bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep learning for automatic mandible segmentation on dental panoramic x-ray images
Authors: Machado Leonardo Ferreira , Watanabe Plauto Christopher Aranha , Rodrigues Giovani Aantonio , Junior Luiz Otavio Murta 
Published: February 2023

Abstract
Many studies in the last decades have correlated mandible bone structure with systemic diseases like osteoporosis. Mandible segmentation, as well as segmentation of other oral structures, is an essential step in studies that correlate oral structures’ conditions with systemic diseases in general. However, manual mandible segmentation is a time-consuming and training-required task that suffers from inter and intra-user variability. Further, the dental panoramic x-ray image (PAN), the most used image in oral studies, contains overlapping of many structures and lacks contrast on structures’ interface. Those facts make both manual and automatic mandible segmentation a challenge. In the present study, we propose a precise and robust set of deep learning-based algorithms for automatic mandible segmentation (AMS) on PAN images. Two datasets were considered. An in-house image dataset with 393 image/segmentation pairs was prepared using image data of 321 image patient data and the corresponding manual segmentation performed by an experienced specialist. Additionally, a publicly available third-party image dataset (TPD) composed of 116 image/segmentation pairs was used to train the models. Four deep learning models were trained using U-Net and HRNet architectures with and without data augmentation. An additional morphological refinement routine was proposed to enhance the models’ prediction. An ensemble model was proposed combining the four best-trained segmentation models. The ensemble model with morphological refinement achieved the highest scores on the test set (98.27%, 97.60%, 97.18%, ACC, DICE, and IoU respectively), with the other models scoring above 95% in all performance metrics on the test set. The present study achieved the highest ranked performance considering all the previously published results on AMS for PAN images. Additionally, those are the most robust results achieved since it was performed over an image set with considerable gender representativeness, a wide age range, a large variety of oral conditions, and images from different imaging scans.
Design and CT imaging of casper, an anthropomorphic breathing thorax phantom
Authors: Laidlaw Josie , Earl Nicolas , Shavdia Nihal , Davis Rayna , Mayer Sarah , Karaman Dmitri , Richtsmeier Devon , Rodesch Pierre-Antoine , Bazalova-Carter Magdalena 
Published: February 2023

Abstract
The goal of this work was to build an anthropomorphic thorax phantom capable of breathing motion with materials mimicking human tissues in x-ray imaging applications. The thorax phantom, named Casper, was composed of resin (body), foam (lungs), glow polyactic acid (bones) and natural polyactic acid (tumours placed in the lungs). X-ray attenuation properties of all materials prior to manufacturing were evaluated by means of photon-counting computed tomography (CT) imaging on a table-top system. Breathing motion was achieved by a scotch-yoke mechanism with diaphragm motion frequencies of 10−20 rpm and displacements of 1 to 2 cm. Casper was manufactured by means of 3D printing of moulds and ribs and assembled in a complex process. The final phantom was then scanned using a clinical CT scanner to evaluate material CT numbers and the extent of tumour motion. Casper CT numbers were close to human CT numbers for soft tissue (46 HU), ribs (125 HU), lungs (−840 HU) and tumours (−45 HU). For a 2 cm diaphragm displacement the largest tumour displacement was 0.7 cm. The five tumour volumes were accurately assessed in the static CT images with a mean absolute error of 4.3%. Tumour sizes were either underestimated for smaller tumours or overestimated for larger tumours in dynamic CT images due to motion blurring with a mean absolute difference from true volumes of 10.3%. More Casper information including a motion movie and manufacturing data can be downloaded from http://web.uvic.ca/~bazalova/Casper/.
G-RANK: an equivariant graph neural network for the scoring of protein–protein docking models
Authors: Kim Ha Young , Kim Sungsik , Park Woong-Yang , Kim Dongsup 
Published: February 2023

Abstract

Motivation
Protein complex structure prediction is important for many applications in bioengineering. A widely used method for predicting the structure of protein complexes is computational docking. Although many tools for scoring protein–protein docking models have been developed, it is still a challenge to accurately identify near-native models for unknown protein complexes. A recently proposed model called the geometric vector perceptron–graph neural network (GVP-GNN), a subtype of equivariant graph neural networks, has demonstrated success in various 3D molecular structure modeling tasks.

Results
Herein, we present G-RANK, a GVP-GNN-based method for the scoring of protein-protein docking models. When evaluated on two different test datasets, G-RANK achieved a performance competitive with or better than the state-of-the-art scoring functions. We expect G-RANK to be a useful tool for various applications in biological engineering.

Availability and implementation
Source code is available at https://github.com/ha01994/grank.

Contact
kds@kaist.ac.kr

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Follicular fluid progesterone downregulated HPGD and COX2 in granulosa cells via suppressing NF-ĸB in endometriosis
Authors: Li Jing-Yi , Chen Jian-Peng , Qian Yu-Li , Ma Jun-Yan , Ni Fei-Da , Lin Yi-Feng , Zhang Run-Ju , Ying Yue , Zhang Yan-Ye , Wang Si-Wen , Huang Yun , Liu Juan , Tu Mi-Xue , Ying Yan-Yun , Wu Yi-Qing , Wu Xue-Chen , Wu Bing-Bing , Zhu Bo , Zhang Dan 
Published: February 2023

AbstractIncreasing evidences showed that ovulatory dysfunction, possibly caused by luteinized unruptured follicular follicle syndrome (LUFS), is one of the reasons for endometriosis-related infertility. The present study was conducted to explore the potential effect of elevated progesterone in follicular fluid (FF) on ovulation in endometriosis. A prospective study including 50 ovarian endometriosis patients and 50 control patients with matched pairs design was conducted with alterations in FF and peritoneal fluid (PF) components identified by metabolomics analyses and differentially expressed genes in granulosa cells (GCs) identified by transcriptome analysis. Patients with endometriosis exhibited a significantly higher progesterone level in serum, FF, and PF. Granulosa cells from endometriosis patients revealed decreased expression of HPGD, COX-2, and suppressed NF-ĸB signaling. Similarly, progesterone treatment in vitro downregulated HPGD and COX2 expression and suppressed NF-ĸB signaling in granulosa tumor-like cell line KGN (Bena Culture Collection, China) and primarily cultured GCs, as manifested by decreased expressions of IL1R1, IRAK3, reduced pIĸBα/IĸBα ratio, and nucleus translocation of p65. On the contrary, TNF-α treatment increased expression of IL1R1, IRAK3, pIĸBα, p65, and HPGD in GCs. One potential p65 binding site was identified in the promoter region of HPGD by chromatin immunoprecipitation. In conclusion, we found that intrafollicular progesterone might downregulate HPGD and COX-2 in GCs via suppressing the NF-ĸB signaling pathway, shedding light on the mechanism underlying the endometriosis-related ovulatory dysfunction.
The autism spectrum among transgender youth: default mode functional connectivity
Authors: Strang John F , McClellan Lucy S , Li Sufang , Jack Allison E , Wallace Gregory L , McQuaid Goldie A , Kenworthy Lauren , Anthony Laura G , Lai Meng-Chuan , Pelphrey Kevin A , Thalberg Alexandra E , Nelson Eric E , Phan Jenny M , Sadikova Eleonora , Fischbach Abigail L , Thomas John , Vaidya Chandan J 
Published: February 2023

Abstract
The common intersection of autism and transgender identities has been described in clinical and community contexts. This study investigates autism-related neurophenotypes among transgender youth. Forty-five transgender youth, evenly balanced across non-autistic, slightly subclinically autistic, and full-criteria autistic subgroupings, completed resting-state functional magnetic resonance imaging to examine functional connectivity. Results confirmed hypothesized default mode network (DMN) hub hyperconnectivity with visual and motor networks in autism, partially replicating previous studies comparing cisgender autistic and non-autistic adolescents. The slightly subclinically autistic group differed from both non-autistic and full-criteria autistic groups in DMN hub connectivity to ventral attention and sensorimotor networks, falling between non-autistic and full-criteria autistic groups. Autism traits showed a similar pattern to autism-related group analytics, and also related to hyperconnectivity between DMN hub and dorsal attention network. Internalizing, gender dysphoria, and gender minority-related stigma did not show connectivity differences. Connectivity differences within DMN followed previously reported patterns by designated sex at birth (i.e. female birth designation showing greater within-DMN connectivity). Overall, findings suggest behavioral diagnostics and autism traits in transgender youth correspond to observable differences in DMN hub connectivity. Further, this study reveals novel neurophenotypic characteristics associated with slightly subthreshold autism, highlighting the importance of research attention to this group.
A rare variant of a ruptured sinus of valsalva aneurysm forming an aorto-atrial fistula: a case report and review of literature
Authors: Dayco John S , Dsouza Alyssa , Baciewicz Frank , Cardozo Shaun 
Published: February 2023

AbstractBackgroundSinus of valsalva aneurysms (SOVAs) are infrequent findings and generally diagnosed incidentally. A SOVA may be at risk for rupture, which would lead to an aorto-cardiac shunt. These patients present similarly to decompensated heart failure.Case PresentationWe present a case of a 44-year-old female with a ruptured non-coronary SOVA diagnosed by echocardiogram during evaluation for exertional dyspnoea. A trans-oesophageal echocardiogram (TEE) revealed a 2.1 cm non-coronary SOVA with windsock communication to the right atrium. The patient refused surgery, and two years later, presented with florid right heart failure with preserved left ventricular function. The right ventricle was severely dilated and hypokinetic with right atrial enlargement. After finally agreeing to surgery, a pre-operative catheterization revealed non-obstructive coronaries and a significant left to right shunt with elevated pulmonary pressure. The patient had suboptimal response to diuretic therapy and was sent for successful repair of the aneurysm with the closure of the aorto-atrial fistula via bovine pericardial patch and resolution of the left to right shunt as demonstrated by intra-operative TEE. Her right-sided heart failure symptoms subsequently resolved.DiscussionSOVA is a rare finding but should still be considered in the differential in young and middle-aged patients with symptoms of acute heart failure, hemodynamic compromise, and a new continuous heart murmur. Early surgical repair is highly recommended to prevent acute and long-term complications.
Aboveground responses to belowground root damage detected by non-destructive sensing metrics in three tree species
Authors: Azar Matan , Mulero Gabriel , Oppenheimer-Shaanan Yaara , Helman David , Klein Tamir 
Published: February 2023

Abstract
Root systems form a significant part of tree biomass and function. Yet, roots are hidden from our eyes, making it difficult to track the belowground processes. By contrast, our capacity to detect aboveground changes in trees has been continuously improving using optical methods. Here, we tested two fundamental questions: (1) To what extent can we detect aboveground responses to mechanical damage of the root system? (2) To what extent are roots redundant? We applied three different non-destructive remote sensing means: (1) optical means to derive leaf greenness, (2) infrared means to detect the changes in leaf surface temperature and (3) spectral means to derive five vegetation indices (i.e. the photochemical reflectance index (PRI), the chlorophyll photosynthesis index (CIRed-edge), the anthocyanin reflectance index 1, the structure insensitive pigment index and the normalized difference water index (NDWI)). We recorded the above metrics for hours and days and up to a month following induced root damage in three key Mediterranean tree species: Aleppo pine (Pinus halepensis Mill.), Palestine oak (Quercus calliprinos Webb.) and Carob (Ceratonia siliqua L.). To induce root damage, we removed 25, 50 and 75 percent of the root system in each species and compared it with control saplings. Tree aboveground (canopy) responses to root damage increased over time and with damage level. Leaf warming (up to 3°C) and decreased PRI were the most significant and rapid responses, with temperature differences being visible as early as 2 days following root damage. NDWI and greenness were the least sensitive, with responses detectable only at 75 percent root damage and as late as 14 or 30 days following root damage. Responses varied vastly among species, with carob being the most sensitive and pine being the least. Changes in leaf temperature and PRI indicated that leaf transpiration and photosynthesis were impaired by root damage. Although trees build roots in excess, mechanical damage will eventually decrease transpiration and photosynthesis across tree species.
Quantitative profiling of N-glycosylation of SARS-CoV-2 spike protein variants
Authors: Xie Yongjing , Butler Michael 
Published: February 2023

Abstract
With the global spread of the corona virus disease-2019 pandemic, new spike variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continuously emerge due to increased possibility of virus adaptive amino acid mutations. However, the N-glycosylation profiles of different spike variants are yet to be explored extensively, although the spike protein is heavily glycosylated and surface glycans are well-established to play key roles in viral infection and immune response. Here, we investigated quantitatively the N-glycosylation profiles of seven major emerging spike variants including Original, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Kappa (B.1.671.1), Delta (B.1.671.2), and Omicron (B.1.1.529). The aim was to understand the changing pattern of N-glycan profiles in SARS-CoV-2 evolution in addition to the widely studied amino acid mutations. Different spike variants exhibit substantial variations in the relative abundance of different glycan peaks and subclasses, although no specific glycan species are exclusively present in or absent from any specific variant. Cluster analysis shows that the N-glycosylation profiles may hold the potential for SARS-CoV-2 spike variants classification. Alpha and Beta variants exhibit the closest similarity to the Original, and the Delta variant displays substantial similarity to Gamma and Kappa variants, while the Omicron variant is significantly different from its counterparts. We demonstrated that there is a quantifiable difference in N-glycosylation profiles among different spike variants. The current study and observations herein provide a valuable framework for quantitative N-glycosylation profiling of new emerging viral variants and give us a more comprehensive picture of COVID-19 evolution.
Industrial Property Arbitration in Turkey: An Analysis in Comparison with Swiss Law
Authors: Okur Irem 
Published: February 2023

Abstract
Given the difficulties in international intellectual property litigation, such as jurisdictional issues, choice of law, and recognition and enforcement of foreign judgments, arbitration and other dispute resolution mechanisms may be better tailored to resolve intellectual property disputes. Under Swiss law, these disputes are arbitrable to such an extent that arbitral tribunals seated in Switzerland and state courts are equally competent to rule on the validity of industrial property rights. This paper assesses the arbitrability of industrial property disputes under Turkish law, under which there is neither a specific statutory provision nor an official decision regarding their arbitrability. The paper concludes that disputes arising from industrial property rights should be considered arbitrable under Turkish law, provided that for disputes over the validity of industrial property rights, the arbitral tribunal decides on the industrial property rights’ enforceability and the arbitral award has an inter partes effect. Although submitting industrial property disputes, especially those on employee inventions, to arbitration may in certain cases not be accepted due to the intention to protect the weaker party, employees are obliged to resort to arbitration for the resolution of their employee invention disputes under Turkish law. This paper also examines the resolution of employee invention disputes by way of arbitration from a comparative perspective.
Ruxolitinib Alleviates Inflammation, Apoptosis, and Intestinal Barrier Leakage in Ulcerative Colitis via STAT3
Authors: Li Chunxiao , Xu Yu , Gao Tengjiao , Zhang Shunyao , Lin Zhe , Gu Shaobo , Fang Yi , Yuan Xin , Yu Siyi , Jiang Qi , Lou Zhongze , Zhang Xiuming , Zhang Jie , Wu Qiaoyan , Gu Mengli , Ding Xiaoyun , Sun Jing , Chen Yi 
Published: February 2023

AbstractBackgroundUlcerative colitis (UC) is an idiopathic, chronic inﬂammatory disorder of the colonic mucosa with increasing prevalence and limited management. Ruxolitinib is a new anti- JAK/STAT3 biologic agent that has shown potential in protecting against colitis.MethodsWe first constructed an in vivo UC model and an in vitro colonic epithelial cell inflammation model. Ruxolitinib was administered via gavage in mice. After treatment, colon tissues, cells, and cell lysates were collected and prepared for histological evaluation, immunohistochemistry, immunofluorescence staining, quantitative reverse-transcriptase polymerase chain reaction, Western blotting, terminal deoxynucleotidyl transferase mediated dUTP nick end labeling staining, and cytokine analysis. STAT3 expression was silenced and overexpressed via small interfering RNA and overexpression plasmid transfection, respectively, and quantitative reverse-transcriptase polymerase chain reaction was used to examine the downstream effects.ResultsRuxolitinib administration significantly alleviated colitis both in vivo and in vitro, as manifested by reduced body weight loss, shortened colon lengths, relieved disease activity (measured by the disease activity index), and prolonged survival. A mechanistic study showed that ruxolitinib attenuated nuclear factor kappa B–induced inflammation, reduced apoptosis, and ameliorated epithelial barrier leakage, and thereby reduced colitis activity in vivo. STAT3 knockdown partially reversed the protective effect of ruxolitinib against colitis, while STAT3 overexpression exaggerated the reductions in proinflammatory cytokine levels upon ruxolitinib treatment.ConclusionsWe demonstrate that ruxolitinib alleviates colitis by inhibiting nuclear factor kappa B–related inflammation and apoptosis in addition to restoring epithelial barrier function via STAT3, providing a new strategy for UC treatment.
Remote physiologic monitoring for hypertension in primary care: a prospective pragmatic pilot study in electronic health records using propensity score matching
Authors: Petito Lucia C , Anthony Lauren , Peprah Yaw Amofa , Lee Ji Young , Li Jim , Sato Hironori , Persell Stephen D 
Published: February 2023

Abstract

Objectives
Since 2019, the Centers for Medicare and Medicaid Services covers remote physiologic monitoring (RPM) for blood pressure (BP) per hypertension diagnosis and treatment guidelines. Here, we integrated Omron VitalSight RPM into the health system’s electronic health record to transmit BP and pulse without manual entry, assessed feasibility, and used pragmatic prospective matched cohort studies to assess initial effects in (1) uncontrolled (last two office BP ≥140/90 mmHg) and (2) general (diagnosed hypertension or last office BP ≥140/90 mmHg) hypertension patient populations.

Materials and Methods
Seventeen clinicians at two internal medicine practices were oriented. Eligible patients were aged 65–85 years had Medicare insurance with ≥1 office visit in the previous year. We prospectively identified matched controls (age, sex, BP, and number of office visits in previous year) from other primary care practices within the health system and estimated the association between RPM availability (clinic-level) and patient BP outcomes after 6 months. ClinicalTrials.gov: NCT04604925.

Results
Feasibility. Uptake was low at pilot clinics: 10 physicians prescribed RPM to 118 patients during the 6-month pilot. This included 7% (14/207) of the prespecified uncontrolled hypertension cohort and 3.3% (78/2356) of the general hypertension cohort. Surveyed clinicians (n = 4) reported changing their patients’ medical treatment in response to RPM BPs, although they recommended having a dedicated RN or LPN to review BP readings. Effectiveness. At 6 months, BP control was greater at pilot practices than among matched controls (uncontrolled: 31.4% vs 22.8%; P = .007; general: 64.0% vs 59.7%; P &lt; .001). Systolic BP at last office visit did not differ (mean [SD] 146.0 [15.7] vs 147.1 [15.6]; P = .48) in the uncontrolled population, and was lower in the general population (131.8 [15.7] vs 132.8 [15.9]; P = .04).The frequency of antihypertensive medication changes was similar in both groups (uncontrolled P = .986; general P = .218).

Discussion and Conclusions
Uptake notwithstanding, RPM may have improved BP control. A potential mechanism is increased physician awareness of and attention to uncontrolled hypertension. Barriers to RPM use among physicians require further study.
Separable shape tensors for aerodynamic design
Authors: Grey Zachary J , Doronina Olga A , Glaws Andrew 
Published: February 2023

AbstractAirfoil shape design is a classical problem in engineering and manufacturing. In this work, we combine principled physics-based considerations for the shape design problem with modern computational techniques using a data-driven approach. Modern and traditional analyses of two-dimensional (2D) and three-dimensional (3D) aerodynamic shapes reveal a flow-based sensitivity to specific deformations that can be represented generally by affine transformations (rotation, scaling, shearing, and translation). We present a novel representation of shapes that decouples affine-style deformations over a submanifold and a product submanifold principally of the Grassmannian. As an analytic generative model, the separable representation, informed by a database of physically relevant airfoils, offers: (i) a rich set of novel 2D airfoil deformations not previously captured in the data, (ii) an improved low-dimensional parameter domain for inferential statistics informing design/manufacturing, and (iii) consistent 3D blade representation and perturbation over a sequence of nominal 2D shapes.