bluuebunny/crossref_metadata_2025_split huggingface dataset:
Missense variants in the chromatin remodeler CHD1 are associated with neurodevelopmental disability
Authors: Pilarowski Genay O , Vernon Hilary J , Applegate Carolyn D , Boukas Leandros , Cho Megan T , Gurnett Christina A , Benke Paul J , Beaver Erin , Heeley Jennifer M , Medne Livija , Krantz Ian D , Azage Meron , Niyazov Dmitriy , Henderson Lindsay B , Wentzensen Ingrid M , Baskin Berivan , Sacoto Maria J Guillen , Bowman Gregory D , Bjornsson Hans T 
Published: September 2017

BackgroundThe list of Mendelian disorders of the epigenetic machinery has expanded rapidly during the last 5 years. A few missense variants in the chromatin remodeler CHD1 have been found in several large-scale sequencing efforts focused on uncovering the genetic aetiology of autism.ObjectivesTo explore whether variants in CHD1 are associated with a human phenotype.MethodsWe used GeneMatcher to identify other physicians caring for patients with variants in CHD1. We also explored the epigenetic consequences of one of these variants in cultured fibroblasts.ResultsHere we describe six CHD1 heterozygous missense variants in a cohort of patients with autism, speech apraxia, developmental delay and facial dysmorphic features. Importantly, three of these variants occurred de novo. We also report on a subject with a de novo deletion covering a large fraction of the CHD1 gene without any obvious neurological phenotype. Finally, we demonstrate increased levels of the closed chromatin modification H3K27me3 in fibroblasts from a subject carrying a de novo variant in CHD1.ConclusionsOur results suggest that variants in CHD1 can lead to diverse phenotypic outcomes; however, the neurodevelopmental phenotype appears to be limited to patients with missense variants, which is compatible with a dominant negative mechanism of disease.
Prediction of hyperperfusion phenomenon after carotid artery stenting and carotid angioplasty using quantitative DSA with cerebral circulation time imaging
Authors: Yamauchi Keita , Enomoto Yukiko , Otani Katharina , Egashira Yusuke , Iwama Toru 
Published: September 2017

BackgroundHyperperfusion syndrome after carotid interventions has a low incidence but it can lead to morbidity and mortality.ObjectiveTo evaluate the usefulness of quantitative DSA for predicting hyperperfusion phenomenon (HPP) after carotid artery stenting and angioplasty.MethodsThirty-three consecutive patients with carotid stenosis treated with carotid artery stenting or angioplasty between February 2014 and August 2016 were included. Color-coded digital subtraction angiograms showing the time to maximum contrast intensity of each image pixel were obtained from conventional DSA before and after procedures. The cerebral circulation time (CCT) was defined as the difference in the relative time to maximum intensity between arterial and venous regions of interest set on the angiograms. HPP was diagnosed straight after the procedure with qualitative123I-IMP single-photon emission CT (SPECT). Cut-off points for detecting HPP for preprocedural CCT and periprocedural change of CCT were assessed by receiver operating characteristic analysis using123I-IMP SPECT as reference standard.Results123I-IMP SPECT showed HPP in 4 of 33 patients. In these 4 patients, preprocedural prolongation of CCT (13.0±6.1 vs 7.2±1.3 s; p<0.001) was seen compared with patients without HPP as well as larger periprocedural changes of CCT (5.9±5.7 vs 0.5±1.3 s; p<0.001). The optimal cut-off points of preprocedural CCT and change of CCT for predicting HPP were 8.0 s (100% sensitivity, 69% specificity) and 3.2 s (75% sensitivity, 100% specificity), respectively.ConclusionsPreprocedural prolongation and greater periprocedural change of CCT are associated with the occurrence of HPP. Periprocedural evaluation of CCT may be useful for predicting HPP.
Formative student-authored question bank: perceptions, question quality and association with summative performance
Authors: Walsh Jason L , Harris Benjamin H L , Denny Paul , Smith Phil 
Published: September 2017

AbstractPurpose of the studyThere are few studies on the value of authoring questions as a study method, the quality of the questions produced by students and student perceptions of student-authored question banks. Here we evaluate PeerWise, a widely used and free online resource that allows students to author, answer and discuss multiple-choice questions.Study designWe introduced two undergraduate medical student cohorts to PeerWise (n=603). We looked at their patterns of PeerWise usage; identified associations between student engagement and summative exam performance; and used focus groups to assess student perceptions of the value of PeerWise for learning. We undertook item analysis to assess question difficulty and quality.ResultsOver two academic years, the two cohorts wrote 4671 questions, answered questions 606 658 times and posted 7735 comments. Question writing frequency correlated most strongly with summative performance (Spearman’s rank: 0.24, p=&lt;0.001). Student focus groups found that: (1) students valued curriculum specificity; and (2) students were concerned about student-authored question quality. Only two questions of the 300 ’most-answered' questions analysed had an unacceptable discriminatory value (point-biserial correlation &lt;0.2).ConclusionsItem analysis suggested acceptable question quality despite student concerns. Quantitative and qualitative methods indicated that PeerWise is a valuable study tool.
Detection of human papillomavirus in urine among heterosexual men in relation to location of genital warts and circumcision status
Authors: Aung Ei T , Fairley Christopher K , Tabrizi Sepehr N , Danielewski Jennifer A , Ong Jason J , Chen Marcus Y , Bradshaw Catriona S , Chow Eric P F 
Published: September 2017

ObjectiveHuman papillomavirus (HPV) surveillance is important to monitor the effectiveness of national HPV vaccination programmes. Positivity of HPV in urine in men varies with different sampling methods. We aimed to determine the positivity for detection of HPV-6/11 in urine samples among men in relation to the position of genital warts and circumcision status.MethodWe analysed stored chlamydia-positive urine specimens in young heterosexual men aged less than 25 years attending Melbourne Sexual Health Centre, Australia, between 2004 and 2015, for HPV genotypes. Positivity of HPV-6/11 and high-risk genotypes were stratified according to the position of genital warts and circumcision status. Positivity of HPV-6/11 was calculated using diagnosis of warts as the gold standard. Warts were classified as proximal penile warts from suprapubic area to midshaft of penis, and distal penile warts from distal shaft of penis to meatus.ResultsOf the 934 specimens, 253 (27.1%) men were positive for any HPV and 82 men (8.8%) had genital warts. The ORs of HPV-6/11 detection in urine were 4.63 (95% CI: 1.68 to 12.78) and 40.20 (95% CI: 19.78 to 81.70) times higher among men who had proximal penile warts and distal penile warts, respectively, compared with men who did not have genital warts. Circumcised men were less likely to have high-risk HPV (OR 0.31; 95% CI: 0.14 to 0.65) than uncircumcised men. Uncircumcised men were more likely to have distal penile warts than circumcised men (OR 8.22; 95% CI: 1.34 to 337.46).ConclusionPositivity of HPV-6/11 in urine increases greatly in men with distal penile warts. Circumcised men are less likely to have distal penile warts, any HPV or high-risk HPV detected. Urine is likely to be an alternative sampling method for HPV-6/11 surveillance programme in men in countries with low circumcision rates.
Acceptability and ease of use of mailed HPV self-collection among infrequently screened women in North Carolina
Authors: Anderson Chelsea , Breithaupt Lindsay , Des Marais Andrea , Rastas Charlotte , Richman Alice , Barclay Lynn , Brewer Noel T , Smith Jennifer S 
Published: September 2017

ObjectivesSelf-collection of cervico-vaginal samples for human papillomavirus (HPV) testing has the potential to make cervical cancer screening more accessible to underscreened women. We evaluated the acceptability and ease of use of home-based HPV self-collection within a diverse population of low-income, infrequently screened women.MethodsParticipants were low-income women from North Carolina who had not received Pap testing in 4 or more years. Eligible women received a self-collection kit containing instructions and a brush for home-based sample collection. A total of 227 women returned a self-collected sample by mail and completed a questionnaire to assess their experiences with HPV self-collection. We described acceptability measures and used logistic regression to identify predictors of overall positive thoughts about the self-collection experience.ResultsNearly all women were willing to perform HPV self-collection again (98%) and were comfortable receiving the self-collection kit in the mail (99%). Overall, 81% of participants reported positive thoughts about home-based self-collection. Women with at least some college education and those who were divorced, separated or widowed were more likely to report overall positive thoughts. Aspects of self-collection that participants most commonly reported liking included convenience (53%), ease of use (32%) and privacy (23%). The most frequently reported difficulties included uncertainty that the self-collection was done correctly (16%) and difficulty inserting the self-collection brush (16%).ConclusionsHome-based self-collection for HPV was a highly acceptable screening method among low-income, underscreened women and holds the promise to increase access to cervical cancer screening in this high-risk population.
Functional phenotypes determined by fluctuation-based clustering of lung function measurements in healthy and asthmatic cohort participants
Authors: Delgado-Eckert Edgar , Fuchs Oliver , Kumar Nitin , Pekkanen Juha , Dalphin Jean-Charles , Riedler Josef , Lauener Roger , Kabesch Michael , Kupczyk Maciej , Dahlen Sven-Erik , Mutius Erika von , Frey Urs 
Published: September 2017

RationaleAsthma is characterised by inflammation and reversible airway obstruction. However, these features are not always closely related. Fluctuations of daily lung function contain information on asthma phenotypes, exacerbation risk and response to long-acting β-agonists.ObjectivesIn search of subgroups of asthmatic participants with specific lung functional features, we developed and validated a novel clustering approach to asthma phenotyping, which exploits the information contained within the fluctuating behaviour of twice-daily lung function measurements.MethodsForced expiratory volume during the first second (FEV1) and peak expiratory flow (PEF) were prospectively measured over 4 weeks in 696 healthy and asthmatic school children (Protection Against Allergy – Study in Rural Environments (PASTURE)/EFRAIM cohort), and over 1 year in 138 asthmatic adults with mild-to-moderate or severe asthma (Pan-European Longitudinal Assessment of Clinical Course and BIOmarkers in Severe Chronic AIRway Disease (BIOAIR) cohort). Using enrichment analysis, we explored whether the method identifies clinically meaningful, distinct clusters of participants with different lung functional fluctuation patterns.Measurements and main resultsIn the PASTURE/EFRAIM dataset, we found four distinct clusters. Two clusters were enriched in children with well-known clinical characteristics of asthma. In cluster 3, children from a farming environment predominated, whereas cluster 4 mainly consisted of healthy controls. About 79% of cluster 3 carried the asthma-risk allele rs7216389 of the17q21locus. In the BIOAIR dataset, we found two distinct clusters clearly discriminating between individuals with mild-to-moderate and severe asthma.ConclusionsOur method identified dynamic functional asthma and healthy phenotypes, partly independent of atopy and inflammation but related to genetic markers on the17q21locus. The method can be used for disease phenotyping and possibly endotyping. It may identify participants with specific functional abnormalities, potentially needing a different therapeutic approach.
A new genus of Anacardiaceae fossil wood from El Bosque Formation (Eocene), Chiapas, Mexico
Authors: Pérez-Lara Diana K. , Castañeda-Posadas Carlos , Estrada-Ruiz Emilio 
Published: September 2017

ABSTRACTWe describe a new fossil wood from the El Bosque Formation (Eocene) in Chiapas, southern Mexico. It has a combination of features found in the Anacardiaceae, including distinct growth rings, diffuse porosity, vessels solitary and in radial multiples of 2–3, simple perforation plates, medium to large alternate intervessel pits, vessel-ray parenchyma pits rounded and elongate with reduced borders, septate and non-septate fibers, axial parenchyma scanty paratracheal, vasicentric, apotracheal diffuse, Kribs heterogeneous rays type IIA, and multiseriate rays with radial canals. The mosaic of features of this wood supports the erection of a new genus, Bosquesoxylon Pérez-Lara, Castañeda-Posadas et Estrada-Ruiz. This new genus of anacardiaceous fossil wood extends our knowledge of this family’s history and offers hints on the possible relationships with floras from other localities worldwide, especially North America and Asia.
Selektivitas alat tangkap purse seine di Pangkalan Pendaratan Ikan Muara Angke
Authors: Pamenan Azlhimsyah R. , Sunarto Sunarto , Nurruhwati Isni 
Published: September 2017

Alat tangkap purse seine adalah alat tangkap terbanyak kedua yang digunakan nelayan di PPI Muara Angke setelah alat tangkap bouke ami. Tujuan dari penelitian ini adalah menganalisis tingkat selektivitas alat tangkap purse seine berdasarkan hasil tangkapannya. Pengumpulan data dilakukan dengan melakukan survey di PPI Muara Angke Jakarta dari 10 Mei - 1 Juni 2016. Data hasil tangkapan ikan dikumpulan dari 4 unit alat tangkap purse seine dengan masing-masing alat tangkap 1 kali trip. Analisis data meliputi komposisi jenis hasil tangkapan dan ukuran panjang cagak pertama matang gonad hasil tangkapan utama. Hasil Penelitian menunjukan bahwa alat tangkap purse seine menangkap sebanyak 14 spesies dengan jumlah total hasil tangkapan 75.945 ekor dengan bobot 9.092 kg.Â Komposisi hasil tangkapan sampingan lebih mendominasi yaitu sebesar 78,7% dibanding hasil tangkapan utama 21,3%. Panjang cagak ikan tangkapan utama yang telah mencapai ukuran matang gonad mencapai 50,1% dari total seluruh ikan yang diukur. Secara umum, dengan melihat faktor yang digunakan untuk mengukur tingkat selektivitas alat tangkap, purse seine tergolong alat tangkap yang memiliki tingkat selektivitas yang rendah.Kata Kunci : Purse Seine, Hasil Tangkapan, Selektivitas. Purse seine fishing gears is the second most fishing gears which is used by fisherman in muara angke fishing port after bouke ami fishing gears. The purpose of this research is to analyzed the selectivity level of purse seine fishing gears based on fishing catch. The data collection was collected in muara angke fishing port between 10 mei â€“ 1 juni 2016. The data of fishing catch is collected from 4 unit of purse seine fishing gears with 1 trip from each unit. The data analysis exminesÂ the composisition of fishing catch and fork length of first maturity fish. The result from this research seeing that purse seine catch 14 different species from the total 75.945 fishes with 9.092 kg total weight. By-catch composistion is 78,7% more high than main catch composition 21,3%. The fork length of main catch which is have maturity size is just 50,1% from fishes were measured. Generally. From seeing theÂ used factor to measurre the level of fishing gears selectivity, purse seine fishing gears is classffied to the fishing gears that have poor selectivity level.Keywords : Purse Seine, Fishing catch, Selectivity
Kondisi habitat dan keragaman nekton di hulu Daerah Aliran Sungai Wampu, Kabupaten Langkat, Provinsi Sumatera Utara
Authors: Muhtadi Ahmad , Dhuha Orbita R. , Desrita Desrita , Siregar Toibullah , Muammar Muammar 
Published: September 2017

The study was conducted to determine the condition of the habitat and the diversity of fish in the watershed of Wampu. The habitat conditions was determined by measuring parameters of temperature, brightness, current velocity, depth, DO, pH, type of substrate, the width and the width of the river. Nekton was sampled using electrofishing units at voltage of 15 volt and 9 amperes. The characteristic of upstream watershed was large stones substrate, gravel, and sand with a fast flow and clear waters. Physical-chemical parameters of waters in the upper watersheds Wampu is still suitable for fish, crabs, and shrimp to live in good condition. A total of 15 species of fishes and one species of freshwater crab and one species of freshwater prawns were recorded during the study. There were two species of mahseer were recorded, namely; Tor soro and T. tambra. The higher diversity index (H ') was recorded in the Bahorok River with a value of 4.5 followed by Berkail River (3.45) and Landak River with a value of 2.46.Penelitian ini dilakukan untuk mengetahui kondisi habitat dan keragaman ikan di DAS Wampu. Pengukuran kondisi habitat dengan mengukur parameter suhu, kecerahan, kecepatan arus, kedalaman, DO, pH, jenis substrat, lebar dan lebar badan sungai. Jenis nekton ditangkap dengan alat backpack electrofishing units dimana arus listrik yang dihasilkan bersumber dari batere 15 volt dan 9 ampere. Kondisi habitat pada bagian hulu DAS Wampu yaitu bertipe substrat batu besar, kerikil, dan pasir dengan arus yang sedang - besar serta perairan yang jernih. Parameter fisika-kimia perairan di hulu DAS Wampu masih layak dan cocok untuk habitat ikan, kepiting dan udang. Selama penelitian nekton yang terkoleksi sebanyak 15 jenis ikan dan 1 jenis kepiting air tawar serta 1 jenis udang air tawar. Pada survei ini ditemukan dua jenis ikan Tor yakni T. soro, dan T. Tambra. Keanekaragaman (H') tertinggi terdapat pada Sungai Bahorok dengan nilai 4,5 diikuti Sungai Berkail dengan nilai 3,45, dan Sungai Landak dengan nilai 2,46.
Keragaman, kerapatan dan penutupan lamun di Pulau Biak, Papua
Authors: Dewi Citra S. U. , Subhan Beginer , Arafat Dondy 
Published: September 2017

The purpose of this study were to evaluate the diversity, density, and covering area of seagrass in Biak Island, Papua. Methodology that used in this study were combination of line intercept and quadrat transects, which drawn perpendicular to the shoreline. The results showed that there were 9 species of seagras found in Biak Island and it was categorized as high category. The density was renged from 450 ind/m2 to 898 ind/mand the covering area was between 60% to 80%.Penelitian ini bertujuan untuk mengetahui keragaman, kerapatan jenis lamun dan penutupan lamun di Pulau Biak. Metode yang digunakan dalam penelitian ini adalah transek kuadrat dan transek garis, yang ditarik tegak lurus dari garis pantai. Hasil penelitian menunjukkan bahwa keragaman jenis lamun di Pulau Biak tergolong tinggi, karena ditemukan delapan jenis lamun, dari 13 jenis lamun yang ada di Indonesia. Jenis lamun yang beragam di Pulau Biak diikuti juga dengan kerapatan lamun di setiap stasiun, yaitu pada kisaran 450 individu/m2 hingga 898 ind/m2. Kondisi ini seiring dengan penutupan lamun yang tergolong tinggi, yaitu berkisar antara 60% hingga 80%.
Status padang lamun di Pulau Talago, Madura dan potensinya sebagai bahan baku bioaktif
Authors: Sukandar Sukandar , Dewi Citra S.U. 
Published: September 2017

The aims of the study were to evaluate the status of the seagrass beds in Talango Island in relation to diversity, density, and percentage area of seagrass; and to analyze the potential of seagrass as bioactive compounds by calculating the crude extract, which is produced. Data were collected in August 2016 using the transect quadrat method, perpendicular to the shoreline, on the north side of Talango Island. Extraction of seagrass leaves was carried from November to December 2016 at Exploration Fisheries Resources Laboratory FPIK UB, using polar, semi-polar and non-polar solvents. The results showed that the water quality on Talango Island is in good condition with water temperatures of 30.70C, average salinity 310 ppt , dissolved oxygen of 8 mg /L and pH 7. There were four species of seagrass found on Talango Island, namely Enhalus acoroides, Cymodocea serulata, Halophila ovalis, and Halodule pinifolia. Where H. pinifolia has has the highest density, while Enhalus acoroides has the highest covering area. Seagrass leaf that used in this study is E. acoroides, and produces raw extract about 0.8% non-polar compounds, 1.73% of polar compounds, and 0.13% semi-polar compounds. This raw extract shows that seagrass leaf has potential as bioactive compound.Penelitian ini bertujuan untuk mengetahui status padang lamun di Pulau Talango, meliputi keragaman jenis, kerapatan jenis, penutupan jenis padang lamun dan menganalisis potensi pemanfaatannya sebagai bahan baku bioaktif, dengan menghitung rendemen ekstrak kasar yang dihasilkan.Pengambilan data dilakukan pada Bulan Agustus 2016, dengan menggunakan metode transek kuadrat yang ditarik tegak lurus terhadap garis pantai, di sisi utara Pulau Talango.Ekstraksi daun lamun dilakukan pada Bulan November – Desember 2016 di Laboratorium Eksplorasi Sumberdaya Perikanan FPIK UB, dengan menggunakan pelarut polar, semi polar, dan non polar. Hasil penelitian menunjukkan bahwa perairan di Pulau Talango berada pada kondisi yang cukup baik, ditunjukkan dengan nilai suhu sebesar 30,70C, salinitas 310/00, konsentrasi oksigen terlarut (DO) sebesar 8mg/L, dan nilai pH sebesar 7. Terdapat empat jenis lamun yang ditemukan di Pulau Talango, yaitu Enhalus acoroides, Cymodocea serulata, Halophila ovalis, dan Halodule pinifolia.Halodule pinifolia adalah lamun dengan kerapatan jenis tertinggi, sementara Cymodocea serulata adalah lamun dengan kerapatan jenis terendah. Daun lamun yang digunakan dalam penelitian adalah jenis Enhalus acoroides, dan menghasilkan rendemen ekstrak kasar sebesar 0,8% senyawa non polar, 1,73% senyawa polar, dan 0,13% senyawa semi polar. Rendemen yang dihasilkan menunjukkan bahwa ekstrak daun lamun ini memiliki potensi untuk diuji kandungan bioaktifnya.