tbuckley/cabot-search huggingface dataset:
Model selection applied to 750 outpatient ICD-9 codes identifies hazards important for all-cause cancer mortality in 2 million veterans with 14 years of follow-up.
Authors: Benjamin McMahon, Sayera Dhaubhadel, Nicolas Hengartner, Ioana Danciu, Tate Janet, Amy Justice
Journal: Journal of Clinical Oncology (2020)

2053 Background: Cost-benefit analysis before undergoing cancer treatments can involve a broad array of factors, yet existing statistical algorithms are limited to a few of the most commonly observed competing risks. Using 20 years of Veteran medical records from the Veteran’s Administration, we identify a broad array of outpatient descriptors providing contributions to computed mortality comparable in size to common cancers. Methods: 1,911,632 Veterans born between 1927 and 1968 with medical records extending from October 1, 2000 until either recorded death after October 1, 2005 (47%) or observation during CY 2019 were split equally into age-matched test and training sets. The 20 year-long record was split into three intervals: 5 years during which ICD codes were tallied, 14 years of waiting, and establishment of continuation in care during 2019. The 750 most common outpatient ICD9 codes were recorded as present/absent for each patient and used in a generalized linear model to predict subsequent mortality, subject to LASSO model selection and 10-fold cross validation. Gender was included as a covariate as well as age at time of prediction, up to the 4 th power. Results: The C-statistic for predicting mortality in 14 years of follow-up was 0.835 on training data and 0.833 on test data when using the 498 codes selected by LASSO. Prevalent codes with the largest model coefficients were (ICD 9 code: model coefficient, # alive/# deceased in test set) congestive heart failure (428.0: 0.66, 9k/48k), chronic airway obstruction (496.: 0.60, 42k/105k), and tobacco use disorder (305.1: 0.54, 107k/123k), while the prevalent codes most protective in comparison to baseline were hyperlipidemia (272.4: -0.21, 211k/225k) and colon cancer screening (V76.51: -0.16, 49k/39k). In comparison, observed cancer ICD 9 coefficients were lung (162.9: 1.03, 1k/7k), colon (153.9: 0.18, 3.1k/7.0k), and prostate (185.: 0.06, 16k/32k). 74 predictors contribute with coefficients greater than colon cancers, such as ‘no household member able to render care’ (V60.4: 0.28, 1.1k/4.2k). Conclusions: A wide variety of structured data contribute at a similar level of importance in prediction of 14-year mortality. While various selection biases, co-linearity of predictors, differences in treatments, and missing data are significant impediments to utilization of predictive models in clinical practice, we have demonstrated an ability to identify and quantify predictors from a large data set with model selection techniques.
Headache and sleep disorders
Authors: 燕兰云, 万琪
Journal: BMJ (2010)

头痛和睡眠障碍是临床常见的疾病,两者常并存于同一患者.偏头痛、紧张型头痛(TTH)、丛集性头痛和少见的睡眠性头痛(HH)是与睡眠相关性较大的原发性头痛[1],失眠和睡眠呼吸暂停是与头痛相关性较大的睡眠障碍[2]。
The role of continuity of systematic treatment and rehabilitation in patients with metastatic colorectal cancer in elderly and senile age.
Authors: Iuliia Vladimirovna Alekseeva, Tatiana Semiglazova, Elena Tkachenko, Boris Kasparov, Nadezhda Brish, Larisa Valentinovna Filatova, Vladislav Semiglazov, Aleksey Belyaev, Veronika Klimenko, Svetlana Protsenko, Gulfiya Midhatovna Teletaeva, Dilorom H. Latipova
Journal: Journal of Clinical Oncology (2020)

e16041 Background: The concomitant pathology, cancer and geriatric status affect the organism of a sick elderly person. In routine clinical practice elderly patients require comprehensive geriatric assessment (CGO). Despite many treatment strategies for elderly patients with metastatic colorectal cancer (mCRC), there are no use of rehabilitation programs and the assessment of their impact on the treatment tolerability and survival. Methods: The study includes patients with newly diagnosed mCRC stage IV, receiving the first line of chemotherapy (FOLFOX). Patients are given CGO before starting chemotherapy and in dynamics.The following scales are used for geriatric examination: Cumulative Illness Rating Scale for Geriatrics (CIRS-G); Activities of Daily Living (ADL); Daily instrumental activity scale (IADL); Mini nutritional assessment (MNA); Clock Drawing Test (CDT); Geriatric depression scale (GDS). Results: At the moment 29 patients are included in the study. According the results of CGO we determined that elderly and middle-aged patients are similar in cognitive, mental, and nutritional status, but they have statistically significant differences on the MMSE scale (P=0,014). In both groups patients have a decrease in IADL and cognitive functions, the presence of depression. Elderly patients (&gt; 60 years old) are more likely to experience chronic pain (P&lt;0.05) and increased blood pressure (P&lt;0.05) (Table). Conclusions: The management tactics of patients with mCRC in elderly age shouldn't be based only on chronological age, ECOG or the Karnovsky index, that don't reflect functional disorders in patients of the older age group. It is necessary to define algorithms for medical rehabilitation in cancer patients of the older age group. A CGO is aimed at developing a medical rehabilitation plan together with an elderly patient and his environment, and an algorithm for supporting his health status during and after specialized treatment. [Table: see text]
Internet-based assessment technology for age-related cognitive impairment
Authors: Jia Zhiying, Dong Minye, Shi Zhensu, Li Guohong, Jin Chunlin, Chen Jie
Journal: BMJ (2019)

With the population aging, the number of elderly with Alzheimer′s disease or other types of dementia is increasing, which seriously threatens the health and quality of life in elderly. The early screening and detection of dementia among high-risk population and appropriate interventional measures would delay the disease course, and maintain patients′ self-care abilities and dignity. Computerized neuropsychological assessment devices are economic and efficient, and suitable for screening in large population. This article reviews the theory, characteristics and application of internet-based neuropsychological assessment for age-related cognitive impairment, as well as the prospect in the future studies.


Key words: 
Cognitive impairment; Internet technology; Screening
Radiomic texture analysis correlates with PDAC patient outcomes on SM-88.
Authors: Allyson J. Ocean, Ronald Lee Korn, Semmie Kim, Andre Burkett, Ziad Hindosh, Zak Nolte, Giuseppe Del Priore
Journal: Journal of Clinical Oncology (2020)

e16776 Background: SM-88 (racemetyrosine) is a dysfunctional tyrosine derivative; previous studies demonstrated a well-tolerated profile with encouraging efficacy. Recent advances in image analysis using Quantitative Textural Analysis (QTA) have uncovered non-invasive biomarkers that correlate with molecular drivers of cancer and prognostic signatures of response in PDAC. Earlier radiomic data from subjects treated with SM-88 showed a positive correlation between circulating tumor cells and tumor texture at baseline. This study extends those findings to focus on radiomic changes associated with SM-88 doses in a Phase II dose escalation trial (NCT03512756). Methods: Retrospective evaluation of 18 subjects with &gt;1 prior therapy, ECOG PS &lt;2, with no restriction on size, number, or locations of mets, and had baseline (BL) and follow up (FUP) contrast enhanced CTs. Subjects received &gt; 1 cycle of SM-88 at either 460mg (n = 8) or 920mg (n = 10) QD oral doses. CTs were analyzed by the QTA platform (TexRad, Essex, UK) for tumor texture. The largest met of each subject was selected using portal venous phase images. A region of interest was posited on the axial slice with the longest tumor diameter and features automatically generated using voxel resampling to correct for scanner variability across subjects and time points. Results were displayed as histogram frequency curves (HFCs) of pixel densities (Hounsfield Units). First order HFC analysis (mean, StDev, MPP, skewness, kurtosis) at spatial scale filters (SSF) ranging from no filter, to fine, to coarse texture (SSF:0, SSF:2, SSF:6, respectively) were reported. Results: Subjects whose largest lesions showed greater changes in tumor texture at FUP vs. BL were more likely to develop tumor progression (StDev in PD (n = 10) vs SD (n = 7) (1 N/A): -0.07 vs -0.25, p = 0.05). Greater tumor textural changes were associated with poor survival at 180 days (Skewness: Chi-Sq. = 4.81, p = 0.03; HR = 4.1 for above median □Skew ssf3 ). There was a negative change in FUP kurtosis vs BL in the 6 subjects who developed new lesions vs the 12 who did not (mean □kurtosis = -0.67 vs +2.63, p = 0.05). Greater change in tumor texture on FUP vs BL scans was seen in the 460mg vs 920mg group (MPP LD = -0.29, MPP HD = -0.04; p = 0.05) suggesting more tumor stability (less change in texture and better outcomes) was associated with the 920mg dose. Conclusions: Tumor lesions in subjects on 920mg of SM-88 were less likely to show a change in tumor texture and were associated with better outcomes. Using radiomic QTA, less tumor texture variability from baseline may be associated with better outcomes in PDAC subjects.
Color Doppler ultrasonography in assessment of activity of ulcerative colitis
Authors: Jie Zhang, Hong-qiu Han, Xiao-cang Cao
Journal: BMJ (2012)

Sixty patients with ulcerative colitis (UC),including 28 males and 32 females were enrolled in the study.Color Doppler ultrasonographic scans were performed and the disease activity was estimated base on the Sourtherland score index (DAI).On the sonography the colon with active inflammatory disease showed bowel wall thickening,alteration of layers structure or even discrimination and increased vascular signals.Using DAI as the gold standard,the sensitivity,specificity,positive predictive value,negative predictive value and accurate rate for ultrasonography in assessment of UC activity were 90.0％ (36/40),75.0％ ( 15/20),87.8％ (36/41),78.9％ (15/19),85.0％ (51/60),respectively.In conclusion,Color Doppler ultrasonography provides a convenient technique for assessment of bowel involvement and inflammatory activity in ulcerative colitis with high sensitivity and accuracy.

Key words: 
Ultrasonography, Doppler;  Colitis,ulcerative
Evaluation of the effectiveness of dyslipidemia health management in a community
Authors: Jian-dong Zhang, Ning Zhuang, Li-juan Gao
Journal: BMJ (2011)

In the Jinsong district of Beijing,345 patients with dyslipidemia were selected for study.Health management was implemented for one year,during which time,monitoring,analysis,and evaluation of the health of individuals and groups was conducted; health advice and guidance were given with regard to health risk factors.After the one-year intervention,the average daily dietary intake of salt,oil,and meat was reduced by 2,4,and 18 g,respectively,and the average daily intake of vegetables increased by 45 g.The average levels of body mass index,systolic blood pressure,diastolic blood pressure,total cholesterol,triglycerides,and low-density lipoprotein cholesterol were reduced by 0.47 kg/m2,3.0 mm Hg ( 1 mm Hg =0.133 kPa),1.6 mm Hg,0.76 mmol/L,0.83 mmol/L,and 0.42 mmol/L,respectively,while the average level of high-density lipoprotein cholesterol increased by 0.05 mmol/L.All the differences were significant.

Key words: 
Dyslipidemias; Health management
Comparison of three minimally invasive surgical methods in treatment of impacted upper-ureteral calculi
Authors: Yunyan Wang, Bing Zhong, Junsong Meng, Xiaosong Yang, Peijin Hou
Journal: BMJ (2017)

One hundred and fifty patients with impacted upper-ureteral calculi were treated with ureteroscopic lithotripsy (URSL group, n=58), percutaneous nephrolithotomy (PCNL group, n=42) or retroperitoneal laparoscopic ureterolithotomy (RPLU group, n=50) from April 2011 to August 2015. The operative time, length of postoperative hospital stay, stone-free rate and the incidence of postoperative complications were observed and compared among three groups. The stone-free rate of URSL group one month after surgery was 77%, which was significantly lower than PCNL (95%) and RPLU groups (100%) (P<0.05). But the operative time and length of postoperative hospital stay of URSL group [(37.2±5.6)min, (3.9±0.8)d] were significantly shorter than PCNL group[(75.2±6.7)min, (7.9±0.9))d] and RPLU group [(65.3±6.1)min, (8.7±0.9)d] (all P<0.05). The postoperative complication rates of three groups were 8%, 10% and 10%, respectively.


Key words: 
Ureteral calculi, upper; Lithotripsy, Ureteroscopy; Nephrolithotomy, percutaneous; Laparoscopy
Ocular manifestations of granulomatosis with polyangiitis: an analysis of 164 patients
Authors: Di Chen, Hanyi Min, Jiuliang Zhao, Xiaofeng Zeng
Journal: BMJ (2016)

Objective
To review the ophthalmic features of granulomatosis with polyangiitis (GPA).


Methods
Clinical data of 164 GPA patients diagnosed in Peking Union Medical College Hospital during the past 10 years were retrospectively reviewed.


Results
Among 164 patients, 48 (29.3%) had ocular involvement with a male to female ratio of 1.4∶1 and an average age of (45±15) years. Nine patients (5.5%) were first diagnosed at the ophthalmology department. Scleritis (15.9%, 26/164), orbit lesions (13.4%, 22/164) and peripheral corneal ulcer (9.1%, 15/164) were the three most common ophthalmic complications. Twenty-two patients (13.4%) had positive findings in the orbit imaging. Six patients (3.7%, 6/164) lost their vision due to GPA.


Conclusion
The ocular manifestations of GPA are diverse and complicated. GPA may affect every component of the eye, sclera, orbit and cornea are the most frequently affected sites of the eye.


Key words: 
Wegener granulomatosis; Eye manifestations; Diagnosis
Mobile internet and cloud computing promotes the development of electronic health record
Authors: Hui Gong, Weili Yan, Liyin Jin, Tao Zhang, Daoping Song, Ping Lu, Huiyun Tang
Journal: BMJ (2018)

Currently, electronic health records (EHR) are largely created and maintained by physicians, and used just as an electronic record. In future, EHR will be a tool of information sharing and patients may participate in decision making for their own health with this tool. This article summarizes the concept of EHR, the problems it faces and how the mobile internet and cloud computing can promote the development of EHR.


Key words: 
Medical informatics; Computer communication networks; Electronic health records
Developmental regulation of canonical and small ORF translation from mRNAs
Authors: Pedro Patraquim, Muhammad Ali Shahzad Mumtaz, José Ignacio Pueyo, Julie Louise Aspden, Juan-Pablo Couso
Journal: Genome biology (2020)

Ribosomal profiling has revealed the translation of thousands of sequences outside annotated protein-coding genes, including small open reading frames of less than 100 codons, and the translational regulation of many genes. Here we present an improved version of Poly-Ribo-Seq and apply it to Drosophila melanogaster embryos to extend the catalog of in vivo translated small ORFs, and to reveal the translational regulation of both small and canonical ORFs from mRNAs across embryogenesis.We obtain highly correlated samples across five embryonic stages, with nearly 500 million putative ribosomal footprints mapped to mRNAs, and compare them to existing Ribo-Seq and proteomic data. Our analysis reveals, for the first time in Drosophila, footprints mapping to codons in a phased pattern, the hallmark of productive translation. We propose a simple binomial probability metric to ascertain translation probability. Our results also reveal reproducible ribosomal binding apparently not resulting in productive translation. This non-productive ribosomal binding seems to be especially prevalent amongst upstream short ORFs located in the 5' mRNA leaders, and amongst canonical ORFs during the activation of the zygotic translatome at the maternal-to zygotic transition.We suggest that this non-productive ribosomal binding might be due to cis-regulatory ribosomal binding and to defective ribosomal scanning of ORFs outside periods of productive translation. Our results are compatible with the main function of upstream short ORFs being to buffer the translation of canonical canonical ORFs; and show that, in general, small ORFs in mRNAs display markers compatible with an evolutionary transitory state towards full coding function.
Development of a novel liquid biopsy test to diagnose and locate gastrointestinal cancers.
Authors: Yuying Wang, Jianchao Zheng, Zhilong Li, Ruijingfang Jiang, Jiaxi Peng, Jianlong Sun, Guanghui Yang, Xin-Rong Yang, Ao Huang, Yupeng Wang, Yuan Jie, Xuanhui Liu, Feng Gao, Xiaojian Wu, Dansong WANG, Wenchuan Wu, Wenhui Lou, Jian Zhou, Jia Fan
Journal: Journal of Clinical Oncology (2020)

1557 Background: Cancers of the gastrointestinal (GI) system, including esophagus, stomach, pancreas, gallbladder, liver, bile duct, colon, and rectum are estimated to account for 38% of all cancer incidences and nearly 46% of cancer-related deaths in China. We conducted a multi-center study to evaluate the feasibility of using genetic and epigenetic abnormalities in plasma cfDNA to diagnose and locate GI cancers. Methods: We performed parallel genetic and epigenetic profiling of plasma cfDNA from hepatocellular carcinoma (HCC), colorectal cancer (CRC) and pancreatic cancer (PC) patients as well as age-matched healthy individuals by ultra-deep sequencing targeting cancer driver genes, and by targeted bisulfite sequencing covering genome-wide CpG islands, shelves, and shores. Results: Using a pre-specified mutation scoring system, we found that cfDNA mutation profiling achieved a sensitivity of 59.6%, 67.2%, and 46.8% for detecting HCC (n = 322), CRC (n = 244) and PC (n = 141) respectively, with a specificity of 95% in healthy controls (n = 207). For 901 plasma cfDNA samples that underwent methylome profiling, we first applied a machine learning approach to classify each cancer type versus healthy controls in the training cohort (HCC: n = 125; CRC: n = 105; PC: n = 97; healthy individuals: n = 84). Random Forest models with 10-fold cross validation achieved an AUC of 0.96±0.04,0.89±0.06, 0.91±0.07 for HCC, CRC, and PC, respectively. Further analyses were performed on the validation cohort, including 172 HCC patients, 162 CRC patients, 60 PC patients, and an independent cohort of healthy individuals (HCC validation: n = 63; HCC independent validation: n = 109; CRC validation: n = 104; CRC external validation: n = 58; PC validation: n = 60; healthy controls: n = 96). The trained model achieved a sensitivity of 83.1% (specificity = 95.8%), 89.5% (specificity = 95.8%), and 76.7% (specificity = 91.7%) for HCC, CRC, and PC, respectively. Using regional methylation markers from diagnostic models for individual cancer types, we built a tissue-of-origin classification model, which achieved a cross-validation accuracy of 83.3% in the training cohort and an accuracy of 80.1% in the validation cohort in assigning correct cancer types. Conclusions: Plasma cfDNA methylome profiling identified effective biomarkers for the detection and tissue-of-origin determination of GI cancers, and outperformed mutation-based detection approach. Therefore, a liquid biopsy test capable of detecting and locating GI cancers is feasible and may serve as a valuable tool for early detection and intervention.
Mitigating the risks of surgery during the COVID-19 pandemic
Authors: Paul S Myles, Salome Maswime
Journal: The Lancet (2020)

Mitigating the risks of surgery during the COVID-19 pandemicIn response to the evolving COVID-19 pandemic, most governments and professional bodies recommended cancellation of elective surgery.This action was important to free up hospital bed capacity and ensure supplies of personal protective equipment (PPE), as well as to protect patients and health-care workers.In The Lancet, The COVIDSurg Collaborative 1 report 30-day results of an international cohort study assessing postoperative outcomes in 1128 adults with COVID-19 who were undergoing a broad range of surgeries ( 605[53•6%] men and 523 [46•4%] women; 214 [19•0%] aged <50 years, 353 [31•3%] aged 50-69 years, and 558 [49•5%] aged ≥70 years).Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection was diagnosed postoperatively in more than two-thirds of the patients (806 [71•5%]).The primary outcome was overall postoperative mortality at 30 days and the rate was high at 23•8% (268 of 1128 patients).Pulmonary complications occurred in 577 (51•2%) patients and 30-day mortality in these patients was 38•0% (219 of 577), accounting for 82•6% (219 of 265) of all deaths.Risk factors for mortality were patient age of 70 years or older, male sex, poor preoperative physical health status, emergency versus elective surgery, malignant versus benign or obstetric diagnosis, and more extensive (major vs minor) surgery.The high proportion of
Under detected causes of renal failure:analysis of 80 cases
Authors: Ai-neng Liao, Ai-ping Chen, Hong-bin Zhong, Wen-sheng Wu, Zhe Jin, Xiao-hua Wang
Journal: BMJ (2008)

Clinical data of 80 patients with renal failure due to under detected causes(from January 1998 to June 2007)were retrospectively analyzed.Of 66 patients with acute renal failure(ARF),rhabdomyolysis was found in 45,tumor in 15,anti-neutrophil cytoplasmic antibody(ANCA)related vasculitis in 2,infective endocarditis in 2,and hemolytic uremic syndrome in 2.Of 14 patients with chronic renal failure(CRF),primary hypothyroidism was seen in 3,multiple myeloma in 4,amyloidosis in 2,analgesic nephropathy in 3,and renal tuberculosis in 2.

Key words: 
Renal Failure; Diagnosis
Gene editing to induce FOXP3 expression in human CD4 <sup>+</sup> T cells leads to a stable regulatory phenotype and function
Authors: Yuchi Honaker, Nicholas Hubbard, Yufei Xiang, Logan Fisher, David Hagin, Karen Sommer, Yumei Song, Soo Jung Yang, Christina Lopez, Tori Tappen, Elizabeth M. Dam, Iram Khan, Malika Hale, Jane H. Buckner, Andrew M. Scharenberg, Troy R. Torgerson, David J. Rawlings
Journal: Science Translational Medicine (2020)

Gene editing to insert a strong promoter upstream of endogenous FOXP3 conferred T reg -like properties and functions to primary human CD4 + T cells.