possibly entry into arthropod vector host cells. It is well documented thatFrankliniella occidentalisis one of seven competent thrips vectors of TSWV transmission to plant hosts, however, the insect molecules that interact with viral proteins, such as GN, during infection and dissemination in thrips vector tissues are unknown. The goals of this project were to identify TSWV-interacting proteins (TIPs) that interact directly with TSWV GNand to localize expression of these proteins in relation to virus in thrips tissues of principle importance along the route of dissemination. We report here the identification of six TIPs from first instar larvae (L1), the most acquisition-efficient developmental stage of the thrips vector. Sequence analyses of these TIPs revealed homology to proteins associated with the infection cycle of other vector-borne viruses. Immunolocalization of the TIPs in L1s revealed robust expression in the midgut and salivary glands ofF. occidentalis, the tissues most important during virus infection, replication and plant-inoculation. The TIPs and GNinteractions were validated using protein-protein interaction assays. Two of the thrips proteins, endocuticle structural glycoprotein and cyclophilin, were found to be consistent interactors with GN. These newly discovered thrips protein-GNinteractions are essential towards better understanding of transmission of persistent propagative plant viruses by their vectors, as well as for developing new strategies of insect pest management and virus resistance in plants.Importance StatementThrips-transmitted viruses cause devastating losses to numerous food crops worldwide. For negative-sense RNA viruses that infect plants, the arthropod serves as a host as well by supporting virus replication in specific tissues and organs of the vector. The goal of this work was to identify vector/host proteins that bind directly to the viral attachment protein and thus may play a role in the infection cycle in the insect. Using the model plant bunyavirus, tomato spotted wilt virus (TSWV), and the most efficient thrips vector, we identified and validated six TSWV-interacting proteins fromFrankliniella occidentalisfirst instar larvae. Two proteins, an endocuticle structural glycoprotein and cyclophilin, were able to interact directly with the TSWV attachment protein, GN, in insect cells. The TSWV GN-interacting proteins provide new targets for disrupting the virus-vector interaction and could be putative determinants of vector competence.
Influence of prior beliefs on perception in early psychosis: effects of illness stage and hierarchical level of belief
Authors: Haarsma J. , Knolle F. , Griffin J.D. , Taverne H. , Mada M. , Goodyer I.M. ,   the NSPN Consortium, Fletcher P.C. , Murray G.K. 
Published: September 2018

AbstractAlterations in the balance between prior expectations and sensory evidence may account for faulty perceptions and inferences leading to psychosis. However, uncertainties remain about the nature of altered prior expectations and the degree to which they vary with the emergence of psychosis. We explored how expectations arising at two different levels – cognitive and perceptual – influenced processing of sensory information and whether relative influences of higher and lower level priors differed across people with prodromal symptoms and those with psychotic illness. In two complementary auditory perception experiments, 91 participants (30 with first episode psychosis, 29 at clinical risk for psychosis, and 32 controls) were required to decipher a phoneme within ambiguous auditory input. Expectations were generated in two ways: an accompanying visual input of lip movements observed during auditory presentation, or through written presentation of a phoneme provided prior to auditory presentation. We determined how these different types of information shaped auditory perceptual experience, how this was altered across the prodromal and established phases of psychosis, and how this relates to cingulate glutamate levels assessed by magnetic resonance spectroscopy. The psychosis group relied more on high level cognitive priors compared to both healthy controls and those at clinical risk for psychosis, and more on low level perceptual priors than the clinical risk group. The risk group were marginally less reliant on low level perceptual priors than controls. The results are consistent with previous theory that influences of prior expectations in psychosis in perception differ according to level of prior and illness phase.General scientific summaryWhat we perceive and believe on any given moment will allow us to form expectations about what we will experience in the next. In psychosis, it is believed that the influence of these so-called perceptual and cognitive ‘prior’ expectations on perception is altered, thereby giving rise to the symptoms seen in psychosis. However, research thus far has found mixed evidence, some suggesting an increase in the influence of priors and some finding a decrease. Here we test the hypothesis that perceptual and cognitive priors are differentially affected in individuals at-risk for psychosis and individuals with a first episode of psychosis, thereby partially explaining the mixed findings in the literature. We indeed found evidence in favour of this hypothesis, finding weaker perceptual priors in individuals at-risk, but stronger cognitive priors in individuals with first episode psychosis.
Identification of SMARCD1 as a syndromic intellectual disability gene that is required for memory and context-dependent regulation of neuronal genes in Drosophila
Authors: Nixon Kevin C.J. , Rousseau Justine , Stone Max H. , Sarikahya Mohammed , Ehresmann Sophie , Mizuno Seiji , Matsumoto Naomichi , Miyake Noriko ,   DDD study
Published: September 2018

AbstractMutations in several genes encoding components of the SWI/SNF chromatin remodeling complex cause syndromic intellectual disability (ID). Here, we report on 5 individuals with mutations in the SMARCD1 gene, presenting with ID, developmental delay, hypotonia, feeding difficulties, and small extremities. The mutations were proven to be de novo in 4 of the 5 individuals. Mutations in other SWI/SNF components cause Coffin-Siris, Nicolaides-Baraitser, or other syndromic ID disorders. Although the individuals presented here have some clinical overlap with these disorders, they lack the typical facial dysmorphisms. To gain insight into the function of SMARCD1 in neurons, we investigated the Drosophila ortholog, Bap60, in postmitotic memory-forming neurons of the adult Drosophila mushroom body (MB). Targeted knockdown of Bap60 in the MB of adult flies causes defects in long-term memory. Mushroom body specific transcriptome analysis revealed that Bap60 is required for context-dependent expression of genes involved in neuron function and development in juvenile flies when synaptic connections are actively being formed in response to experience. Taken together, we identify SMARCD1 mutations as a novel cause of ID, and establish a role for the SMARCD1 ortholog Bap60 in regulation of neurodevelopmental genes during a critical time window of juvenile adult brain development that is essential in establishing neuronal circuits that are required for learning and memory.
Mind the Gap: Identifying What Is Missed When Searching Only the Broad Scope with PubMed Clinical Queries
Authors: Sperr Edwin V. 
Published: September 2018

ObjectivePubMed Clinical Queries are subdivided into “Broad” and “Narrow” versions. These versions are tuned to maximize either retrieval or sensitivity using two different sets of keywords and MeSH headings. While a searcher might assume that all items retrieved by Filter name/Narrow would also be found in the set Filter name/Broad, this is not explicitly guaranteed. It is the purpose of this study to quantify the overlap between these two sets and confirm whether Filter/Narrow is always a subset of Filter/Broad.MethodsFor each of the five PubMed Clinical Queries, PubMed was searched for citations matching the query Filter/Narrow NOT Filter/Broad. This number was compared with that for Filter/Broad to compute a “degree of discordance” between the two sets. This process was then repeated for the MeSH headings for “Medicine” and “Diseases” as well as for a set of test searches.ResultsFour of the five Clinical Queries returned citations using Filter/Narrow that were not found with Filter/Broad. Discordances between the sets Broad and Narrow were generally modest for “Etiology”, “Diagnosis” and “Clinical prediction guides”. “Prognosis” was notably more discordant – a searcher could easily miss one Prognosis/Narrow citation for every ten citations she retrieves when using Prognosis/Broad alone for a given search.ConclusionsUsers of the Clinical Queries apart from “Therapy” who are interested in retrieving as many relevant citations as possible should consider combining Filter/Narrow together with Filter/Broad in their search strategy. This is particularly true for “Prognosis”, as otherwise the risk of missing relevant citations is substantial.
Skin microbiome modulation induced by probiotic solutions
Authors: Paetzold Bernhard , Willis Jesse R. , Lima Joao , Knodlseder Nastassia , Quist Sven R. , Gabaldón Toni , Güell Marc 
Published: September 2018

BackgroundThe skin is colonized by a large number of microorganisms, of which most are beneficial or harmless. However, disease states of skin have specific microbiome compositions that are different from those of healthy skin. Gut microbiome modulation through fecal transplant has proven as a valid therapeutic strategy in diseases such as Clostridium difficile infections. Therefore, techniques to modulate the skin microbiome composition may become an interesting therapeutic option in diseases affecting the skin such as psoriasis or acnes vulgaris.Here we have used mixtures of different skin microbiome components to alter the composition of a recipient skin microbiome.ResultsWe show that after sequential applications of a donor microbiome, the recipient microbiome becomes similar to that of the donor. After intervention, an initial, week-long phase is characterized by dominance of donor strains. The level of engraftment depends on the composition of the recipient and donor microbiomes, and the applied bacterial load. We observed higher engraftment using a multi-strain donor solution with recipient skin rich in Cutibacterium acnes subtype H1 and Leifsonia.ConclusionsWe have demonstrated the use of living bacteria to modulate skin microbiome composition.
Defining the transcriptional and post-transcriptional landscapes ofMycobacterium smegmatisin aerobic growth and oxygen limitation
Authors: Martini M. Carla , Zhou Ying , Sun Huaming , Shell Scarlet S. 
Published: September 2018

AbstractThe ability ofMycobacterium tuberculosisto infect, proliferate, and survive during long periods in the human lungs largely depends on the rigorous control of gene expression. Transcriptome-wide analyses are key to understanding gene regulation on a global scale. Here, we combine 5’-end-directed libraries with RNAseq expression libraries to gain insight into the transcriptome organization and post-transcriptional mRNA cleavage landscape in mycobacteria during log phase growth and under hypoxia, a physiologically relevant stress condition. Using the model organismMycobacterium smegmatis, we identified 6,090 transcription start sites (TSSs) with high confidence during log phase growth, of which 67% were categorized as primary TSSs for annotated genes, and the remaining were classified as internal, antisense or orphan, according to their genomic context. Interestingly, over 25% of the RNA transcripts lack a leader sequence, and of the coding sequences that do have leaders, 53% lack a strong consensus Shine-Dalgarno site. This indicates that likeM. tuberculosis,M. smegmatiscan initiate translation through multiple mechanisms. Our approach also allowed us to identify over 3,000 RNA cleavage sites, which occur at a novel sequence motif. The cleavage sites show a positional bias toward mRNA regulatory regions, highlighting the importance of post-transcriptional regulation in gene expression. We show that in low oxygen, a condition associated with the host environment during infection, mycobacteria change their transcriptomic profiles and endonucleolytic RNA cleavage is markedly reduced, suggesting a mechanistic explanation for previous reports of increased mRNA half-lives in response to stress. In addition, a number of TSSs were triggered in hypoxia, 56 of which contain the binding motif for the sigma factor SigF in their promoter regions. This suggests that SigF makes direct contributions to transcriptomic remodeling in hypoxia-challenged mycobacteria. Our results show thatM. smegmatisandM. tuberculosisshare a large number of similarities at the transcriptomic level, suggesting that similar regulatory mechanisms govern both species.