bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract LB519: Bimodality of gene expression in cancer patients as interpretable biomarkers for drug sensitivity
Authors: Haibe-Kains Benjamin , Ba-alawi Wail 
Published: June 2022

Abstract
Identifying biomarkers predictive of cancer cells’ response to drug treatment constitutes one of the main challenges in precision oncology. Recent large-scale cancer pharmacogenomic studies have opened new avenues of research to develop predictive biomarkers by profiling thousands of human cancer cell lines at the molecular level and screening them with hundreds of approved drugs and experimental chemical compounds. Many studies have leveraged these data to build predictive models of response using various statistical and machine learning methods. However, a common challenge in these methods is the lack of interpretability as to how they make the predictions, hindering the clinical translation of these models. To alleviate this issue, we used the recent logic modeling approach to develop a new machine learning pipeline that explores the space of bimodally expressed genes in multiple large in vitro pharmacogenomic studies and builds multivariate, nonlinear, yet interpretable logic-based models predictive of drug response. We showcased the performance of the approach in a compendium of the three largest in vitro pharmacogenomic data sets to build robust and interpretable models for 101 drugs that span 17 drug classes with high validation rate in independent datasets. These results along with in vivo validation support a better translation of gene expression biomarkers between model systems using bimodal genes.
Citation Format: Benjamin Haibe-Kains, Wail Ba-alawi. Bimodality of gene expression in cancer patients as interpretable biomarkers for drug sensitivity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB519.
Abstract LB528: A microglia associated gene signature predicts survival risk in glioma patients
Authors: Jiang Chongming , Schaafsma Evelien , Zhao Yanding , Nguyen Thinh , Zhu Kenneth , Cheng Chao 
Published: June 2022

Abstract
Background: Gliomas are common tumors that affect the brain and spinal cord. A complex tumor microenvironment is one of the leading reasons for a poor prognosis in glioma patients. Microglia, as part of the immune microenvironment of gliomas, may facilitate glioma growth and invasion. However, the correlation between the microglia abundance and glioma prognosis has not been clarified.
Method: Our goal was to examine the relationship between microglia abundance and glioma prognosis. We analyzed the single-cell RNA sequences of human and mouse glioma cells to identify microglia marker genes. Then, we built a LASSO Cox regression model of microglia abundance signatures in gliomas. The Cancer Genome Atlas (TCGA) dataset (Low-grade gliomas, LGG) was used as the training cohort. The Repository of Molecular Brain Neoplasia Data (REMBRANDT) dataset and Chinese Glioma Genome Atlas (CGGA) dataset was used to validate the model as the validation cohorts.
Findings: Overall survival was significantly lower in those with a high level of microglia infiltration. Additionally, we found that microglia could interact with the tumor microenvironment and genomic features of gliomas, making microglia abundance negatively associated with the prognosis of glioma patients. Microglia abundance was positively correlated with immune genes expression and immune-related pathways. By applying our LASSO Cox regression model to gliomas, we found that patients with high-risk scores had significantly shorter overall survival (OS) than those with low-risk scores.
Conclusions: Taken together, our findings suggest that microglia abundance may be negatively associated with survival in gliomas. Based on the novel microglia abundance signatures, we developed a high accuracy LASSO Cox regression model. In this study, we demonstrated that the model accurately predicted the prognosis of glioma patients and could offer new therapeutic targets for microglial-directed therapies.
Keywords: Gliomas; Microglia abundance; LASSO Cox regression; TCGA; Signature.- 1 -
Citation Format: Chongming Jiang, Evelien Schaafsma, Yanding Zhao, Thinh Nguyen, Kenneth Zhu, Chao Cheng. A microglia associated gene signature predicts survival risk in glioma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB528.
Abstract LB541: The cysteine rich protein 61 (Cyr61) contributes to tumor proliferation and invasion via HGF (hepatocyte growth factor) mediated NFkB signaling pathway in human hepatocellular carcinoma
Authors: Jung Jiyoon , Koh sungae , Lee Kyunghee , Kim Jaeryong 
Published: June 2022

Abstract
Background: CCN growth factor family regulates a variety of biological events such as cell proliferation, cell invasion, cell differentiation, apoptosis, and growth inhibition. Cysteine-rich protein 61 (Cyr61) is one of six secreted proteins in the CCNs. It has been shown that Cyr61 plays an important role in tumorigenesis and carcinogenesis in glioma, breast cancer, and gastric cancer, and others. However, Cyr61 has not yet been elucidated on the tumorigenesis, proliferation, and invasion of hepatocellular carcinoma, and needs to be researched and discovered. In this study, the HGF-mediated association of Cyr61, interleukin-8 (IL-8), and NF-κB (Nuclear factor kappa-light-chain-enhancer of activated B cells) and cancer cell proliferation and invasion were investigated in two types of hepatoma cell lines.
Methods: In this study, cell culture, cDNA microarray analysis, western blotting, Real-time Polymerase chain reaction, Zymography, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, Cyr61 knock-down with short hairpin RNA (shRNA), chromatin immunoprecipitation assay, Standard two chamber invasion assay.
Results: First, we confirmed that the expression level of Cyr61 was up-regulated by HGF (hepatocyte growth factor) in hepatoma cells. To identify associated pathway of HGF-induced Cyr61 about IL-8, NF-κB expression, the cells were treated with PI3K (Phosphoinositide 3-kinase) inhibitor (LY294002) and then analyzed by Western blotting. The HGF-mediated IL-8 and NF-κB levels were decreased with LY294002. The role for Cyr61 associated with IL-8 and NF-κB was determined by knock down cell of Cyr61. Cyr61-sh RNA cells showed a decreased level of IL-8 and NF-κB. HGF-mediated cell proliferation and invasion were decreased in Cyr61 knock down cell.
Conclusions: These results suggest that Cry61 plays an important role in cell proliferation and metastasis in hepatocellular carcinoma, and Cry61 may be a novel target for the prevention of progression and treatment of hepatocellular carcinoma.
Citation Format: Jiyoon Jung, sungae Koh, Kyunghee Lee, Jaeryong Kim. The cysteine rich protein 61 (Cyr61) contributes to tumor proliferation and invasion via HGF (hepatocyte growth factor) mediated NFkB signaling pathway in human hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB541.
Association of Common and Rare Genetic Variation in the 3‐Hydroxy‐3‐Methylglutaryl Coenzyme A Reductase Gene and Cataract Risk
Authors: Ghouse Jonas , Ahlberg Gustav , Skov Anne Guldhammer , Bundgaard Henning , Olesen Morten S. 
Published: June 2022

Background

Results from animal models and observational studies have raised concerns regarding the potential cataractogenic effects of statin treatment. We investigated whether common and rare genetic variants in
HMGCR
are associated with cataract risk, to gauge the likely long‐term effects of statin treatment on lenticular opacities.

Methods and Results

We used genotyping data and exome sequencing data of unrelated European individuals in the UK Biobank to test the association between genetically proxied inhibition of
HMGCR
and cataract risk. First, we constructed an
HMGCR
genetic score consisting of 5 common variants weighted by their association with low‐density lipoprotein cholesterol. Second, we analyzed exome sequencing data to identify carriers of predicted loss‐of‐function mutations in
HMGCR
. Common and rare variants in aggregate were then tested for association with cataract and cataract surgery. In an analysis of >402 000 individuals, a 38.7 mg/dL (1 mmol/L) reduction in low‐density lipoprotein C by the
HMGCR
genetic score was associated with higher risk for cataract (odds ratio, 1.14 [95% CI, 1.00–1.39],
P
=0.045) and cataract surgery (odds ratio, 1.25 [95% CI, 1.06–1.48],
P
=0.009). Among 169 172 individuals with
HMGCR
sequencing data, we identified 32 participants (0.02%), who carried a rare
HMGCR
predicted loss‐of‐function variant. Compared with noncarriers, heterozygous carriers of
HMGCR
predicted loss‐of‐function had a higher risk of developing cataract (odds ratio, 4.54 [95% CI, 1.96–10.53],
P
=0.001) and cataract surgery (odds ratio, 5.27 [95% CI, 2.27–12.25]
, P
=5.37×10
−4
). In exploratory analyses, we found no significant association between genetically proxied inhibition of
PCSK9, NPC1L1
, or circulating low‐density lipoprotein cholesterol levels (
P
>0.05 for all) and cataract risk.

Conclusions

We found that genetically proxied inhibition of the
HMGCR
gene mimicking long‐term statin treatment associated with higher risk of cataract. Clinical trials with longer follow‐up are needed to confirm these findings.
Neural Reinstatement Tracks Spread of Attention between Object Features in Working Memory
Authors: Printzlau Frida A. B. , Myers Nicholas E. , Manohar Sanjay G. , Stokes Mark G. 
Published: June 2022

Abstract
Attention can be allocated in working memory (WM) to select and privilege relevant content. It is unclear whether attention selects individual features or whole objects in WM. Here, we used behavioral measures, eye-tracking, and EEG to test the hypothesis that attention spreads between an object's features in WM. Twenty-six participants completed a WM task that asked them to recall the angle of one of two oriented, colored bars after a delay while EEG and eye-tracking data were collected. During the delay, an orthogonal “incidental task” cued the color of one item for a match/mismatch judgment. On congruent trials (50%), the cued item was probed for subsequent orientation recall; on incongruent trials (50%), the other memory item was probed. As predicted, selecting the color of an object in WM brought other features of the cued object into an attended state as revealed by EEG decoding, oscillatory α-power, gaze bias, and improved orientation recall performance. Together, the results show that attentional selection spreads between an object's features in WM, consistent with object-based attentional selection. Analyses of neural processing at recall revealed that the selected object was automatically compared with the probe, whether it was the target for recall or not. This provides a potential mechanism for the observed benefits of nonpredictive cueing in WM, where a selected item is prioritized for subsequent decision-making.
A Gamma Parameterization for Precipitating Particle Size Distributions Containing Snowflake Aggregates Drawn from Five Field Experiments
Authors: Duffy George , Posselt Derek J. 
Published: June 2022

Abstract
In this study, we investigate the tendencies of gamma parameters for particle size distributions (PSDs) containing snowflake aggregates in orographic, convective, and stratiform clouds, above snowstorms and above rainstorms, in temperatures ranging from 0° to −45°C. We find a strong relationship between μ and Λ but no dependence on temperature. Higher μ are observed during the experiments sampling winter snowstorms, and lower μ are observed during experiments sampling frozen clouds above convective and orographic storms. We find that a gamma function with a μ of −1.25 provides the best average representation of PSD shape and the most accurate representation of PSD moments related to mass and reflectivity. We also provide a lookup table of maximum particle size boundaries that can be used to parameterize incomplete gamma functions with negative μ values.

Significance Statement
In many weather models and satellite retrieval algorithms, frozen clouds and precipitation are governed by the same assumptions even though they develop through different growth processes. This paper provides recommendations for snowflake aggregate size distributions that reflect natural conditions, and these recommended assumptions are demonstrated to improve estimates of mass and radar reflectivity. We studied a variety of storms, such as thunderstorms, snow storms, and winter rainstorms, and we found that our model for snowflake aggregates was nearly identical in all observed conditions.
The Impact of Primary Care Physicians on the Surgical Presentation and Outcomes of Colorectal Cancer in Vulnerable Populations
Authors: Balan Naveen , Braschi Caitlyn , Kirkland Patrick , Kaji Amy H. , Chen Kathryn T. 
Published: June 2022

Background Multiple socioeconomic and clinical factors have been implicated in the health disparities that exist amongst vulnerable populations with colorectal cancer. Efforts have been directed toward addressing these factors to improve outcomes. We evaluate the impact of primary care physicians (PCP) on the surgical presentation and outcomes of colorectal cancer at a safety-net hospital. Methods A retrospective chart review of 331 patients diagnosed with colorectal adenocarcinoma between 2014 and 2020 at a single-institution urban county medical center. Results The cohort was predominantly male (59%) and Hispanic (52.1%). Thirty-two percent of patients had a PCP at time of diagnosis. Patients with PCPs compared to those without PCPs had significantly lower rates of acute presentation (perforation or obstruction) (17.0 vs 38.1%, P < .001), higher rates of surgical resection (83.0 vs 70.7%, P = .016), and were less likely to have metastatic disease at presentation (20.4 vs 33.5%, P = .02). Overall, having a PCP also improved probability of survival (HR 1.36, P < .04). Conclusion Having a PCP at the time of colorectal cancer diagnosis is associated with improved outcomes in a safety-net population, with significant differences in surgical presentation and resection.
Off-Label Use of Ciprofloxacin/Dexamethasone Drops in the Pediatric Upper Airway: Case Presentation and Review of Adverse Effects
Authors: Ben-Dov Tom , Yang Jackie , April Max M. 
Published: June 2022

Objective: This report describes a new observation of hyperglycemia in a child with Type 1 diabetes after off-label use of otic ciprofloxacin/dexamethasone drops in the nasal passage and reviews previous reports of adverse endocrine effects from intranasal corticosteroids in pediatric patients. Methods: We describe the clinical case and conducted a literature review of MEDLINE (PubMed) and EMBASE. Results: A 9-month-old female with a history of Type 1 diabetes who underwent unilateral choanal atresia repair was started on 1 week of ciprofloxacin 0.3%/dexamethasone 0.1% otic drops twice a day for choanal obstruction with granulation tissue. While the patient’s airway patency improved, average daily blood glucose increases by 40 to 50 points were noted on the patient’s continuous glucose monitor. The hyperglycemia resolved within 2 days after switching to mometasone furoate 0.05% spray. We also review 21 pediatric otolaryngology cases of iatrogenic Cushing’s syndrome associated with on- and off-label use of topical steroid suspensions in the airway. Patients ranged from 3 months to 16 years in age and used doses of 50 μg/day to 2 mg/day. Conclusion: This is the first reported pediatric case of increased blood glucose levels associated with intranasal steroid suspensions, to the best of our knowledge. Counseling families on precise dose administration and potential endocrine disturbances is critical when prescribing these medications for off-label use in infants and small children, particularly among patients with underlying endocrine disorders such as diabetes.
The Better By Moving study: A multifaceted intervention to improve physical activity in adults during hospital stay
Authors: Geelen Sven JG , Giele Boukje M , Veenhof Cindy , Nollet Frans , Engelbert Raoul HH , van der Schaaf Marike 
Published: June 2022

Objective ‘Better By Moving’ is a multifaceted intervention developed and implemented in collaboration with patients and healthcare professionals to improve physical activity in hospitalized adults. This study aimed to understand if, how and why ‘Better By Moving’ resulted in higher levels of physical activity by evaluating both outcomes and implementation process. Design Mixed-methods study informed by the Medical Research Council guidance. Setting Tertiary hospital. Participants Adult patients admitted to surgery, haematology, infectious diseases and cardiology wards, and healthcare professionals. Measures Physical activity was evaluated before and after implementation using the Physical Activity Monitor AM400 on one random day during hospital stay between 8 am and 8 pm. Furthermore, the time spent lying on bed, length of stay and discharge destination was investigated. The implementation process was evaluated using an audit trail, surveys and interviews. Results There was no significant difference observed in physical activity (median [IQR] 23 [12–51] vs 27 [17–55] minutes, P = 0.107) and secondary outcomes before-after implementation. The intervention components’ reach was moderate and adoption was low among patients and healthcare professionals. Patients indicated they perceived more encouragement from the environment and performed exercises more frequently, and healthcare professionals signalled increased awareness and confidence among colleagues. Support (priority, resources and involvement) was perceived a key contextual factor influencing the implementation and outcomes. Conclusion Although implementing ‘Better By Moving’ did not result in significant improvements in outcomes at our centre, the process evaluation yielded important insights that may improve the effectiveness of implementing multifaceted interventions aiming to improve physical activity during hospital stay.
Analysis of medical appointments for patients with overweight and obesity in a public hospital of Lima, Peru: a cross-sectional study of audio-recorded consultations
Authors: Torres-Nolasco Maria Felix , Ruiz Eloy F , Tarazona-Meza Carla , Lazo-Porras María , Málaga Germán 
Published: June 2022

Objective To describe the content of overweight and obesity counseling performed in a public Peruvian hospital. Methods We audio-recorded 40 visits of patients with overweight or obesity from the internal medicine, cardiology, endocrinology, and family medicine services at Cayetano Heredia Hospital. Fragments of the recordings in which counseling was performed were transcribed and codified. We established a checklist to score each counseling session and performed descriptive analyses. Results Complete counseling (including weight, nutrition, and physical activity) was performed in 32.5% of consultations. The average time spent in counseling was 1.72 minutes. Counseling on weight loss was performed in 65% of consultations, nutrition in 65%, and physical activity in 35%. On average, 8 of 26 checklist items were fulfilled per appointment. Weight loss goals were established in 15% of visits. The most frequent diet recommendations were eating more fruits and vegetables (32.5%) and eating fewer carbohydrates (30.0%). Suggested physical activities were walking (10.0%), running (7.5%), and playing any sport (7.5%). Conclusions Complete counseling was only addressed in one-third of the appointments, and most counseling was superficial without considering therapeutic goals. This suggests the need to include lifestyle counseling in consultations, regardless of the medical specialty or patient’s background condition.
Intra-articular Damage and Patient Outcome Comparison Between Athletes and Nonathletes After Hip Arthroscopy
Authors: Shapira Jacob , Glein Rachel M. , Yelton Mitchell J. , Maldonado David R. , Lall Ajay C. , Domb Benjamin G. 
Published: June 2022

Background: The body of literature comparing hip arthroscopy between athletes and nonathletes is relatively scarce. Analyzing these groups can help to shed light on the severity of intra-articular damage and end-stage osteoarthritis that may result from participation in strenuous activities. Purpose: (1) To compare the intra-articular damage at the time of hip arthroscopy between athletes and nonathletes, and (2) to compare the pre- and postoperative outcomes between the groups. Study Design: Cohort study; Level of evidence, 3. Methods: Patients were considered eligible for analysis if they had received a primary hip arthroscopy between August 2008 and June 2018, were participating in competitive athletics, and had preoperative baseline scores and minimum 2-year follow-up for the following patient-reported outcomes: modified Harris Hip Score, Nonarthritic Hip Score (NAHS), Hip Outcome Score–Sports Specific Subscale, and visual analog scale. Propensity score matching was used to match eligible patients in a 1:1 ratio to patients who were not participating in any sports greater than a recreational level before surgery. Results: A total of 234 patients were included. There were no significant differences in the severity of labral tears, ligamentum teres tears, or cartilage damage ( P > .05). The procedures performed between cohorts were similar ( P > .05). The athlete population had higher preoperative means scores for the modified Harris Hip Score and NAHS (each P < .001). Likewise, the athlete population had higher postoperative means scores for the NAHS, Hip Outcome Score–Sports Specific Subscale, and visual analog scale ( P = .031, P = .030, and P = .032, respectively). Additionally, the athlete cohort reported higher minimum 2-year outcomes than the nonathlete cohort for the 12-Item Short Form Health Survey (mental component; P = .003) and Veterans RAND 12-Item Health Survey (mental component, P = .032; physical component, P = .005). Conclusion: At the time of hip arthroscopy, athletes demonstrate similar intra-articular damage to their nonathlete counterparts. Given their higher preoperative scores, it is possible that athletes better tolerate the damage to the hip joint. Despite their strenuous activities and potentially higher tolerance to pain, athletes should not necessarily be expected to have greater severity of intra-articular pathology.
British Association for Sexual Health and HIV (BASHH) United Kingdom national guideline on the management of Trichomonas vaginalis 2021
Authors: Sherrard Jackie , Pitt Rachel , Hobbs Kate Russell , Maynard Michelle , Cochrane Eleanor , Wilson Janet , Tipple Craig 
Published: June 2022

The main objective of this guideline is to assist practitioners in managing individuals diagnosed with Trichomonas vaginalis (TV). It offers recommendations on the diagnostic tests, treatment regimens and health promotion principles needed for the effective management of TV. It covers the management of the initial presentation, as well as how to prevent transmission and future re-infection. It is aimed primarily at people aged 16 years or older presenting to health care professionals, working in departments offering specialist care in sexually transmitted infection (STI) management within the United Kingdom. However, the principles of the recommendations are applicable across all levels of STI care providers (N.B. non-specialist services may need to develop, where appropriate, local care pathways).