bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning 3D Semantic Scene Graphs with Instance Embeddings
Authors: Wald Johanna , Navab Nassir , Tombari Federico 
Published: January 2022

AbstractA 3D scene is more than the geometry and classes of the objects it comprises. An essential aspect beyond object-level perception is the scene context, described as a dense semantic network of interconnected nodes. Scene graphs have become a common representation to encode the semantic richness of images, where nodes in the graph are object entities connected by edges, so-called relationships. Such graphs have been shown to be useful in achieving state-of-the-art performance in image captioning, visual question answering and image generation or editing. While scene graph prediction methods so far focused on images, we propose instead a novel neural network architecture for 3D data, where the aim is to learn to regress semantic graphs from a given 3D scene. With this work, we go beyond object-level perception, by exploring relations between object entities. Our method learns instance embeddings alongside a scene segmentation and is able to predict semantics for object nodes and edges. We leverage 3DSSG, a large scale dataset based on 3RScan that features scene graphs of changing 3D scenes. Finally, we show the effectiveness of graphs as an intermediate representation on a retrieval task.
A pilot study on comparison of subjective titration versus remotely controlled mandibular positioning during polysomnography and drug-induced sleep endoscopy, to determine the effective protrusive position for mandibular advancement device therapy
Authors: Kazemeini Elahe , Op de Beeck Sara , Vroegop Anneclaire , Van Loo Dorine , Willemen Marc , Verbraecken Johan , Braem Marc J. , Vanderveken Olivier M. , Dieltjens Marijke 
Published: January 2022

Abstract
Study objectives
The aim of this pilot study was to evaluate the clinical effectiveness of subjective titration versus objectively guided titration during polysomnography (PSG) and drug-induced sleep endoscopy (DISE) in mandibular advancement device (MAD) therapy for patients with obstructive sleep apnea (OSA).

Methods
In this pilot cross-over study, patients underwent three titration procedures in randomized order: (1) subjective titration, (2) PSG-guided titration using a remotely controlled mandibular positioner (RCMP) and (3) DISE-assisted titration using RCMP. After each titration procedure, patients used the MAD for 1 month at the targeted protrusion obtained according to the preceding titration procedure. For each procedure, a follow-up PSG was performed after 1 month of MAD use in order to evaluate the efficacy of the MAD.

Results
Ten patients were included in the study. Overall, no significant differences in targeted optimal protrusion compared to maximal comfortable protrusion among the three titration methods were observed. There was no significant difference in reduction in AHI. In this study, PSG titration correctly classified 50% of patients as ‘responder’. A higher predictive accuracy was found for DISE titration with a sensitivity of 83.3% and a specificity of 100%.

Conclusions
This pilot randomized cross-over trial showed no differences in optimal mandibular positioning and corresponding efficacy of MAD between subjective titration, DISE titration or PSG titration.
Arsenic Detection Using Surface Plasmon Resonance Sensor With Hydrous Ferric Oxide Layer
Authors: Mustapha Kamil Yasmin , Al-Rekabi Sura Hmoud , Abu Bakar Muhammad Hafiz , Fen Yap Wing , Mohammed Husam Abduldaem , Mohamed Halip Nor Hafizah , Alresheedi Mohammed Thamer , Mahdi Mohd Adzir 
Published: January 2022

AbstractThe lethality of inorganic arsenic (As) and the threat it poses have made the development of efficient As detection systems a vital necessity. This research work demonstrates a sensing layer made of hydrous ferric oxide (Fe2H2O4) to detect As(III) and As(V) ions in a surface plasmon resonance system. The sensor conceptualizes on the strength of Fe2H2O4 to absorb As ions and the interaction of plasmon resonance towards the changes occurring on the sensing layer. Detection sensitivity values for As(III) and As(V) were 1.083 °·ppb−1 and 0.922 °·ppb−1, respectively, while the limit of detection for both ions was 0.6 ppb. These findings support the feasibility and potential of the sensor configuration towards paving future advancement in As detection systems.
Low-Drift Closed-Loop Fiber Optic Gyroscope of High Scale Factor Stability Driven by Laser With External Phase Modulation
Authors: Yan Jingtao , Miao Lijun , Shen Heliang , Shu Xiaowu , Huang Tengchao , Che Shuangliang 
Published: January 2022

AbstractIn view of the poor scale factor stability of the interferometric fiber optic gyroscope (IFOG), it is a creative method to use laser to drive the IFOG for its better frequency stabilization characteristics instead of the broadband light source. As the linewidth of laser is narrow, the errors of coherent backscattering, polarization coupling, and Kerr effect are reintroduced which cause more noise and drift. This paper studies laser spectrum broadening based on external phase modulation of Gaussian white noise (GWN). The theoretical analysis and test results indicate that this method has a good effect on spectrum broadening and can be used to improve the performance of the laser-driven IFOG. In the established closed-loop IFOG, a four-state modulation (FSM) is adopted to avoid temperature instability of the multifunction integrated-optic chip (MIOC) and drift caused by the electronic circuit in demodulation. The experimental results show that the IFOG driven by broadened laser has the angular random walk noise of 0.003 8 °/√h and the drift of 0.017 °/h, which are 62% and 66% better than those without modulation respectively, of which the drift has reached the level of the broadband light source. Although the noise still needs further reduction, its scale factor stability is 0.38 ppm, which has an overwhelming advantage compared with the traditional IFOG.
Skew Polynomial Rings: the Schreier Technique
Authors: Ánh Phạm Ngọc 
Published: January 2022

AbstractSchreier bases are introduced and used to show that skew polynomial rings are free ideal rings, i.e., rings whose one-sided ideals are free of unique rank, as well as to compute a rank of one-sided ideals together with a description of corresponding bases. The latter fact, a so-called Schreier-Lewin formula (Lewin Trans. Am. Math. Soc.145, 455–465 1969), is a basic tool determining a module type of perfect localizations which reveal a close connection between classical Leavitt algebras, skew polynomial rings, and free associative algebras.
Revisiting the Limits of Atmospheric Temperature Retrieval From Cosmic‐Ray Measurements
Authors: Riádigos Irma , González‐Díaz Diego , Pérez‐Muñuzuri Vicente 
Published: January 2022

AbstractA priori, cosmic‐ray measurements offer a unique capability to determine the vertical profile of atmospheric temperatures directly from ground. However, despite the increased understanding of the impact of the atmosphere on cosmic‐ray rates, attempts to explore the technological potential of the latter for atmospheric physics remain very limited. In this paper, we examine the intrinsic limits of the process of cosmic‐ray data inversion for atmospheric temperature retrieval, by combining a detection station at ground with another one placed at an optimal depth, and making full use of the angular information. With that aim, the temperature‐induced variations in cosmic rays (c.r.) rates have been simulated resorting to the theoretical temperature coefficients WT(h, θ, Eth) and the temperature profiles obtained from the ERA5 atmospheric reanalysis. Muon absorption and Poisson statistics have been included to increase realism. The resulting c.r. sample has been used as input for the inverse problem and the obtained temperatures compared to the input temperature data. Relative to early simulation works, performed without using angular information and relying on underground temperature coefficients from a suboptimal depth, our analysis shows a strong improvement in temperature predictability for all atmospheric layers up to 50 hPa, nearing a factor 2 error reduction. Furthermore, the temperature predictability on 6‐h intervals stays well within the range 0.8–2.2 K. Most remarkably, we show that it can be achieved with small‐area m2‐scale muon hodoscopes, amenable nowadays to a large variety of technologies. For mid‐latitude locations, the optimal depth of the underground station is around 20 m.
Hydro‐Mechanical Measurements of Sheared Crystalline Rock Fractures With Applications for EGS Collab Experiments 1 and 2
Authors: Meng Meng , Frash Luke P. , Li Wenfeng , Welch Nathan J. , Carey J. William , Morris Joseph , Neupane Ghanashyam , Ulrich Craig , Kneafsey Timothy 
Published: January 2022

AbstractWe present hydro‐mechanical measurements that characterize shear on natural fractures in schist, amphibolite, and rhyolite specimens from the enhanced geothermal system (EGS) Collab Project's Experiment 1 and 2 sites (E1 and E2) at the Sanford Underground Research Facility. We employed a triaxial direct shear method augmented with X‐ray imaging to perform hydroshearing (injection‐induced shearing) and mechanical shearing on naturally fractured specimens at in situ stress conditions. Measurements included fracture permeability, strength, stress‐dependent aperture, shear dilation, and frictional strength. Results reveal that in situ natural fractures must be permeable, weak, and shear‐oriented to be hydrosheared, and only a subset of the observable in situ fractures were suitable. When sheared, the fracture permeability typically increased by a factor of 10 or more and this increase was retained over time. However, shear slip did not always result in permeability increase. High phyllosilicate content associated with exceptionally weak fractures exhibited poor or even decreased permeability after stimulation. These measurements in combination with site data were used to conduct a slip‐tendency analysis for different fracture sets, and we selected the top candidate natural fractures for hydroshearing at the EGS Collab sites. We also found that the lower in situ shear stress and stronger fractures at the E2 site make hydroshearing more challenging than at the E1 site. Overall, the methods and analysis used in our work can be applied to any geothermal project to identify in situ joint sets that are best suited for hydroshearing, which in turn can help to optimize well placement and energy production.
T cell apoptosis characterizes severe Covid-19 disease
Authors: André Sonia , Picard Morgane , Cezar Renaud , Roux-Dalvai Florence , Alleaume-Butaux Aurélie , Soundaramourty Calaiselvy , Cruz André Santa , Mendes-Frias Ana , Gotti Clarisse , Leclercq Mickaël , Nicolas Alexandre , Tauzin Alexandra , Carvalho Alexandre , Capela Carlos , Pedrosa Jorge , Castro António Gil , Kundura Lucy , Loubet Paul , Sotto Albert , Muller Laurent , Lefrant Jean-Yves , Roger Claire , Claret Pierre-Géraud , Duvnjak Sandra , Tran Tu-Anh , Racine Gina , Zghidi-Abouzid Ouafa , Nioche Pierre , Silvestre Ricardo , Droit Arnaud , Mammano Fabrizio , Corbeau Pierre , Estaquier Jérôme 
Published: January 2022

AbstractSevere SARS-CoV-2 infections are characterized by lymphopenia, but the mechanisms involved are still elusive. Based on our knowledge of HIV pathophysiology, we hypothesized that SARS-CoV-2 infection-mediated lymphopenia could also be related to T cell apoptosis. By comparing intensive care unit (ICU) and non-ICU COVID-19 patients with age-matched healthy donors, we found a strong positive correlation between plasma levels of soluble FasL (sFasL) and T cell surface expression of Fas/CD95 with the propensity of T cells to die and CD4 T cell counts. Plasma levels of sFasL and T cell death are correlated with CXCL10 which is part of the signature of 4 biomarkers of disease severity (ROC, 0.98). We also found that members of the Bcl-2 family had modulated in the T cells of COVID-19 patients. More importantly, we demonstrated that the pan-caspase inhibitor, Q-VD, prevents T cell death by apoptosis and enhances Th1 transcripts. Altogether, our results are compatible with a model in which T-cell apoptosis accounts for T lymphopenia in individuals with severe COVID-19. Therefore, a strategy aimed at blocking caspase activation could be beneficial for preventing immunodeficiency in COVID-19 patients.
AHR EXPRESSION ON VIL1-EXPRESSING COLONIC EPITHELIAL CELLS IS ESSENTIAL FOR I3C-MEDIATED PROTECTION AGAINST COLITIS
Authors: Saxena Archana , Mitchell Chandani , Stanley Shanieka , Wilson Keisha , Rutkovsky Alex , Wisniewski P J , Dopkins Nicholas , Nagarkatti Mitzi , Nagarkatti Prakash , Busbee Philip 
Published: January 2022

Abstract
Ulcerative colitis (UC) is a chronic, idiopathic inflammatory disease that affects the colon and is characterized by localized tissue injury and disruption of the intestinal epithelial barrier. Pathophysiology of UC includes genetic predisposition, epithelial barrier defects, dysregulated immune responses, microbial dysbiosis, and environmental factors. Several therapeutic interventions for colitis have been identified, but many current treatments have various negative side effects, which is alarming given the incidence of UC is increasing around the world. Thus a search for safe therapeutic strategies to control the pathogenesis of colitis is still greatly needed. Previous studies from our laboratory reported that indole-3-carbinol (I3C), a natural plant product and ligand for the aryl hydrocarbon receptor (AhR), exhibited protective effects against colitis through innate lymphoid type 3 (ILC3) cells in an interleukin-22 (IL-22) dependent manner. The aim of this study was to ascertain the possible role of AhR in vil1-expressing colonic epithelial cells (CECs) during I3C-mediated protection against colitis. Using in vivo mouse studies and in vitro primary CEC organoid cultures, we investigated how key intestinal regulatory mediators (e.g. mucins and anti-microbial peptides, or AMPs) were altered in the absence or presence of AhR in CECs during I3C treatment under colitis or colitis-like conditions. We generated conditional AhR knockout mice in vil1-expressing CECs using the cre-flox system and induced colitis using the dextran sodium sulfate (DSS) model. Our results showed that the mice with AhR deficiency in CECs (AV mice) lost the protective effects of I3C treatment during colitis. Results showed that AV mice had a higher disease score and increased inflammation in the colon when compared to wild type (WT) or littermate (LM) controls. In addition, after treatment with I3C during DSS-induced colitis, AV mice were not able to prevent colitis-associated gut microbial dysbiosis even though flow cytometry analysis revealed AV mice were still capable of increasing IL-22 production by ILC3s in the colon. This suggested that the IL-22-ILC3 immune cell response was not the only major mechanism involved in I3C-mediated protection against colitis and regulation of the gut microbiome. Whole transcriptome analysis of RNA isolated from enriched CECs of experimental mice was performed and results showed significant altered expression of several microRNAs, mucins (muc3 and muc13), and tight junction proteins in AV mice when compared to wild type (WT) or littermate (LM) controls. PCR gene expression data and direct effects of I3C on CECs using colonic organoids from WT and AV mice validated these results. Collectively, these data showed that AhR expression in CECs play a critical role in I3C-mediated prevention of colitis.
EFFECTIVENESS OF ANTI-TNF THERAPY COMPARED TO IMMUNE MODULATOR FOR PREVENTION OF SURGICAL RECURRENCE IN PEDIATRIC CD
Authors: Egberg Matthew , Zhang Xian , Phillips Michael , Kappelman Michael 
Published: January 2022

Abstract

BACKGROUND
Crohn’s disease (CD) is an immune-mediated, chronic inflammatory disease without a present cure. Surgical intervention for disease complications is common among CD patients, however post-operative strategies to prevent disease recurrence represent a critical knowledge gap, particularly in the pediatric CD population. Although adult CD data suggest effectiveness of anti-Tumor Necrosis Factor (TNF) therapies for prevention of recurrence, similar evidence is scarce for the pediatric population. We sought to evaluate the effectiveness of anti-TNF monotherapy compared to immune modulator (methotrexate or thiopurine) monotherapy for prevention of surgical recurrence in pediatric CD patients using a large, geographically diverse administrative claims database.

METHODS
We analyzed pediatric (≤18 years) patients with CD who underwent ≥1 intestinal resection within the IQVIA Legacy PharMetrics Adjudicated Claims database between 2007 and 2018. IQVIA data contain longitudinal, de-identified patient-level claims for medical, surgical, and pharmacy encounters. IQVIA captures over 100 health plans with nearly 80 million insurance plan enrollees. We selected patients with ≥1 International Classification of Diseases 9thor 10thclinical modification (ICD-9/10) code for CD and ≥1 Current Procedural Terminology (CPT) code for a large and/or small bowel resection. We excluded patients with ≥3 encounters with an ICD-9/10 diagnosis code for ulcerative colitis (UC) or ≥1 UC code in the month of the index resection. We identified patients prescribed anti-TNF monotherapy and those prescribed immune modulators (thiopurine or methotrexate) monotherapy within 90 days of resection and compared rates of surgical recurrence. Analyses included descriptive statistics for the post-surgical cohort as well as time to surgical recurrence using Kaplan-Meier curves.

RESULTS
A total of 399 pediatric CD patients underwent an intestinal resection between 2007-2018 within the IQVIA database. Among those, 212 were prescribed either an anti-TNF monotherapy (109; 51%) or immune modulator monotherapy (103; 49%) within 90 days of resection. The median age of the treated cohort was 16 years (interquartile range (IQR) 14, 17) with 48% females. Over 60% of intestinal resections were ileo-cecectomies/colectomies. Thirteen (6.1%) patients required a repeat resection. Differences in median time to surgical recurrence were not statistically significant (Figure 1). Post-operative therapy was highly correlated with pre-operative therapy (p-value &lt;0.001).

CONCLUSION
Our results do not suggest a clear benefit of anti-TNF monotherapy versus immune modulator therapy for post-operative prophylaxis of pediatric Crohn’s disease. Randomized comparative effectiveness trials evaluating a range of outcomes including clinical and endoscopic recurrence are needed.
SAFFRON AS AN ADJUVANT THERAPY IN ULCERATIVE COLITIS PATIENTS
Authors: Ashktorab Hassan , Oppong-Twene Philip , Maecker Holden Terry , Chirumamilla Lakshmi , Kibreab Angesom , Nabi Eiman , Laiyemo Adeyinka , Brim Hassan 
Published: January 2022

Abstract

BACKGROUND
In the search for alternative or supplemental treatment for Ulcerative Colitis (UC), we studied saffron (Crocus Sativus) in a UC clinical trial, as an additional intervention to improve clinical manifestations of UC through its anti-inflammatory and anti-reactive oxygen species properties.

METHODS
This study is an open-label single-center pilot study conducted at Howard University. Patients with UC (n=3) in remission with mild-moderate disease received 50mg of Saffron twice daily for a period of 8-weeks. Inflammatory markers CRP measured in serum, calprotectin in feces, and the others (TNFα, INFγ, IL-6, IL-2, IL-17a, and IL-10) from PMA/ionomycin stimulated PBMCs by CyTOF, at baseline compared to 8-weeks Saffron treatment. Partial Mayo scoring was used for clinical response, the health-related quality of life questionnaire (HQoL) along with Hamilton Depression Rating Scale (HDRS) was used to assess the patient’s quality of Life as the primary endpoints. 16sDNA was performed on stool DNA for gut microbiome.

RESULTS
Significant calprotectin improvement was noticed in 2 out of 3 patients receiving saffron after 8 weeks compared to baseline. There was an improvement of Partial Mayo Score, pro-inflammatory markers TNFα, INFγ, IL-6, IL-2, IL-17a decreased while anti-inflammatory IL-10 increased. A wash-out period of 8 weeks reversed the calprotectin improvement while the second cycle of saffron treatment restored the calprotectin improvement level after 8-week in the 2 patients enrolled in the washout period. There was no drug-related adverse event during the study. Saffron’s effects on the gut microbiome composition in UC patients showed a decrease in gamma Proteobacteria, and enrichment in Ruminococcaceae.

CONCLUSIONS
Saffron improved clinical response for the main UC indicator fecal calprotectin and in Partial Mayo Scores. We observed significant improvement in patient’s symptoms such as abdominal pain, diarrhea, and rectal bleeding. Therefore, using saffron supplements, along with conventional medicines, may have beneficial impacts on UC patients and reduce the need for immunosuppressants in these patients.
SIMPLE SUGAR TRIGGERS SPONTANEOUS COLITIS DEVELOPMENT INIL10
-/- MICE
Authors: Khan Shahanshah , Zaki Hasan 
Published: January 2022

Abstract
The Western diet characterized by high fat and high sugar is considered a risk factor for inflammatory bowel disease (IBD) such as colitis. However, the precise role of sugar in colitis pathogenesis is poorly understood. We, therefore, investigated the role of glucose, a simple sugar, in colitis pathogenesis using IBD susceptible Il10-/- mice. We fed healthy 14-week old Il10-/- mice with 10% glucose in drinking water for 5 week and monitored body weight changes. Sugar fed Il10-/- mice spontaneously developed severe colitis, characterized by higher body weight loss and increased diarrhea, and shorter colon lengths. In agreement, there was higher expression of pro-inflammatory cytokines and chemokines in glucose-fed mice. Since colitis induction in Il10-/- mice is microbiota dependent, development of spontaneous colitis is often irregular. To induce colitis uniformly in all mice, glucose-fed and control Il10-/- mice were treated with a piroxicam-fortified diet. Alternatively, healthy Il10-/- mice were administered with a piroxicam-fortified diet for 5 days followed by feeding with high-glucose or regular drinking water. In both instances, glucose-fed Il10-/- mice lost more body weight and developed worse colitis. Increased colitis pathogenesis of glucose-fed Il10-/- mice was associated with increased inflammatory response, activation of inflammatory signaling pathways, induction of cell death, and erosion of mucus layer. Consistent to reduced mucus layer, there was increased bacterial colonization on the colonic mucosa and higher activity of bacteria-derived mucolytic enzymes in the gut lumen of sugar-fed Il10-/- mice. Notably, high sugar diets altered the composition of gut microbiota, particularly the abundance of mucus degrading bacteria, such as Akkermansia muciniphila and Bacteroides sp., was increased. Together these data suggest that high-sugar diet predisposes spontaneous colitis and enhances colitis pathogenesis by promoting the growth of mucus degrading bacteria in the gut of Il10-/- mice.