tbuckley/cabot-search huggingface dataset:
Trends of Research Output of Allopathic Medical Students Matching Into Dermatology, 2007-2018
Authors: Jatin Narang, Anna Eversman, Mehak Kalra, Frederick Morgan, Elizabeth Obi, Emma R. Russell, Angela H. Wei, David X. Zheng, Wilhemina Osei-Koomson, Amy S. Nowacki, Bryan T. Carroll, Timmie R. Sharma
Journal: JAMA Dermatology (2021)

<h3>Importance</h3> According to the National Residency Matching Program's biennial Charting Outcomes in the Match (NRMP ChOM) reports, the mean number of research items of matched allopathic dermatology applicants has nearly tripled since 2007, rising from 5.7 to 14.7. Research items are self-reported by applicants and serve as an approximation of research output. Because the NRMP research items field is unverified and reported as an aggregate of several different research pursuits, it may not be an accurate representation of applicant research output. <h3>Objective</h3> To determine if the rise in NRMP-reported data is associated with a rise in verifiable, indexed publications from matched allopathic dermatology applicants from 2007 to 2018. <h3>Design, Setting, and Participants</h3> Cross-sectional study including a bibliometric analysis on accepted applicant research output among 2234 matched allopathic dermatology applicants, with a total of 6229 publications, in dermatology residency programs for the years 2007, 2009, 2011, 2014, 2016, and 2018. <h3>Main Outcome and Measures</h3> The primary outcomes were the mean number of peer-reviewed indexed publications and mean number of NRMP ChOM research items. Secondary outcomes assessed the quality of indexed publications by analyzing article type and journal of publication. <h3>Results</h3> From 2007 to 2018, the mean number of indexed publications per matched dermatology applicant increased from 1.6 to 4.7 (203% increase). Indexed publications consistently compose a minority of NRMP ChOM research items (28.8% across the 6 years of the study). Nonindexed research items increased at more than double the rate of indexed publications. Bibliometric analysis showed that all other types of publications are increasing at a rate of 6 to 9 times that of basic science publications, dermatology-related publications increased at 5 times the rate of non-dermatology publications, and publications in lower–impact factor dermatology journals increased at 4 times the rate of publications in higher–impact factor dermatology journals. <h3>Conclusions and Relevance</h3> This cross-sectional study provides data on the research output of matched dermatology applicants. Indexed publications compose a minority of NRMP research items. Medical student self-reports of research output may emphasize research quantity over quality.
Abstract 10796: Early and Late Readmission Rates for Heart Failure Hospitalizations in Patients With Preserved and Reduced Ejection Fraction: Insights From the Nationwide Readmission Database 2010-2016
Authors: Ahmed Elkaryoni, Jonathan Enriquez
Journal: Circulation (2019)

Introduction: Heart failure (HF) readmission is common and associated with unfavorable outcomes and financial burden. Although the focus is often on 30-day readmission, HF patients remain at risk o...
Trends in Incidence and Transmission Patterns of COVID-19 in Valencia, Spain
Authors: Carolina Romero García, Adina Iftimi, Álvaro Briz-Redón, Massimiliano Zanin, Maria Otero, Mayte Ballester, José de Andrés, Giovanni Landoni, Dolores de las Marinas, Juan Carlos Catalá Bauset, Jesus Mandingorra, José Conca, Juan Correcher, Carolina Ferrer, Manuel Lozano
Journal: JAMA Network Open (2021)

<h3>Importance</h3> Limited information on the transmission and dynamics of SARS-CoV-2 at the city scale is available. <h3>Objective</h3> To describe the local spread of SARS-CoV-2 in Valencia, Spain. <h3>Design, Setting, and Participants</h3> This single-center epidemiological cohort study of patients with SARS-CoV-2 was performed at University General Hospital in Valencia (population in the hospital catchment area, 364 000), a tertiary hospital. The study included all consecutive patients with COVID-19 isolated at home from the start of the COVID-19 pandemic on February 19 until August 31, 2020. <h3>Exposures</h3> Cases of SARS-CoV-2 infection confirmed by the presence of IgM antibodies or a positive polymerase chain reaction test result on a nasopharyngeal swab were included. Cases in which patients with negative laboratory results met diagnostic and clinical criteria were also included. <h3>Main Outcomes and Measures</h3> The primary outcome was the characterization of dissemination patterns and connections among the 20 neighborhoods of Valencia during the outbreak. To recreate the transmission network, the inbound and outbound connections were studied for each region, and the relative risk of infection was estimated. <h3>Results</h3> In total, 2646 patients were included in the analysis. The mean (SD) age was 45.3 (22.5) years; 1203 (46%) were male and 1442 (54%) were female (data were missing for 1); and the overall mortality was 3.7%. The incidence of SARS-CoV-2 cases was higher in neighborhoods with higher household income (β<sub>2</sub>[for mean income per household] = 0.197; 95% CI, 0.057-0.351) and greater population density (β<sub>1</sub>[inhabitants per km<sup>2</sup>] = 0.228; 95% CI, 0.085-0.387). Correlations with meteorological variables were not statistically significant. Neighborhood 3, where the hospital and testing facility were located, had the most outbound connections (14). A large residential complex close to the city (neighborhood 20) had the fewest connections (0 outbound and 2 inbound). Five geographically unconnected neighborhoods were of strategic importance in disrupting the transmission network. <h3>Conclusions and Relevance</h3> This study of local dissemination of SARS-COV-2 revealed nonevident transmission patterns between geographically unconnected areas. The results suggest that tailor-made containment measures could reduce transmission and that hospitals, including testing facilities, play a crucial role in disease transmission. Consequently, the local dynamics of SARS-CoV-2 spread might inform the strategic lockdown of specific neighborhoods to stop the contagion and avoid a citywide lockdown.
A multicenter observational study of cs-131 seeds embedded in a collagen carrier tile in intracranial brain neoplasms: Trial in progress.
Authors: K. Stuart Lee, Matthew Peach, Clark C Chen, Kathryn Dusenbery, Clara Ferreira, Colette Shen, Sivakumar Jaikumar, Michael W McDermott, Rupesh Kotecha, David J McCracken, Adam W Nowlan, Erin M. Dunbar, John E Trusheim, David James Monyak, John Wanebo, Mehee Choi, David Brachman, Lisa Misell
Journal: Journal of Clinical Oncology (2021)

TPS2073 Background: Brachytherapy is an efficacious means for radiation delivery in the treatment of a spectrum of central nervous system tumors. Traditional brachytherapy methods have been limited by uneven dose distribution, complicated workflow, extended procedural times, the cost of dedicated equipment, and frequent adverse events. To address these issues, a permanently implanted device with Cs-131 radiation seeds embedded in a bioresorbable collagen carrier tile (GammaTile [GT], GT Medical Technologies, Tempe, AZ USA) was developed. Described as surgically targeted radiation therapy (STaRT) to distinguish it from external beam radiation therapy, the device is FDA-cleared for use in newly diagnosed malignant intracranial neoplasms and recurrent intracranial tumors, and has demonstrated excellent safety and local control outcomes in early commercial use. Methods: The overarching primary objectives of this multicenter, prospective, observational (phase IV) registry study are to evaluate “real-world” clinical outcomes and patient reported outcomes that measure the safety and efficacy of STaRT using the GT device. The registry is planned for 600 prospectively enrolled subjects at up to 50 enrolling sites. All adult patients undergoing surgical resection of brain tumors of any pathology with intra-operative GT placement are eligible for enrollment, upon consent. Information on patient demographics, tumor pathology, overall survival, adverse events related to radiation or surgery, and quality of life (FACT-Br and LASA) will be collected. Serial MRIs will be collected, and timing of surgical bed recurrence and/or distant recurrence will be collected. Data will be collected at 1-, 3-, 6-, 9-, 12-, 18-, and 24-months, then every 6 months through 5 years. Results will be used to benchmark clinical outcomes of GT therapy, allow for comparisons to other existing treatments, and facilitate the design of future clinical trials. Enrollment opened on November 15, 2020, and seven subjects have been enrolled to date at three centers. This study will be the first observational study of resection plus STaRT, delivered by Cs-131 sources in permanently implanted bioresorbable collagen tile carriers, and will allow for evaluation of this treatment approach in a real world setting, as well as provide an information platform for cross-comparison of results obtained from ongoing GT clinical trials. Clinical trial information: NCT04427384.
The Tim3-galectin-9 interactions in the tumor microenvironment of nasopharyngeal cancer.
Authors: Dora Lai Wan Kwong, Ngar-Woon Kam, Wai Chun Tse, Sing Hei Lok, George Tsao, Victor Ho-Fun Lee
Journal: Journal of Clinical Oncology (2021)

2629 Background: The complex cell interactions within the tumor microenvironment (TME) have become a crucial point in cancer research. Yet, the cell interactions might not only depend on the frequency of immune cells, but also on the inter-individual distances as cells might interact via soluble factors and/or cell-cell contact. Accordingly, the mapping of TME has recently gained importance. The aim of this study is to investigate the alternations between galectin-9 (G9) and its natural immunosuppressive receptor, T cell immunoglobulin and mucin domain 3 (Tim3) in nasopharyngeal cancer (NPC). Methods: Using multiplexed quantitative immunofluorescence, we measured the levels of G9 and Tim3 in 95 NPC patients cancerous and 8 normal specimens in tissue microarray format. Cell densities and cell-to-cell distances were quantified. The interaction between G9-expressing tumor cell lines and T cells were also studied. Results: G9-expressing tumor cells were detected in all NPC cases and were significantly higher than normal tissue. Elevated G9 was associated with shorter overall survival (OS: 89% vs 70.5% at 7 years, p: 0.019). Incremental percentages of Tim3 + cells were shown in top 10% cases strongly positive for G9-expressing tumor cells. The number of Tim3 + cells was calculated at 15µm intervals from the nearest G9-expressing tumor cells, of which a significant difference of Tim3 + cells was observed at the 0-15µm distance from G9-expressing cell in cancerous compared to normal tissues. Epithelial short distances were associated with a unfavourable prognosis. Observed short distance were hypothesized to represent Tim3 + cells actively interacting with G9-expressing tumor cells. Accordingly, In vitro cocultured of G9-ovexpressing NPC cell lines induced Tim3 expression on T cells which suppressed the T-cell mediate cytotoxicity on tumor cells. Conclusions: Our findings indicate a specific preexisting profile of Tim3 + and G9-expressing tumor cells and demonstrated that Tim3 + cells were mainly found intratumorally within 15µm of a NPC cell. The relevance of Tim3 + and G9 + distances reflect a potential marker of their functional interaction. Our results could have important implications for clinical therapeutic strategies. Since high G9 expression have poorer OS, they would deserve a different therapeutic strategy.[Table: see text]
Preliminary safety and efficacy results from phase 1 studies of DZD9008 in NSCLC patients with EGFR Exon20 insertion mutations.
Authors: James Chih-Hsin Yang, Mengzhao Wang, Paul Mitchell, Jian Fang, Weiqi Nian, Chao-Hua Chiu, Jianying Zhou, Yanqiu Zhao, Wu-Chou Su, D. Ross Camidge, Tsung-Ying Yang, Viola Weijia Zhu, Michael Millward, Yun Fan, Wen Tsung Huang, Ying Cheng, Liyan Jiang, Li Zheng, Xiuhui Ye, Pasi A. Janne
Journal: Journal of Clinical Oncology (2021)

9008 Background: There are no approved targeted therapies for EGFR exon20 insertion (exon20ins) mutant NSCLC. DZD9008 is a rationally designed selective, irreversible EGFR exon20ins inhibitor being studied in two ongoing phase 1/2 studies (NCT03974022 and CTR20192097). Methods: The objectives of the studies are to assess the safety, tolerability, pharmacokinetics, and preliminary anti-tumor efficacy of DZD9008 in NSCLC with EGFR or HER2 mutations. Both studies include dose escalation and expansion cohorts. Pooled analysis is applied to define recommended phase 2 dose (RP2D). Results: Between July 9, 2019 and February 5, 2021, 97 NSCLC patients with EGFR or HER2 mutations were dosed with DZD9008 (dose range: 50 mg to 400 mg, once daily). M/F: 44/53; 59 with EGFR exon 20. DZD9008 was well tolerated up to 400 mg (MTD) once daily. The DLTs were diarrhea and cardiac arrhythmia. The most common TEAEs were diarrhea (grade 3, 5.2%) and skin rash (grade 3, 1%). DZD9008 showed approximately dose-proportional PK, with a half-life of around 50 hours. Fifty-six patients with &gt; 16 different EGFR exon20ins mutations had &gt; 1 post-treatment efficacy assessment. Prior therapies: median 2 (range 1 - 10), prior chemotherapy 92.9% (52/); prior TKI 44.6% (25/56) including 1 patient had poziotinib treatment; 42.9% (24/56) with brain metastasis. Partial response was observed at ≥ 100 mg dose levels. At the RP2D dose of 300 mg once daily, the objective response rate was 48.4% (15/31), and disease control rate (DCR) was 90.3% (28/31). Responses were observed in 2 patients with prior JNJ-61186372 treatment. Anti-tumor activity was observed across different EGFR exon20ins mutation subtypes. By data cut-off, the median treatment duration was 100 days (range 1 – 422). The longest duration of response was over 6 months, and 18 out of 22 responders are still responding. Conclusions: DZD9008 showed a favorable safety profile and promising anti-tumor efficacy in pre-treated NSCLC with EGFR exon20ins mutations. The updated data will be presented at the meeting. DZD9008 is currently in phase II clinical development (NCT03974022). Clinical trial information: NCT03974022.
Treatment outcomes for stage T1b-2 esophagogastric adenocarcinomas.
Authors: Maria Diab, Lana Khalil, Subir Goyal, Jeffrey M. Switchenko, Olatunji B. Alese, Mehmet Akce, Christina Wu, Bassel F. El-Rayes, Walid Labib Shaib
Journal: Journal of Clinical Oncology (2021)

e16085 Background: Treatment of localized esophageal, gastroesophageal junction (GEJ), and stomach cancer is neoadjuvant therapy with either chemoradiation or chemotherapy followed by surgery. Treatment for T1b-2 stage disease is not well evaluated and this stage is underrepresented in prospective studies. The aim of this study is to evaluate survival outcomes among the three treatment modalities (neoadjuvant chemotherapy (NACT), neoadjuvant chemoradiation (NACRT), and upfront surgery (US)) in this population using the National Cancer Database (NCDB). Methods: Patients (pts) with clinical stage T1b-2N0 and any pathological stage (excluding metastatic) adenocarcinoma of the esophagus, GEJ, and stomach treated with neoadjuvant therapy or upfront surgery, with or without adjuvant chemotherapy (AC), were identified between 2004 and 2015 in the NCDB. Univariate and multivariable analyses were conducted, and Kaplan-Meier analysis and Cox proportional hazard models were used to identify the association between the three treatment modalities and overall survival (OS). Results: A total of 2260 pts were analyzed. The median follow-up was 66.6 months. The median age was 67 years. Most pts were White (86%) and male (77%). 1018 (45%) had moderately-differentiated grade, while 946 (42%) had poorly-differentiated/undifferentiated grade. The most common site of disease was the lower third of esophagus (34.1%). 161 pts (7%) received NACT, of whom 45 pts received AC; 537 pts (24%) received NACRT, of whom 40 pts received AC. 1562 pts (69%) underwent US, of whom 146 pts received AC. US with AC was associated with the best survival, followed by NACT with AC; median OS was 90.1 and 86.8 months for surgery with AC and NACT with AC, respectively. NACRT was associated with the worst survival (39.5 and 40.2 months with and without AC, respectively). The 5-year OS rates were 59.8%, 58.5%, 52.1%, 44.9%, 37.3%, and 37.8%, for US, NACT, and NACRT, with and without AC, respectively. The rate of tumor upstaging was highest in the NACT group, followed by the NACRT group, and lowest in the US group. Postsurgically, 62 (39%) and 48 (30%) pts in the NACT group and 198 (37%) and 161 (30%) pts in the NACRT group had upstaging in their T and N stages, respectively, compared to 214 (13%) and 326 (21%) pts in the US group. For the 1107 pts who also had pathological T1b-2N0 stage disease following US, no difference in survival was observed with or without AC. Conclusions: Upfront surgery with adjuvant chemotherapy and perioperative chemotherapy are associated with the best survival compared to preoperative radiotherapy. This is the largest study to address the best approach for the treatment of T1b-2 stage disease.
Leveraging artificial intelligence for pandemic preparedness and response: a scoping review to identify key use cases
Authors: Ania Syrowatka, Masha Kuznetsova, Ava Alsubai, Adam L. Beckman, Paul A. Bain, Kelly Jean Thomas Craig, Jianying Hu, Gretchen Purcell Jackson, Kyu Rhee, David W. Bates
Journal: npj Digital Medicine (2021)

Artificial intelligence (AI) represents a valuable tool that could be widely used to inform clinical and public health decision-making to effectively manage the impacts of a pandemic. The objective of this scoping review was to identify the key use cases for involving AI for pandemic preparedness and response from the peer-reviewed, preprint, and grey literature. The data synthesis had two parts: an in-depth review of studies that leveraged machine learning (ML) techniques and a limited review of studies that applied traditional modeling approaches. ML applications from the in-depth review were categorized into use cases related to public health and clinical practice, and narratively synthesized. One hundred eighty-three articles met the inclusion criteria for the in-depth review. Six key use cases were identified: forecasting infectious disease dynamics and effects of interventions; surveillance and outbreak detection; real-time monitoring of adherence to public health recommendations; real-time detection of influenza-like illness; triage and timely diagnosis of infections; and prognosis of illness and response to treatment. Data sources and types of ML that were useful varied by use case. The search identified 1167 articles that reported on traditional modeling approaches, which highlighted additional areas where ML could be leveraged for improving the accuracy of estimations or projections. Important ML-based solutions have been developed in response to pandemics, and particularly for COVID-19 but few were optimized for practical application early in the pandemic. These findings can support policymakers, clinicians, and other stakeholders in prioritizing research and development to support operationalization of AI for future pandemics.
Association of gut microbiota and metabolites with tumor response to immune checkpoint inhibitors in patients with unresectable hepatocellular carcinoma.
Authors: Pei-Chang Lee, Chi-Jung Wu, Ya-Wen Hung, Chieh-Ju Lee, Yee Chao, Ming-Chih Hou, Yu-Lun Kuo, Shih-Hsuan Chou, Yi-Hsiang Huang
Journal: Journal of Clinical Oncology (2021)

e16165 Background: Immunotherapy with checkpoint inhibitors (ICI) is a promising treatment for unresectable hepatocellular carcinoma (HCC), but lack of effective biomarker to predict treatment response. Gut microbiome could modulate tumor response to immunotherapy in melanoma; but its effects on HCC are still unclear. Methods: From May 2018 to April 2020, 94 patients received ICI treatment for unresectable HCC (uHCC) in Taipei Veterans General Hospital, the feces samples were prospectively collected before ICI treatment. Finally, 20 patients with radiology proven objective tumor responses (OR; 3 complete responses and 17 partial responses) following immunotherapy, and 21 randomly selected patients with progressive disease (PD) were enrolled for fecal microbiota and metabolites investigation. In addition, feces from 17 healthy volunteers were taken as normal control. Results: Although the alpha diversity was not significantly different among groups, the principal component analysis of Bray-Curtis distance showed a significant clustering of fecal microbiota between HCC patients and healthy volunteers. The significant bacterial dissimilarity was observed between OR and PD patients following immunotherapy (p = 0.016 and 0.019 by Anoism and Adonis tests, respectively). According to linear discriminant analysis (LDA) effect size (LEfSe), a prominence of Prevotella usually regarded as a pathogenic bacterium, was more abundant in HCC patients with PD to ICI treatment. While Veillonella, Lachnospiraceae, Lachnoclostridium, Lactobacillales, Streptococcaceae and Ruminococcaceae were predominant in patients with OR (LDA score [log10] &gt; 3). In addition, primary bile acids, including murocholic acid, α and β-muricholic acids, and secondary bile acids, including ursodeoxycholic acid, ursocholic acid, tauro-ursodeoxycholic acid, and taurohyocholic acid were significantly dominant in the feces of patients with OR to ICI treatment. Correlation network analysis in patients with OR showed significant linkages between Lachnoclostridium, Ruminococcus and secondary bile acids. Conclusions: Fecal microbiota and bile acids are associated with the response to immunotherapy for uHCC patients. These findings highlight the potential role of microbiota as a biomarker and strategy to enhance response to immunotherapy by modifying gut microbiota for uHCC.
Stereotactic body radiotherapy versus conventional external beam radiotherapy in patients with painful spinal metastases: an open-label, multicentre, randomised, controlled, phase 2/3 trial
Authors: Arjun Sahgal, Sten D Myrehaug, Shankar Siva, Giuseppina L Masucci, Pejman J Maralani, Michael Brundage, James Butler, Edward Chow, Michael G Fehlings, Mathew Foote, Zsolt Gabos, Jeffrey Greenspoon, Marc Kerba, Young Lee, Mitchell Liu, Stanley K Liu, Isabelle Thibault, Rebecca K Wong, Maaike Hum, Keyue Ding, Wendy R Parulekar
Journal: The Lancet Oncology (2021)
Landscape and selection of vaccine epitopes in SARS-CoV-2
Authors: Christof C. Smith, Kelly S. Olsen, Kaylee M. Gentry, Maria Sambade, Wolfgang Beck, Jason Garness, Sarah Entwistle, Caryn Willis, Steven Vensko, Allison Woods, Misha Fini, Brandon Carpenter, Eric Routh, Julia Kodysh, Timothy O’Donnell, Carsten Haber, Kirsten Heiss, Volker Stadler, Erik Garrison, Adam M. Sandor, Jenny P. Y. Ting, Jared Weiss, Krzysztof Krajewski, Oliver C. Grant, Robert J. Woods, Mark Heise, Benjamin G. Vincent, Alex Rubinsteyn
Journal: Genome Medicine (2021)

Early in the pandemic, we designed a SARS-CoV-2 peptide vaccine containing epitope regions optimized for concurrent B cell, CD4
Nontraumatic tube method for detecting a vessel responsible for colonic diverticular hemorrhage
Authors: Koichiro Kawano, Mamoru Takenaka, Reiko Kawano, Daisuke Kagoshige, Takao Kato, Katsuhisa Nishi, Masatoshi Kudo
Journal: Endoscopy (2021)

Colonic diverticular hemorrhage has been reported as the most common cause of lower gastrointestinal bleeding [1] [2] [3]. In colorectal diverticular hemorrhage, active bleeding, nonbleeding visible vessels, and adherent clot (indicating active bleeding or nonbleeding visible vessels when removed) are defined as stigmata of recent hemorrhage (SRH) [4].
The seroprevalence of SARS-CoV-2 antibodies among health care workers before the era of vaccination: a systematic review and meta-analysis
Authors: İlker Kayı, Bahar Madran, Şiran Keske, Özge Karanfil, Jose Ramon Arribas, Natalia Psheniсhnaya, Nicola Petrosillo, Mehmet Gönen, Önder Ergönül
Journal: Clinical Microbiology and Infection (2021)