tbuckley/cabot-search huggingface dataset:
Post-partum detention of insolvent women and their newborns in Lubumbashi, Democratic Republic of the Congo: a cross-sectional survey
Authors: Karen D Cowgill, Abel Ntambue
Journal: The Lancet Global Health (2017)

BackgroundIn the Democratic Republic of the Congo (DR Congo), maternal mortality is high, government financing for health care negligible, and 80% of people live in poverty. Women unable to pay hospital charges may be detained in hospital beyond the standard 3 days after an uncomplicated birth or 10 days after a caesarean. Here, we aimed to document policy and practice around detention of women in the maternity ward of a large government hospital in Lubumbashi, DR Congo.MethodsIn a cross-sectional survey of post-partum women in the Jason Sendwe Hospital's maternity ward, we collected information on socioeconomic, demographic, and obstetric characteristics, and recorded the number of mother-infant pairs detained for non-payment of medical fees. We conducted semi-structured interviews with clinical staff and administrators about policy, and did a retrospective record review to identify the number of mother-infant pairs that had been detained for non-payment in 2014 and 2015.FindingsOf 85 women in the maternity ward and eligible for discharge between August 5 and September 15, 2016, 46 (54%) were detained for non-payment of medical fees. Median duration of detention was 5 days (range 1–30) and amounts owed were between US$8 and $611 (median $317). All the detained women in this study had received emergency care for delivery-related complications. To leave, four women went into debt, three sold belongings, and 14 were released when a politician paid their bills; 25 had not resolved their detention by study end on (September 15, 2016). From the retrospective record review, we identified 2446 deliveries at Sendwe hospital in 2014 and 2015; of these, 716 files included discharge data, and we retrospectively identified 108 cases of post-partum detention. From interviews with ten hospital clinical staff and administrators, we noted that detention of post-partum women and their infants for non-payment of hospital fees is accepted practice, and that hospital and staff depend on revenue from the maternity unit for hospital operating costs, including staff salaries.InterpretationCost recovery can increase out-of-pocket payments and limit access to care for health-care users. Dependence on user fees has also put health-care providers and facility administrators in a difficult situation, since money for their salaries and supplies must come out of revenues, which may be insufficient if users do not pay. We hope our findings about reasons for, and the frequency of, detention for non-payment of fees will support proposals for changes in policy and alternative models of health-care financing in DR Congo. Such changes would improve quality and access to care and reduce or eliminate the human rights violation of post-partum detention of women who cannot pay hospital fees.FundingNone.
Description of initial treatment for newly diagnosed metastatic carcinoid (cNET) and pancreatic neuroendocrine (pNET) patients.
Authors: Sarah Bobiak, Michael A. Choti, Al B. Benson, Jonathan R. Strosberg, Mark Bloomston, Emily K. Bergsland, Carrie C. Zornosa, Matthew Kulke, Eric K. Nakakura, Manisha H. Shah, James C. Yao
Journal: Journal of Clinical Oncology (2012)

e14542 Background: There is limited descriptive information regarding treatment (tx) patterns for NET from clinic practice data. The primary aim of this analysis was to describe initial tx among NET pts as a first step in understanding tx patterns for NET. Methods: The National Comprehensive Cancer Network (NCCN) Oncology Outcomes Database was queried to identify newly diagnosed pts presenting to 7 NCCN institutions with a confirmed metastatic cNET or pNET diagnosis in 2004 or 2005. Pts with a minimum of 5 years of follow up or confirmed death were included in the analysis. Pt demographics, clinical characteristics, initial tx, and 5-year survival were described. Results: Among 187 cNET pts, 52% were male, median age at diagnosis was 58, and 51% alive. Approximately 58% had a known primary tumor; 65% of which were in the small bowel. Most cNET pts (85%) presented with symptoms, 33% had carcinoid syndrome. Initial tx included surgical therapy in 43%, drug therapy in 41%, and other therapies in 16%. The majority (82%) had imaging prior to treatment, among which 79% had a CT scan and 35% had somatostatin receptor scintigraphy (SRS). The most frequent biomarker test was for CGA (performed in 64 pts, elevated in 53). Of 76 cNET pts receiving initial drug therapy, 82% were treated with a somatostatin analog (SA); others received chemotherapy or targeted therapy. Kaplan-Meier (K-M) curves indicated a 5-year survival of 62% and 56% among pts receiving surgery or drug therapy as initial tx, respectively. Among 104 pNET pts, 61% were male, median age at diagnosis was 54, and 41% alive. Approximately 82% presented with symptoms among which 25% were hormone related. Among the 84% of pts imaged prior to treatment, CT scan was most common (79%) and 38% had SRS. The most common initial tx among pNET pts was drug therapy (56%); 60% received a SA; 31% received chemotherapy. Only 25% underwent surgery as initial tx. K-M curves indicated a 5-year survival of 63% among surgical pts in contrast to 31% for pts whose initial tx was drug therapy. Conclusions: Initial tx among the majority of pts was either surgery or drug therapy. Among cNET and pNET pts receiving drug therapy, 82% (n=62) and 60% (n=35) respectively, received an SA.
Beyond <i>Jeopardy!</i>: Harnessing IBM's Watson to improve oncology decision making.
Authors: Peter Bach, Marjorie Glass Zauderer, Ayca Gucalp, Andrew S. Epstein, Larry Norton, Andrew David Seidman, Aryeh Caroline, Alexander Grigorenko, Aleksandra Bartashnik, Isaac Wagner, Jeffrey Keesing, Martin Kohn, Franny Hsiao, Mark Megerian, Rick J Stevens, Jennifer Malin, John Whitney, Mark G. Kris
Journal: Journal of Clinical Oncology (2013)

6508 Background: Electronic decision support is increasingly prevalent in clinical practice. Traditional tools map guidelines into an interactive platform. An alternative method builds on experience-based learning. Methods: Memorial Sloan-Kettering (MSK), IBM and WellPoint teamed to develop IBM Watson – a cognitive computing system leveraging natural language processing (NLP), machine learning (ML) and massive parallel processing – to help inform clinical decision making. We made a prototype for lung cancers using manufactured and anonymized patient cases. We configured this tool to read medical language and extract specific attributes from each case to identify appropriate treatment options benchmarked against MSK expertise, anonymized patient cases and published evidence. Treatment options reflect consensus guidelines and MSK best practices where guidelines are not granular enough to match treatments to unique patients. Analysis and building accuracy is ongoing and iterative. Results: 420 manufactured and 525 anonymized patient cases trained the initial models. Early results show accuracy improvement in NLP and ML in identifying treatment options (Table). All treatment plans were guideline adherent. A proportion of cases showed the need to incorporate tailored treatment plans reflecting MSK’s practice beyond guidelines – e.g. 11% of cases required addressing a site of critical metastasis before initiating guideline supported treatment. Conclusions: IBM Watson is extracting information from free text medical records that supports building ML models to assist in selecting treatments for persons with lung cancers. This tool can select treatment options from consensus guidelines, and, through ML, it will identify personalized treatment plans. Training is ongoing to improve individualized decision making and optimize the web-based tool that connects with IBM Watson. [Table: see text]
Semi-automated method for detecting cancer in pancreas
Authors: S. Nayak, B. B. Biswal, H. P. Dave
Journal: Journal of Clinical Oncology (2004)

4248 Background: Pancreatic cancer is the second most common gastrointestinal malignancy in the Unites States, where it ranks 4th among all cancers as a cause of death. There is no screening program for this cancer. We describe a non-invasive, semi-automated approach to screening. Methods: Images were registered using the method of maximization of mutual information (MMI) algorithms. The MMI algorithm is automated and requires no prior processing of the images as is commonly required for a number of existing registration techniques. For this study, a few points from the pancreatic region were used to trace out the entire pancreas. The image segmentation is based on the integration of edge and region information. A homogeneity criterion based on clustering analysis and convex hull construction is used for pancreas detection. Both CT and MRI images of the pancreas from 10 subjects with pancreatic cancer were used. Results: The image registration algorithm was able to realign both CT and MRI pancreatic images within 1mm accuracy in 9 of the 10 subjects. The region-growing algorithm was also able to reliably outline the entire pancreas after a few seed pixels from the pancreas were selected. Using the thresholding algorithm using Otsu's method, a difference between the healthy tissues and cancerous tissue was observed. A bimodal distribution was observed. A clustering method was then used to determine the cancerous region. Conclusions: In conclusion, semi-automated methods for analyzing multimodal images of the pancreas is presented. Results obtained from this will not only lead to assisting clinicians in detecting and overlaying of pancreatic images, but will also lead to more quantitative analysis. No significant financial relationships to disclose.
Palliative care pharmacists as advocates to conduct advance care planning.
Authors: Joseph Ma, Alexandra Dullea, Chelsea Hagmann, Michelle Russell, Arlene Cramer, Yael Cohen-Arazi, Eric Roeland
Journal: Journal of Clinical Oncology (2017)

73 Background: Advance care planning (ACP) is a process whereby individuals consider their end-of-life (EoL) treatment preferences and make them known to caregivers and clinicians in the event of decisional incapacity. We previously reported a focused ACP intervention led by a clinical social worker (J Palliat Med 2016). Based on this trial’s initial success, we aimed to evaluate this approach when led by a pharmacist. To date, no data exists regarding pharmacist-led ACP discussions. Methods: Advanced stage cancer patients were screened at a single, academic oncology palliative care clinic. Training of the pharmacist included observation of ACP interventions conducted by the clinical social worker, didactic lectures, and role playing. Subjects engaged in a 1-hour ACP intervention with a palliative care pharmacist within 4 weeks of consent. Details of the ACP intervention were documented in the electronic medical record and AD/POLST completion was encouraged but not required. The study outcome was the identification of an informed proxy. After the patient’s death, proxies were contacted to determine if EoL wishes were achieved. Descriptive analyzes were performed. Results: Patient demographics were 22 patients, who were mostly woman (n = 13), Caucasian (n = 17), married (n = 14), with a mean age ± SD of 60.3 ± 10.5 years and with gastrointestinal (n = 5) and genitourinary (n = 5) as the most common primary cancers. After the ACP intervention by the pharmacist, 21 of 22 patients identified an informed proxy. The most commonly identified proxy was a spouse (n = 13). Fourteen (64%) subjects completed an AD/POLST after the ACP intervention. As of October 2016, 27% (6/22) of patients have died. Four out of 6 patients died in a setting consistent with their EoL wishes. Mean time to death from ACP intervention was 133±132 days. Sixteen subjects remain in surveillance. Conclusions: Preliminary results suggest that a pharmacist can conduct ACP discussions to identify an informed HCP. To date, the majority of patients achieved a death concordant with their EoL wishes.
Prediction of the therapeutic response to paclitaxel by gene expression profiling in neoadjuvant chemotherapy for breast cancer
Authors: M. Yoshimoto, M. Makita, S. Nishimura, K. Tada, F. Kasumi, F. Akiyama, Y. Hoshikawa, Y. Miki, M. Matsuura, T. Noda
Journal: Journal of Clinical Oncology (2004)

500 Background: Paclitaxel is one of the most active agents for breast cancer, but the sensitivity is heterogeneous. In order to avoid unnecessary treatment, identification of a reliable predictive marker is desired to distinguish between patients who are likely to respond and those who are not. We report the discovery of a gene expression profile that predicts response to paclitaxel in breast cancer patients. Methods: We took core needle samples from 75 patients with primary breast cancer (size > 3cm) before treatment and then assessed tumor response to neoadjuvant weekly paclitaxel (80 mg/m2 ×12 cycles) under IC. Clinical response rate was 75%, and pCR rate was 3%. Patents were divided into five groups according to clinical and pathological responses (Group-1, extremely resistant; Grp-2, resistant; Grp-3, moderate responder; Grp-4, responder; Grp-5, high responder). RNA extracted from biopsy samples using microdissection method were profiled on cDNA microarrays of 23,000 human transcripts. Differentially expressed 197 genes between high responder (n=7) and extremely resistant (n=7) groups were selected by Mann-Whittney U-test (p<0.05). Secondly, machine-learning method (AdaBoost) was performed to determine the greatest estimated accuracy between 24 responders (Grp-3,4,5) and 16 non-responders (Grp-1,2), and high-scored predictive set of 23 genes were selected. At the time of this submission, tests were performed on 40 pts. Results: In leave-one-out cross validation analysis using the 23 genes, all responders and non-responders were correctly classified with an accuracy of 100%. Correlation between RNA expression measured by the arrays and semiquantitative RT-PCR was also ascertained. Conclusions: If validated, this gene expression profile could allow development of a clinical test for paclitaxel sensitivity, and may help physicians to select individual patients who are likely to benefit from paclitaxel. No significant financial relationships to disclose.
Turkish National Breast Cancer Registry.
Authors: Kadri Altundag, Esra Dumanli, Mehmet Aliustaoglu, Dogan Uncu, Metin Ozkan, Irfan Cicin, Ugur Coskun, Tamer Elkiran, Murat Kocer, Abdurrahman Isikdogan, Aziz Karaoglu, Salim Basol Tekin, Nilufer Avci, Arife Ulas, Berna Oksuzoglu, Feyyaz Ozdemir, Saadettin Kilickap, Mahmut Gumus, Suleyman Buyukberber, Mustafa Benekli
Journal: Journal of Clinical Oncology (2015)

e12654 Background: Breast cancer (BC) is the most common cancer in women in Turkey. Studies investigating BC epidemiology in Turkey are retrospective case series providing limited information. We developed a BC registry to define BC clinical characteristics in Turkish women Methods: Pts presenting to medical oncology clinics were prospectively registered after October 2012 in 28 centers. Clinical and pathological characteristics were recorded. Results: 13749 pts (128 males [0.9%]) were registered. Median age was 53 yrs (20-93). Pts > 65 and < 35 yrs constituted 20.9% and 4.2% of the whole population, respectively. Elderly pts > 75 yrs were 4.1%. Most pts were postmenopausal (52.3%). Invasive ductal carcinoma was most common (82.6%) with grades I ( 10.3%), II (54%), III (35.7%). ER and PR were positive in 71.1% and 65.8%, respectively. Considering 12949 patients diagnosed in 2003 and later, 27.7% was positive with IHC and/or FISH testing. Molecular subtypes were as follows: luminal A/B 76.4%, triple negative 11.1% and Her2 type 8.6%. Initial stages at diagnosis were: I (15.5%), II (44%), III (23.4%), IV (7.2%). 2262 pts developed metastasis: bone (57%), liver (24.8%), lung (23.4%) and others. Most pts had single organ metastasis (61.6%). Curative/palliative surgery was done in 91%: modified radical mastectomy (58%), breast-conserving surgery (30.5%). Neoadjuvant chemo was used in 8.2%, and of those only 18.6% received neoadjuvant trastuzumab. Pts with early BC received adjuvant chemo (79.1%) with AC (66.3%) and taxanes (31.8%). Radiotherapy was used in 49.3%. Of patients treated after 2003, 17.5% used adjuvant trastuzumab. Adjuvant hormonal therapies were used in 52.5% with tamoxifen (60%) and aromatase inhibitors. Of metastatic BC pts detected either at diagnosis or follow up 87.8% received first-line chemo. Most pts received taxane-based regimens while only 16.3% received first-line trastuzumab. Conclusions: This study is the first comprehensive BC registry performed in Turkey with HR and Her2 status. Patient characteristics and demographics are similar to Western countries including biomarker data. Lower rates of triple negative and Her2-type BC deserves further exploration. Survival data and prognostic variables will be presented at the meeting.
GISAID: Global initiative on sharing all influenza data – from vision to reality
Authors: Yuelong Shu, John McCauley
Journal: Eurosurveillance (2017)

Preview this article: GISAID: Global initiative on sharing all influenza data – from vision to reality, Page 1 of 1 < Previous page | Next page > /docserver/preview/fulltext/eurosurveillance/22/13/eurosurv-22-30494-1-1.gif
The Promise of Pharmacogenomics in Reducing Toxicity during Acute Lymphoblastic Leukemia Maintenance Treatment
Authors: Shoshana Rudin, Marcus Marable, R. Stephanie Huang
Journal: Genomics Proteomics & Bioinformatics (2017)

Abstract Pediatric acute lymphoblastic leukemia (ALL) affects a substantial number of children every year and requires a long and rigorous course of chemotherapy treatments in three stages, with the longest phase, the maintenance phase, lasting 2–3 years. While the primary drugs used in the maintenance phase, 6-mercaptopurine (6-MP) and methotrexate (MTX), are necessary for decreasing risk of relapse, they also have potentially serious toxicities, including myelosuppression, which may be life-threatening, and gastrointestinal toxicity. For both drugs, pharmacogenomic factors have been identified that could explain a large amount of the variance in toxicity between patients, and may serve as effective predictors of toxicity during the maintenance phase of ALL treatment. 6-MP toxicity is associated with polymorphisms in the genes encoding thiopurine methyltransferase (TPMT), nudix hydrolase 15 (NUDT15), and potentially inosine triphosphatase (ITPA), which vary between ethnic groups. Moreover, MTX toxicity is associated with polymorphisms in genes encoding solute carrier organic anion transporter family member 1B1 (SLCO1B1) and dihydrofolate reductase (DHFR). Additional polymorphisms potentially associated with toxicities for MTX have also been identified, including those in the genes encoding solute carrier family 19 member 1 (SLC19A1) and thymidylate synthetase (TYMS), but their contributions have not yet been well quantified. It is clear that pharmacogenomics should be incorporated as a dosage-calibrating tool in pediatric ALL treatment in order to predict and minimize the occurrence of serious toxicities for these patients.
Recall rate in a semi-annual breast surveillance program for high-risk women.
Authors: Hiroyuki Abe, Rodrigo Santa Cruz Guindalini, Elias Obeid, Linda J. Patrick-Miller, Angela R. Bradbury, Marion S. Verp, Susan Hong, Kristen Wroblewski, Greg S. Karczmar, Gillian Newstead, Olufunmilayo I. Olopade
Journal: Journal of Clinical Oncology (2013)

11084 Background: High recall rate and unnecessary biopsies are a concern with screening mammogram (MMG) and magnetic resonance imaging (MRI) in young women at high risk for breast cancer. The aim of this study is to investigate the overall recall rate (ORR) and its consequences in a semi-annual MRI surveillance protocol. Methods: A multi-modality surveillance program for women at high-risk for breast cancer was initiated in 2004. Yearly MMG was supplemented with semi-annual MRI. After 5 years of this protocol, an additional 5 years of follow-up with yearly MMG and MRI were offered only to mutation carriers. Defining positive screening as BIRADS 0, 4 and 5, ORR were analyzed and biopsies findings characterized. Fisher’s exact test was performed to evaluate association between the effect of MMG density, menopausal status, mutation status, age (&lt;50y or &gt; 50y), and previous breast cancer with recalls. Results: With a mean follow-up of 3.6 years, 226 patients (pts) underwent 1,467 MRI and 851 MMG. Among 56 abnormal MRI and 18 abnormal MMG, 62 pts (27%) were recalled for further tests (6 recalled at two screening episodes). The MRI and MMG ORR were 3.8% and 2.1%, respectively. Only six cases (8.8%) were abnormal for both tests. Overall, 50 additional breast ultrasound, 10 additional MMG, 8 additional MRI were performed. Of the 40 biopsies in 38 pts (2 pts were biopsied twice), 11 cancers were detected (ductal in situ: 3; invasive: 7 ductal and 1 lobular). Abnormal MRI findings led to 37 biopsies, of which 10 (27%) detected cancers. One high-grade ductal carcinoma in situ was exclusively detected by MMG. The first and second MRI screening rounds together showed 27/56 (66%) abnormal findings which led to 23/40 (58%) of the biopsies, and detected 5/11 (45%) of the tumors. No statistically significant predictors of recall were identified (p &lt; 0.05). Conclusions: Semi-Annual MRI protocol did not show increased ORR when compared to annual MRI/MMG surveillance. Approximately two-thirds of all recalls were in the first two rounds of screening which is consistent with previous results. Ongoing work will evaluate clinical and MRI features associated with recall to improve practice. Clinical trial information: NCT00989638.