tbuckley/cabot-search huggingface dataset:
High-Quality <i>Arabidopsis Thaliana</i> Genome Assembly with Nanopore and HiFi Long Reads
Authors: Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye
Journal: Genomics Proteomics & Bioinformatics (2021)

Abstract Arabidopsis thaliana is an important and long-established model species for plant molecular biology, genetics, epigenetics, and genomics. However, the latest version of reference genome still contains a significant number of missing segments. Here, we reported a high-quality and almost complete Col-0 genome assembly with two gaps (named Col-XJTU) by combining the Oxford Nanopore Technologies ultra-long reads, Pacific Biosciences high-fidelity long reads, and Hi-C data. The total genome assembly size is 133,725,193 bp, introducing 14.6 Mb of novel sequences compared to the TAIR10.1 reference genome. All five chromosomes of the Col-XJTU assembly are highly accurate with consensus quality (QV) scores &amp;gt; 60 (ranging from 62 to 68), which are higher than those of the TAIR10.1 reference (ranging from 45 to 52). We completely resolved chromosome (Chr) 3 and Chr5 in a telomere-to-telomere manner. Chr4 was completely resolved except the nucleolar organizing regions, which comprise long repetitive DNA fragments. The Chr1 centromere (CEN1), reportedly around 9 Mb in length, is particularly challenging to assemble due to the presence of tens of thousands of CEN180 satellite repeats. Using the cutting-edge sequencing data and novel computational approaches, we assembled a 3.8-Mb-long CEN1 and a 3.5-Mb-long CEN2. We also investigated the structure and epigenetics of centromeres. Four clusters of CEN180 monomers were detected, and the centromere-specific histone H3-like protein (CENH3) exhibited a strong preference for CEN180 Cluster 3. Moreover, we observed hypomethylation patterns in CENH3-enriched regions. We believe that this high-quality genome assembly, Col-XJTU, would serve as a valuable reference to better understand the global pattern of centromeric polymorphisms, as well as the genetic and epigenetic features in plants.
Euthanasia and assisted dying: the illusion of autonomy—an essay by Ole Hartling
Authors: Ole Hartling
Journal: BMJ (2021)

As a medical doctor I have, with some worry, followed the assisted dying debate that regularly hits headlines in many parts of the world. The main arguments for legalisation are respecting self-determination and alleviating suffering. Since those arguments appear self-evident, my book Euthanasia and the Ethics of a Doctor’s Decisions—An Argument Against Assisted Dying 1 aimed to contribute to the international debate on this matter.

I found it worthwhile to look into the arguments for legalisation more closely, with the hope of sowing a little doubt in the minds of those who exhibit absolute certainty in the matter. This essay focuses on one point: the concept of “autonomy.”

(While there are several definitions of voluntary, involuntary, and non-voluntary euthanasia as well as assisted dying, assisted suicide, and physician assisted suicide, for the purposes of brevity in this essay, I use “assisted dying” throughout.)

Currently, in richer countries, arguments for legalising assisted dying frequently refer to the right to self-determination—or autonomy and free will. Our ability to self-determine seems to be unlimited and our right to it inviolable. The public’s response to opinion poll questions on voluntary euthanasia show that people can scarcely imagine not being able to make up their own minds, nor can they imagine not having the choice. Moreover, a healthy person answering a poll may have difficulty imagining being in a predicament where they simply would not wish to be given the choice.

I question whether self-determination is genuinely possible when choosing your own death. In my book, I explain that the choice will always be made in the context of a non-autonomous assessment of your quality of life—that is, an assessment outside your control.1

All essential decisions that we make are made in relation to other people. Our decisions are affected by other people, and …
A national audit of oral propranolol for the treatment of infantile haemangiomas
Authors: C. Cotter, L. Solman, C. Flohr
Journal: British Journal of Dermatology (2021)

Infantile haemangiomas (IH) affect up to 4% of infants and are the most common tumour of infancy. Although self-limiting, some lesions can lead to visual impairment, airway obstruction, ulceration or cosmetic disfigurement and require intervention. Oral propranolol, a nonselective beta-blocker was serendipitously identified as an effective treatment of IH in 2008 and is now recommended as first-line therapy for complicated lesions.
Chicago’s Stay-at-Home Mandate—The Need to Improve on Domestic Violence Prevention and Response
Authors: Amy Bonomi, Rashmi Gangamma, Theresa H. Cruz
Journal: JAMA Network Open (2021)

Louisa Baidoo, BA; Tanya L. Zakrison, MD, MPH; Gillian Feldmeth, BS; Stacy Tessler Lindau, MD, MAPP; Elizabeth L. Tung, MD, MS
Elevated 123I-MIBG Activity in Intramuscular Hemangioma
Authors: Wei Wang, Xu Yang, Jigang Yang
Journal: Clinical Nuclear Medicine (2020)

A 3-year-old boy with high-risk neuroblastoma underwent 123I-MIBG scan to evaluate the disease status after surgery and chemotherapy. 123I-MIBG SPECT/CT demonstrated liver metastasis. In addition, mildly increased uptake in the inferior left erector spinae was noted. Contrast-enhanced CT suggested intramuscular hemangioma. The 123I-MIBG accumulation in the intramuscular hemangioma persisted during the follow-up scan, whereas the abnormal activity in the liver was resolved.
Smart magnetic resonance imaging-based theranostics for cancer
Authors: Beatriz Brito, Thomas W Price, Juan Gallo, Manuel Bañobre-López, Graeme J Stasiuk
Journal: Theranostics (2021)

Smart theranostics are dynamic platforms that integrate multiple functions, including at least imaging, therapy, and responsiveness, in a single agent. This review showcases a variety of responsive theranostic agents developed specifically for magnetic resonance imaging (MRI), due to the privileged position this non-invasive, non-ionising imaging modality continues to hold within the clinical imaging field. Different MRI smart theranostic designs have been devised in the search for more efficient cancer therapy, and improved diagnostic efficiency, through the increase of the local concentration of therapeutic effectors and MRI signal intensity in pathological tissues. This review explores novel small-molecule and nanosized MRI theranostic agents for cancer that exhibit responsiveness to endogenous (change in pH, redox environment, or enzymes) or exogenous (temperature, ultrasound, or light) stimuli. The challenges and obstacles in the design and
The expressed mutational landscape of microsatellite stable colorectal cancers
Authors: Anita Sveen, Bjarne Johannessen, Ina A. Eilertsen, Bård I. Røsok, Marie Gulla, Peter W. Eide, Jarle Bruun, Kushtrim Kryeziu, Leonardo A. Meza-Zepeda, Ola Myklebost, Bjørn A. Bjørnbeth, Rolf I. Skotheim, Arild Nesbakken, Ragnhild A. Lothe
Journal: Genome Medicine (2021)

Abstract Background Colorectal cancer is the 2nd leading cause of cancer-related deaths with few patients benefiting from biomarker-guided therapy. Mutation expression is essential for accurate interpretation of mutations as biomarkers, but surprisingly, little has been done to analyze somatic cancer mutations on the expression level. We report a large-scale analysis of allele-specific mutation expression. Methods Whole-exome and total RNA sequencing was performed on 137 samples from 121 microsatellite stable colorectal cancers, including multiregional samples of primary and metastatic tumors from 4 patients. Data were integrated with allele-specific resolution. Results were validated in an independent set of 241 colon cancers. Therapeutic associations were explored by pharmacogenomic profiling of 15 cell lines or patient-derived organoids. Results The median proportion of expressed mutations per tumor was 34%. Cancer-critical mutations had the highest expression frequency (gene-wise mean of 58%), independent of frequent allelic imbalance. Systematic deviation from the general pattern of expression levels according to allelic frequencies was detected, including preferential expression of mutated alleles dependent on the mutation type and target gene. Translational relevance was suggested by correlations of KRAS / NRAS or TP53 mutation expression levels with downstream oncogenic signatures ( p &lt; 0.03), overall survival among patients with stage II and III cancer ( KRAS / NRAS : hazard ratio 6.1, p = 0.0070), and targeted drug sensitivity. The latter was demonstrated for EGFR and MDM2 inhibition in pre-clinical models. Conclusions Only a subset of mutations in microsatellite stable colorectal cancers were expressed, and the “expressed mutation dose” may provide an opportunity for more fine-tuned biomarker interpretations.
High-dimensional immune phenotyping of blood cells by mass cytometry in patients infected with hepatitis C virus
Authors: Jacobus Herderschee, Tytti Heinonen, Craig Fenwick, Irene T. Schrijver, Khalid Ohmiti, Darius Moradpour, Matthias Cavassini, Giuseppe Pantaleo, Thierry Roger, Thierry Calandra, K. Aebi-Popp, A. Anagnostopoulos, M. Battegay, E. Bernasconi, J. Böni, D.L. Braun, H.C. Bucher, A. Calmy, M. Cavassini, A. Ciuffi, G. Dollenmaier, M. Egger, L. Elzi, J. Fehr, J. Fellay, H. Furrer, C.A. Fux, H.F. Günthard, D. Haerry, B. Hasse, H.H. Hirsch, M. Hoffmann, I. Hösli, M. Huber, C.R. Kahlert, L. Kaiser, O. Keiser, T. Klimkait, R.D. Kouyos, H. Kovari, B. Ledergerber, G. Martinetti, B. Martinez de Tejada, C. Marzolini, K.J. Metzner, N. Müller, D. Nicca, P. Paioni, G. Pantaleo, M. Perreau, A. Rauch, C. Rudin, A.U. Scherrer, P. Schmid, R. Speck, M. Stöckle, P. Tarr, A. Trkola, P. Vernazza, G. Wandeler, R. Weber, S. Yerly
Journal: Clinical Microbiology and Infection (2021)
포스터발표 : 컨벤션홀 특설 발표장 ; Cyclooxygenase-2 억제제에 의한 간암세포의 caspase 의존 내인성 세포자멸사
Authors: 김은영, 송일한, 백두산, 임상수, 신기철, 신현덕, 윤세영, 김석배, 신정은, 김홍자
Journal: Clinical and Molecular Hepatology (2008)
Haematological malignancies in sub-Saharan Africa: east Africa as an example for improving care
Authors: Clement D Okello, Nixon Niyonzima, Marta Ferraresso, Sylivestor Kadhumbula, Henry Ddungu, Katherine Tarlock, Joyce Balagadde-Kambugu, Abrahams Omoding, Louis Ngendahayo, Alfred Karagu, Julius Mwaiselage, John M Harlan, Thomas S Uldrick, Suzanne D Turner, Jackson Orem
Journal: The Lancet Haematology (2021)
Odevixibat: First Approval
Authors: Emma D. Deeks
Journal: Drugs (2021)

Odevixibat (Bylvay™) is a small molecule inhibitor of the ileal bile acid transporter being developed by Albireo Pharma, Inc. for the treatment of various cholestatic diseases, including progressive familial intrahepatic cholestasis (PFIC). In July 2021, odevixibat received its first approval in the EU for the treatment of PFIC in patients aged ≥ 6 months, followed shortly by its approval in the USA for the treatment of pruritus in patients aged ≥ 3 months with PFIC. Odevixibat is also in clinical development for the treatment of other cholestatic diseases, including Alagille syndrome and biliary atresia, in various countries. This article summarizes the milestones in the development of odevixibat leading to this first approval for PFIC.
Surgical delays of less than 1 year in Mohs surgery associated with tumor growth in moderately- and poorly-differentiated squamous cell carcinomas but not lower-grade squamous cell carcinomas or basal cell carcinomas: A retrospective analysis
Authors: Jack Lee, Vernon J. Forrester, Wendy M. Novicoff, Darren J. Guffey, Mark A. Russell
Journal: Journal of the American Academy of Dermatology (2021)
P57: Surprising trends in the detection of cutaneous malignancy during the COVID‐19 pandemic
Journal: British Journal of Dermatology (2021)

diagnostic accuracy measure.Two authors independently screened articles, extracted data and assessed quality.Disagreements were resolved by a third reviewer.Ten studies were included, comprising 41 703 patients who underwent TBP and 6203 biopsies.Melanoma in situ (MIS) was diagnosed in 315 (5Á1%) lesions and invasive melanoma in 187 (3Á0%) lesions biopsied.Summary estimates for TBP in diagnosing melanoma were calculated: mean percentage of biopsies positive for MIS or melanoma was 16% (95% confidence interval 11-20); number needed to biopsy (NNB) was 8Á6 (range 2Á3-19Á6); naevus : melanoma ratio was 7Á6 (range 1Á3-18Á6); and the MIS : melanoma ratio was 1Á7 (range 1Á0-3Á5).Regression analysis showed a negative correlation between NNB and MIS : melanoma ratio.Available data regarding the diagnostic accuracy of TBP are heterogeneous owing to variability in the risk profile of cohorts and TBP protocols.Best current estimates suggest that TBP to diagnose melanoma has an acceptable NNB in high-risk patients.However, prospective diagnostic test accuracy studies are needed to gauge accurately the diagnostic accuracy of TBP.
USPSTF found insufficient evidence on benefits and harms of screening for vitamin D deficiency in asymptomatic adults
Authors: KoKo Aung, Thwe Htay
Journal: Annals of Internal Medicine (2021)

ACP Journal ClubSeptember 2021USPSTF found insufficient evidence on benefits and harms of screening for vitamin D deficiency in asymptomatic adultsKoKo Aung, MD, MPH, Thwe Htay, MDKoKo Aung, MD, MPHPaul L. Foster School of Medicine, El Paso, Texas, USA (K.A., T.H.), Thwe Htay, MDPaul L. Foster School of Medicine, El Paso, Texas, USA (K.A., T.H.)Author, Article, and Disclosure Informationhttps://doi.org/10.7326/ACPJ202109210-100 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail Source CitationKrist AH, Davidson KW, Mangione CM, et al. Screening for vitamin D deficiency in adults: US Preventive Services Task Force recommendation statement. JAMA. 2021;325:1436-42. https://pubmed.ncbi.nlm.nih.gov/33847711Clinical Impact RatingsGIM/FP/GP: Public Health: References1 Kahwati LC, LeBlanc E, Weber RP, et al. Screening for vitamin D deficiency in adults: updated evidence report and systematic review for the US Preventive Services Task Force. JAMA. 2021;325:1443-63. [PMID: 33847712] Google Scholar2 Jorde R, Grimnes G. Serum PTH is not a good marker for defining a threshold for vitamin D deficiency. Endocr Connect. 2020;9:396-404. [PMID: 32412426] Google Scholar3 Amrein K, Scherkl M, Hoffmann M, et al. Vitamin D deficiency 2.0: an update on the current status worldwide. Eur J Clin Nutr. 2020;74:1498-1513. [PMID: 31959942] Google Scholar4 Sempos CT, Binkley N. 25-Hydroxyvitamin D assay standardisation and vitamin D guidelines paralysis [Editorial]. Public Health Nutr. 2020;23:1153-64. [PMID: 32301688] Google Scholar5 Waldron JL, Ashby HL, Cornes MP, et al. Vitamin D: a negative acute phase reactant. J Clin Pathol. 2013;66:620-2. [PMID: 23454726] Google Scholar6 Szabo L. Vitamin D, the sunshine supplement, has shadowy money behind it. New York Times. 18 Aug 2018:BU1. Accessed at www.nytimes.com/2018/08/18/business/vitamin-d-michael-holick.html on 17 May 2021. Google Scholar7 Souberbielle JC, Courbebaisse M, Cormier C, et al. When should we measure vitamin D concentration in clinical practice? Scand J Clin Lab Invest Suppl. 2012;243:129-35. [PMID: 22536774] Google Scholar Author, Article, and Disclosure InformationAffiliations: Paul L. Foster School of Medicine, El Paso, Texas, USA (K.A., T.H.)Disclosures: The commentators have reported no disclosures of interest. The forms can be viewed at www.acponline.org/authors/icmje/ConflictOfInterestForms.do?msNum=M20-7320.This article was published at Annals.org on 7 September 2021. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics Cited byImmune Response in Vitamin D Deficient Metastatic Colorectal Cancer Patients: A Player That Should Be Considered for Targeted Vitamin D Supplementation September 2021Volume 174, Issue 9Page: JC100 ePublished: 7 September 2021 Issue Published: September 2021 Copyright & PermissionsCopyright © 2021 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
Endoscopic submucosal dissection of a lateral spreading tumor involving the appendiceal orifice using a multi-traction device.
Authors: Thomas Lambin, Jérémie Albouys, Clara Yzet, Soline Brun, Florian Rostain, Jérôme Rivory, Mathieu Pioche
Journal: Endoscopy (2021)

Endoscopic submucosal dissection (ESD) is the technique of choice for the resection of large superficial colorectal lesions [1], but it can be technically challenging in some situations. For this reason, lesions involving the appendiceal orifice have long been removed surgically. However, recent findings have found that ESD is effective and safe in that situation [2] [3], even for lesions deeply invading the appendiceal orifice (Toyonaga 3 lesions) with the help of traction device [4] [5].
Prevalence of Allergic Reactions After Pfizer-BioNTech COVID-19 Vaccination Among Adults With High Allergy Risk
Authors: Ronen Shavit, Ramit Maoz-Segal, Mona Iancovici-Kidon, Irena Offengenden, Soad Haj Yahia, Diti Machnes Maayan, Yulia Lifshitz-Tunitsky, Stanley Niznik, Shirly Frizinsky, Michal Deutch, Eti Elbaz, Hosney Genaim, Galia Rahav, Itzchak Levy, Anna Belkin, Gili Regev-Yochay, Arnon Afek, Nancy Agmon-Levin
Journal: JAMA Network Open (2021)

<h3>Importance</h3> Allergic reactions among some individuals who received the Pfizer-BioNTech (BNT162b2) COVID-19 vaccine discourage patients with allergic conditions from receiving this vaccine and physicians from recommending the vaccine. <h3>Objective</h3> To describe the assessment and immunization of highly allergic individuals with the BNT162b2 vaccine. <h3>Design, Setting, and Participants</h3> In a prospective cohort study from December 27, 2020, to February 22, 2021, 8102 patients with allergies who applied to the COVID 19 vaccine referral center at the Sheba Medical Center underwent risk assessment using an algorithm that included a detailed questionnaire. High-risk patients (n = 429) were considered "highly allergic" and were immunized under medical supervision. <h3>Exposures</h3> Pfizer-BioNTech (BNT162b2) COVID-19 vaccine. <h3>Main Outcomes and Measures</h3> Allergic and anaphylactic reactions after the first and second doses of BNT162b2 vaccine among highly allergic patients. <h3>Results</h3> Of the 429 individuals who applied to the COVID-19 referral center and were defined as highly allergic, 304 (70.9%) were women and the mean (SD) age was 52 (16) years. This highly allergic group was referred to receive immunization under medical supervision. After the first dose of the BNT162b2 vaccine, 420 patients (97.9%) had no immediate allergic event, 6 (1.4%) developed minor allergic responses, and 3 (0.7%) had anaphylactic reactions. During the study period, 218 highly allergic patients (50.8%) received the second BNT162b2 vaccine dose, of which 214 (98.2%) had no allergic reactions and 4 patients (1.8%) had minor allergic reactions. Other immediate and late reactions were comparable with those seen in the general population, except for delayed itch and skin eruption, which were more common among allergic patients. <h3>Conclusions and Relevance</h3> The rate of allergic reactions to BNT162b2 vaccine, is higher among patients with allergies, particularly among a subgroup with a history of high-risk allergies. This study suggests that most patients with a history of allergic diseases and, particularly, highly allergic patients can be safely immunized by using an algorithm that can be implemented in different medical facilities and includes a referral center, a risk assessment questionnaire, and a setting for immunization under medical supervision of highly allergic patients. Further studies are required to define more specific risk factors for allergic reactions to the BNT162b2 vaccine.
To Deprescribe or Not to Deprescribe Aspirin—A <i>Clear Indication</i> Is the Challenge—Reply
Authors: Jordan K. Schaefer, Xiaowen Kong, Geoffrey D. Barnes
Journal: JAMA Internal Medicine (2021)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Internal Medicine HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Internal Medicine journal
Stem cell-derived neurons reflect features of protein networks, neuropathology, and cognitive outcome of their aged human donors
Authors: Valentina N. Lagomarsino, Richard V. Pearse, Lei Liu, Yi-Chen Hsieh, Marty A. Fernandez, Elizabeth A. Vinton, Daniel Paull, Daniel Felsky, Shinya Tasaki, Chris Gaiteri, Badri Vardarajan, Hyo Lee, Christina R. Muratore, Courtney R. Benoit, Vicky Chou, Seeley B. Fancher, Amy He, Julie P. Merchant, Duc M. Duong, Hector Martinez, Monica Zhou, Fatmata Bah, Maria A. Vicent, Jonathan M.S. Stricker, Jishu Xu, Eric B. Dammer, Allan I. Levey, Lori B. Chibnik, Vilas Menon, Nicholas T. Seyfried, Philip L. De Jager, Scott Noggle, Dennis J. Selkoe, David A. Bennett, Tracy L. Young-Pearse
Journal: Neuron (2021)
P-74 The impact of first-line chemotherapy in elderly patients with advanced pancreatic cancer: A mono-institutional retrospective study
Authors: M. Maratta, M. Chiaravalli, M. Bensi, B. Di Stefano, M. Ribelli, D. Barone, E. Gurreri, F. Monaca, C. Cutigni, C. Bagalà, G. Tortora, L. Salvatore
Journal: Annals of Oncology (2021)
Abstract 16489: Blood Coagulation Status After Transcatheter Aortic Valve Implantation in Patients With/Without Oral Anticoagulant Therapy
Authors: Taiga Katayama, Naoyuki Yokoyama, Yusuke Watanabe, Shinji Takahashi, Hirofumi Hioki, Hirosada Yamamoto, Kazuo Kawasugi, Ken Kozuma
Journal: Circulation (2019)

Introduction: Patients undergoing transcatheter aortic valve implantation (TAVI) with atrial fibrillation or venous thromboembolism were indicated for oral anticoagulant (OAC) therapy. However, coa...