bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein fold recognition based on multi-view modeling
Authors: Yan Ke , Fang Xiaozhao , Xu Yong , Liu Bin 
Published: January 2019

Abstract

Motivation
Protein fold recognition has attracted increasing attention because it is critical for studies of the 3D structures of proteins and drug design. Researchers have been extensively studying this important task, and several features with high discriminative power have been proposed. However, the development of methods that efficiently combine these features to improve the predictive performance remains a challenging problem.

Results
In this study, we proposed two algorithms: MV-fold and MT-fold. MV-fold is a new computational predictor based on the multi-view learning model for fold recognition. Different features of proteins were treated as different views of proteins, including the evolutionary information, secondary structure information and physicochemical properties. These different views constituted the latent space. The ε-dragging technique was employed to enlarge the margins between different protein folds, improving the predictive performance of MV-fold. Then, MV-fold was combined with two template-based methods: HHblits and HMMER. The ensemble method is called MT-fold incorporating the advantages of both discriminative methods and template-based methods. Experimental results on five widely used benchmark datasets (DD, RDD, EDD, TG and LE) showed that the proposed methods outperformed some state-of-the-art methods in this field, indicating that MV-fold and MT-fold are useful computational tools for protein fold recognition and protein homology detection and would be efficient tools for protein sequence analysis. Finally, we constructed an update and rigorous benchmark dataset based on SCOPe (version 2.07) to fairly evaluate the performance of the proposed method, and our method achieved stable performance on this new dataset. This new benchmark dataset will become a widely used benchmark dataset to fairly evaluate the performance of different methods for fold recognition.

Supplementary information
Supplementary data are available at Bioinformatics online.
Benzene metabolite hydroquinone promotes DNA homologous recombination repair via the NF-κB pathway
Authors: Yang Xuejing , Lu Yedan , He Fuhong , Hou Fenxia , Xing Caihong , Xu Peiyu , Wang Qian-Fei 
Published: January 2019

Abstract
Benzene, a widespread environmental pollutant, induces DNA double-strand breaks (DSBs) and DNA repair, which may further lead to oncogenic mutations, chromosomal rearrangements and leukemogenesis. However, the molecular mechanisms underlying benzene-induced DNA repair and carcinogenesis remain unclear. The human osteosarcoma cell line (U2OS/DR-GFP), which carries a GFP-based homologous recombination (HR) repair reporter, was treated with hydroquinone, one of the major benzene metabolites, to identify the potential effects of benzene on DSB HR repair. RNA-sequencing was further employed to identify the potential key pathway that contributed to benzene-initiated HR repair. We found that treatment with hydroquinone induced a significant increase in HR. NF-κB pathway, which plays a critical role in carcinogenesis in multiple tumors, was significantly activated in cells recovered from hydroquinone treatment. Furthermore, the upregulation of NF-κB by hydroquinone was also found in human hematopoietic stem and progenitor cells. Notably, the inhibition of NF-κB activity by small molecule inhibitors (QNZ and JSH-23) significantly reduced the frequency of hydroquinone-initiated HR (−1.36- and −1.77-fold, respectively, P < 0.01). Our results demonstrate an important role of NF-κB activity in promoting HR repair induced by hydroquinone. This finding sheds light on the underlying mechanisms involved in benzene-induced genomic instability and leukemogenesis and may contribute to the larger exploration of the influence of other environmental pollutants on carcinogenesis.
Dynamics in Central–Local Division of the Authority of EIA Approval in China
Authors: Ma Yun 
Published: January 2019

Abstract
In comparison with the dominant ‘consideration model’, the veto arrangement of environmental impact assessment (EIA) in China is a substantive regulatory feature that empowers environmental authorities to impinge on development activities. However, the anticipated efficacies thereof are compromised by the central–local division of EIA approval. The mismatch between high enforcement rates and prevalent non-compliance shows that EIA approval can be easily circumvented, especially at local levels. Recent mass, blanket devolution in a hasty manner, coupled with enthusiastic local responses in watering down EIA approval, raises serious concerns about its appropriateness and effectiveness. The tendency to deregulate by loosening environmental scrutiny and the reinvention of EIA procedures in light of project licensing processes impairs the veto effects of EIA approval. Without formal legislative empowerment in the central–local framework and individualised regulatory impact analysis, the current devolution approach is bound to endanger environmental quality and undermine the legitimacy of the veto arrangement.
Left External Carotid Artery to the Middle Cerebral Artery Bypass with Radial Artery Graft and Clip Reconstruction of a Large Middle Cerebral Artery Fusiform Aneurysm: 3-Dimensional Operative Video
Authors: Cheng Chun-Yu , Qazi Zeeshan , Sekhar Laligam N 
Published: January 2019

Abstract
This 16-yr-old boy presented with episodes of severe headaches, blurred vision, dizziness, and muffled hearing and was discovered to have a large fusiform aneurysm of the left middle cerebral artery (MCA), M1 segment, 20 × 12 mm in dimension. The lenticulostriate arteries were arising proximal and distal to the aneurysm, but the anterior temporal artery was arising from the aneurysm. The aneurysm culminated in the distal M1 segment, and M1 immediately branched into 3 M2 vessels, the lower one being the larger. Due to origin of the lenticulostriate arteries and the anterior temporal artery and patient's age, a bypass was preferred to a flow diversion stent.
He underwent left frontotemporal craniotomy and orbital osteotomy, left cervical external carotid artery exposure followed by radial artery graft extraction. The Sylvian fissure was opened and intracranial ICA was exposed for proximal control. The distal M2 vessels traced back toward the aneurysm. The aneurysm was not clippable and a bypass to the larger inferior M2 branch was performed followed by aneurysm trapping. The radial artery graft bypass was placed from the left external carotid artery to the M2 segment of left MCA, followed by clip reconstruction and occlusion of the MCA aneurysm with the preservation of the anterior temporal branch and the lenticulostriate vessels. The patient had no postoperative complications. At the follow-up, one month after surgery, he was doing well, and his angiogram demonstrated patency of the bypass.
This video shows the management of a complex fusiform M1 aneurysm with bypass and trapping.
Informed consent was obtained from the patient prior to the surgery that included videotaping of the procedure and its distribution for educational purposes. All relevant patient identifiers have also been removed from the video and accompanying radiology slides.
Expanding the toolbox of synthetic riboswitches with guanine-dependent aptazymes
Authors: Stifel Julia , Spöring Maike , Hartig Jörg Steffen 
Published: January 2019

Abstract
Artificial riboswitches based on ribozymes serve as versatile tools for ligand-dependent gene expression regulation. Advantages of these so-called aptazymes are their modular architecture and the comparably little coding space they require. A variety of aptamer-ribozyme combinations were constructed in the past 20 years and the resulting aptazymes were applied in diverse contexts in prokaryotic and eukaryotic systems. Most in vivo functional aptazymes are OFF-switches, while ON-switches are more advantageous regarding potential applications in e.g. gene therapy vectors. We developed new ON-switching aptazymes in the model organism Escherichia coli and in mammalian cell culture using the intensely studied guanine-sensing xpt aptamer. Utilizing a high-throughput screening based on fluorescence-activated cell sorting in bacteria we identified up to 9.2-fold ON-switches and OFF-switches with a dynamic range up to 32.7-fold. For constructing ON-switches in HeLa cells, we used a rational design approach based on existing tetracycline-sensitive ON-switches. We discovered that communication modules responding to tetracycline are also functional in the context of guanine aptazymes, demonstrating a high degree of modularity. Here, guanine-responsive ON-switches with a four-fold dynamic range were designed. Summarizing, we introduce a series of novel guanine-dependent ribozyme switches operative in bacteria and human cell culture that significantly broaden the existing toolbox.
Phylogeny, divergence times and species delimitation of Tonicia (Polyplacophora: Chitonidae) from the eastern Pacific Ocean
Authors: Ibáñez Christian M , Eernisse Douglas J , Méndez Marco A , Valladares Moises , Sellanes Javier , Sirenko Boris I , Pardo-Gandarillas M Cecilia 
Published: January 2019

AbstractThe chiton genus Tonicia is composed of 12 species, 11 of which are found in the eastern Pacific, but the taxonomic status and geographical distribution of these species have long been controversial. In this study, we compare eastern Pacific Tonicia species using molecular systematics. The molecular markers cytochrome oxidase c subunit I (COI), 16S and 18S ribosomal RNA were used to estimate the phylogenetic relationships and divergence times among species. Species delimitations were inferred using a Bayesian generalized mixed Yule coalescent (bGMYC) and a Bayesian Poisson tree processes (bPTP) approach. We assigned southeastern Pacific specimens to nine recognized species based on their morphology, but these were resolved into only six species in our molecular phylogeny, suggesting that three of the recognized morpho species need to be synonymized. The bGMYC and bPTP analyses indicate the existence of six total coalescent groups interpreted as seven species in our gene tree results. Likewise, pairwise genetic distances, phylogenetic estimates and coalescent approaches support only seven lineages when considering specimens that match the nine currently recognized southeastern Pacific Tonicia species. We suggest that the colouration and morphological characters used to identify Tonicia species must be re-examined in depth.
Concomitant Anterior Cruciate Ligament Reconstruction and Temporary Hemiepiphysiodesis in the Skeletally Immature: A Combined Technique
Authors: O’Brien Adam O. , Stokes Julia , Bompadre Viviana , Schmale Gregory A. 
Published: January 2019

Background:
Young athletes with an anterior cruciate ligament (ACL) disruption and limb malalignment pose a treatment dilemma. Little has been published regarding limb malalignment in this population. Our aim is to review the results of combined treatment of an ACL deficient knee and genu valgum in skeletally immature patients.

Methods:
A retrospective review of skeletally immature patients who underwent transphyseal ACL reconstruction and concomitant hemiepiphysiodesis between 2004 and 2015 by 1 surgeon at a single institution was performed. Included patients had at least a year of growth remaining and were followed to skeletal maturity. Patients with a diagnosis of a connective tissue disorder were excluded. Knee stability, rate of retear, the rate of mechanical axis correction, and time to full correction were determined.

Results:
Ninety skeletally immature patients underwent transphyseal ACL reconstruction, 8 of which met inclusion criteria. Mean time to correction of the valgus deformity was 13 months (0.4 degree/mo). No patient required additional surgeries for malalignment. All patients had improvement in knee stability. One patient had a retear of their ACL reconstruction, for a failure rate of 13%. Preoperative mechanical lateral distal femoral angle and mechanical axis deviation corrected to near-neutral alignment for all treated limbs and were significantly different (P=0.001) than those measured preoperatively.

Conclusions:
Promising results were seen for simultaneous correction of genu valgum and transphyseal ACL reconstruction. Treatment of both pathologies in a concomitant surgery can be considered in the appropriate population, with expected results comparable to each procedure in isolation.

Level of Evidence:
Level IV—case series.
Olecranon Fractures in Pediatric Patients With Osteogenesis Imperfecta
Authors: Tayne Samantha , Smith Peter A. 
Published: January 2019

Background:
Osteogenesis imperfecta (OI) is a hereditary disorder characterized by an abnormality of the quality or quantity of type I collagen, leading to bone fragility. Fractures in children with OI may result from minor trauma and have atypical patterns. Previous studies have found a strong relationship between olecranon fractures and OI in pediatric populations, but the characteristics of olecranon fractures within the OI patient population have not been fully described.

Methods:
We reviewed the records of 358 children with a diagnosis of OI. Of those, 29 had at least 1 olecranon fracture. We collected general information relating to the patient’s diagnosis of OI including OI type, fracture history, mobility, and bisphosphonate treatment. Information regarding the fracture, treatment, and the occurrence of bilateral fractures were recorded, as well as weight, height, and axial bone mineral density z-score from the time of the fracture.

Results:
Within our OI population of 358 patients, we found an incidence of olecranon fracture of 8.1% (29 patients). The olecranon fractures occurred predominantly in the type I population (27 of 29). Within the population of patients specifically with OI type I (200 patients) the incidence is 13.5%, with 6% of OI type I patients sustaining bilateral olecranon fractures. The percentage of children with one olecranon fracture subsequently sustaining another on the contralateral side was 41.4%. The mean time to the second fracture was 5 months. The mean age at the time of the first olecranon fracture was 11.9 years old. The average axial bone mineral density z-score was −2.5 for primary fractures. All 12 patients who suffered a contralateral olecranon fracture had OI type I.

Conclusions:
Olecranon fractures in the OI population occur most commonly in patients with type I OI and during early adolescence, a period of rapid growth. There is a high rate of bilateral olecranon fractures, with the contralateral fracture occurring quickly after the primary fracture. Further studies may elucidate risk factors to determine which patients are most likely to fracture the contralateral side and therefore drive treatment and potentially prevention.

Level of Evidence:
Level IV—retrospective cohort study.
Histological Features of Flagellate Erythema
Authors: Ching Daniel , Wood Benjamin A. , Tiwari Shevya , Chan Jonathan , Harvey Nathan T. 
Published: January 2019

Abstract:Flagellate erythema is a distinctive eruption characterized by “whip-like” linear or curvilinear streaks and plaques, occurring mainly on the trunk. It has classically been described in 2 disparate clinical settings: chemotherapy with bleomycin and ingestion of mushrooms (most commonly Shiitake mushrooms). Most of the literature comprises single case reports, often with minimal histological description of rather nonspecific features. We describe in detail the histological features of 3 cases of flagellate erythema (2 related to bleomycin therapy and one related to ingestion of mushrooms) and review the findings described in the literature to define the spectrum of histological changes encountered in this eruption. Our 3 cases showed mild epidermal changes, with spongiosis and variable interface inflammation. All 3 showed a relatively prominent dermal lymphohistiocytic infiltrate, with features suggestive of a lymphocytic vasculopathy extending to at least the mid-reticular dermis. Eosinophils were a prominent component of the inflammatory infiltrate in 2 cases. Our review of the literature identified a total of 45 publications, representing reports of 46 patients, containing histological information. As well as bleomycin- and mushroom-related cases, similar eruptions have been reported in the context of connective tissue disease and other drugs. Although cases related to connective tissue disease show features of the underlying condition, cases secondary to drugs or mushrooms predominantly show features compatible with common patterns of exanthematous/morbilliform drug reaction. In particular, subtle spongiosis and/or interface dermatitis combined with a dermal lymphocytic infiltrate that includes increased numbers of eosinophils is a common finding. Features of a lymphocytic vasculopathy may be seen in a subset of these cases.
Development of a Brief Screen for Symptoms of Posttraumatic Stress Disorder in Young Children: The Young Child PTSD Screen
Authors: Scheeringa Michael S. 
Published: January 2019

ABSTRACT:

Objective:
The ability to reliably detect posttraumatic stress disorder (PTSD) symptoms that require treatment in young children through screening efforts is a critical step toward providing appropriate treatment. The developmental differences in this age group compared to older youths pose challenges for accurate detection. A brief age-appropriate screen has not yet been quantitatively validated. This study aimed to address that gap by creating a rapid and brief screen based on empirical data that focused on sensitivity and face validity for children aged 3 to 6 years.

Methods:
A trauma-exposed group (N = 284) and a non-trauma-exposed group (N = 46), aged 3 to 6 years, were assessed using a semistructured diagnostic interview with their primary caregivers.

Results:
One hundred twenty combinations of items were evaluated for sensitivity, specificity, positive predictive value, negative predictive value, associations with functional impairment, and frequency of false positives. Many combinations of items performed well on these psychometrics, and the final selection of a 6-item screener was influenced by considerations of face validity so that the screen would best reflect the unique symptoms of PTSD.

Conclusion:
The screener proposed is a promising tool that will benefit from additional research to examine its psychometric properties as a stand-alone PTSD screen. Future research ought to include test–retest reliability and replication of these findings in other samples and settings. Eventual uses of a brief screen for PTSD in young children include screening during primary care visits and large-scale screening efforts following disasters, for which cost and time need to be considered.
Evaluating the Accuracy of Hemorrhoids: Comparison Among Specialties and Symptoms
Authors: Idrees Jay J. , Clapp McKenzie , Brady Justin T. , Stein Sharon L. , Reynolds Harry L. , Steinhagen Emily 
Published: January 2019

BACKGROUND:
A large proportion of patients with anorectal complaints are referred to colorectal surgeons with the label of hemorrhoids.

OBJECTIVE:
The purpose of this study was to review presenting symptoms and frequency of accurate diagnosis, as well as to analyze determinants of misdiagnosis to guide educational endeavors.

DESIGN:
This was a retrospective study.

SETTINGS:
The study was conducted at a tertiary care academic center.

PATIENTS:
The charts of patients referred to a colorectal clinic with the diagnosis of hemorrhoids from January 1, 2012, to January 1, 2017, were reviewed.

MAIN OUTCOME MEASURES:
The accuracy of the referring provider’s diagnosis of hemorrhoids was measured.

RESULTS:
Review of charts identified 476 patients with the referral diagnosis of hemorrhoids. The most common presenting symptoms were bleeding (63%; n = 302), pain (48%; n = 228), and protrusion (39%; n = 185). Anal examination (ie, external inspection and/or digital internal examination) was documented in only 48%. The hemorrhoid diagnostic accuracy was 65% (n = 311). Among patients with incorrect hemorrhoid diagnoses (35%; n = 169), actual diagnosis was anal fissure (34%), skin tag (27%), and hypertrophied papilla (6%). One rectal and 2 anal carcinomas were found (0.63%). Compared with general practitioners, gastroenterologists had 86% higher odds of correct diagnosis (OR = 1.86 (95% CI, 1.10–3.10); p = 0.02), whereas the gynecologists had 68% lower odds of correct diagnosis at the time of referral (OR = 0.32 (95% CI, 0.10–0.80); p = 0.02). On multivariable analysis, referring specialty was not predictive of accurate diagnosis. Patients presenting with protrusion had 73% higher odds of accurate diagnosis (OR = 1.7 (95% CI, 1.1–2.7); p = 0.02), whereas patients presenting with pain (OR = 1.6 (95% CI, 1.1–2.5); p = 0.03) or pruritus (OR = 2.5 (95% CI, 1.2–5.0); p = 0.008) were more likely to be misdiagnosed.

LIMITATIONS:
This is a retrospective study. Not all of the charts contained all data points. The number of patients may limit the power of the study to detect some differences.

CONCLUSIONS:
A variety of anorectal complaints are diagnosed as hemorrhoids by providers who have initial contact with the patients. Educational programs directed toward improving physician knowledge can potentially improve diagnostic accuracy and earlier initiation of appropriate care. Presenting symptoms other than protrusion lead to higher rate of misdiagnosis by a referring physician. See Video Abstract at http://links.lww.com/DCR/A847.
Accurate Nipple Areolar Positioning in Nipple-sparing Mastectomy Reconstruction
Authors: Mayer Alexander P. , Goodreau Adam M. , Blanchet Nadia P. 
Published: January 2019

Summary:
Nipple-sparing mastectomy continues to grow in popularity as oncologic indications for preserving the nipple areolar complex have become less stringent and more patients with genetic predispositions to breast cancer seek aesthetically superior prophylactic mastectomy reconstructions. Nonetheless, nipple malposition remains a common and disturbing complication. This article proposes several anatomic variations that predispose to nipple malposition and a strategy to avoid it through a reliable, easily reproducible method of preoperative marking and intraoperative stabilization.