bluuebunny/crossref_metadata_2025_split huggingface dataset:
MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms
Authors: Kim Minji , Zheng Meizhen , Tian Simon Zhongyuan , Lee Byoungkoo , Chuang Jeffrey H. , Ruan Yijun 
Published: November 2019

AbstractThe single-molecule multiplex chromatin interaction data are generated by emerging 3D genome mapping technologies such as GAM, SPRITE, and ChIA-Drop. These datasets provide insights into high-dimensional chromatin organization, yet introduce new computational challenges. Thus, we developed MIA-Sig, an algorithmic solution based on signal processing and information theory. We demonstrate its ability to de-noise the multiplex data, assess the statistical significance of chromatin complexes, and identify topological domains and frequent inter-domain contacts. On chromatin immunoprecipitation (ChIP)-enriched data, MIA-Sig can clearly distinguish the protein-associated interactions from the non-specific topological domains. Together, MIA-Sig represents a novel algorithmic framework for multiplex chromatin interaction analysis.
Clinical malaria and the potential risk of anaemia among preschool-aged children: a population-based study of the 2015–2016 Malawi micronutrient survey
Authors: Ntenda Peter Austin Morton , Chilumpha Sosten , Mwenyenkulu Edward Tisungane , Kazambwe Jane Flora , El-Meidany Walaa 
Published: November 2019

AbstractBackgroundAnaemia and malaria are common and life-threatening diseases among preschool-aged children in many tropical and subtropical areas, and Malawi is no exception. Accordingly, this study aimed to examine the association of referral clinical malaria with anemia (hemoglobin [Hb] < 110 g/L) in preschool-aged children in Malawi.MethodsUsing cross-sectional data obtained from the 2015–2016 Malawi Micronutrient Survey (MNS), multivariate logistic regression models were constructed using surveylogistic to account for the complex survey design. Blood samples of 1051 children aged 6–59 months were evaluated for malaria (using rapid diagnostic test [RDT] – SD BIOLINE Malaria AgP.f/Pan test histidine-rich protein (HRP-II)™), Hb (using HemoCue 301), α-1-acid glycoprotein (AGP), and serum ferritin biomarkers (using simple sandwich enzyme-linked immunosorbent assay technique, ELISA) and inherited blood disorders from dry blood samples (DBS) using polymerize chain reaction (PCR). Diagnosis of clinical malaria was made on the basis of fever and a positive rapid diagnostic test (RDT).ResultsOf the 1051 PSC analysed, 29% had anaemia while 24.4% had a referral to the hospital due to malaria. After adjustments for known confounders, PSC with a history of referral clinical malaria had increased odds of being anaemic (adjusted odds ratio [aOR] = 4.63, 95% confidence interval [CI]: 2.90–7.40),P <  0.0001.ConclusionsThis study found that clinical malaria increased the risk of anaemia in PSC. Thus, elimination of malaria-causing parasites from the PSC’s blood should be rapid and complete in order to prevent the progression of uncomplicated malaria to a chronic infection that can lead to the development of malaria-related anaemia.
Characterization of plasmid-mediated qnrA and qnrB genes among Enterobacteriaceae strains: quinolone resistance and ESBL production in Ismailia, Egypt
Authors: Taha Samaa A. , Omar Hanan Hassan , Hassan wafaa Hassan 
Published: November 2019

AbstractBackgroundPlasmid-mediated quinolone resistance genes (PMQR) are mainly associated with clinical isolates of Enterobacteriaceae and complicate treatment of infections caused by these isolates worldwide. Extended-spectrum-beta-lactamase (ESBL)-producing bacteria are resistant to common antibiotics and also through many mechanisms, ESBL could be disabling other types of antibiotics. This study aimed to assess the prevalence of quinolone resistance and ESBL among Enterobacteriaceae strains and investigated the presence of qnrA and qnrB genes in these strains which were isolated from urinary tract infections in Ismailia, Egypt. Ninety-four Enterobacteriaceae isolates were collected from cases of UTIs admitted to the intensive care unit, Suez-Canal University Hospitals, between October 2017 and January 2018. Antibacterial susceptibility was determined by the disk diffusion method. A polymerase chain reaction assay was used to detect qnrA and qnrB resistance genes in quinolone- and fluoroquinolone-resistant and ESBL strains. Also, ciprofloxacin MIC was determined by the agar dilution method.ResultsResistance rates were 59.6%, 54.3%, 53.2%, 53.2%, and 53.2% to NA, LEV, NOR, CIP, and FX, respectively. Of 56 NA-resistant isolates, 7 (12.5%) and 6 (10.7%) were positive for qnrA and qnrB, respectively, with only one isolate co-harboring both genes. ESBL-producing bacteria was 66.2% of isolates. The MICs for ciprofloxacin ranged from 32–256 μg/ml in ciprofloxacin-resistant isolates.ConclusionOur study shows high resistance rates of Enterobacteriaceae to quinolones and ESBL in our hospital which necessitate appropriate use of these antibiotics to reserve their application for therapy. The prevalence of quinolone-resistant and ESBL-producing Enterobacteriaceae was approximately 60% and 70% respectively.
A randomized trial of medical cannabis (MC) in patients with advanced cancer (AC) to assess impact on opioid use and cancer-related symptoms.
Authors: Zylla Dylan M. , Eklund Justin , Gilmore Grace , Gavenda Alissa , Vazquez-Benitez Gabriela , Pawloski Pamala A. , Arneson Tom , Birnbaum Angela , Dahmer Stephen , Tracy Matthew , Dudek Arkadiusz Z. 
Published: November 2019

109 Background: Higher pain and greater long-term opioid requirements have been associated with shorter survival and decreased quality of life (QOL) in patients with AC. Routine use of MC is limited by a lack of rigorous scientific data and concerns about side effects, legal ramifications, and cost. Methods: 30 patients with stage IV cancer requiring opioids were randomized 1:1 to early cannabis (EC, n=15) vs. delayed cannabis (DC, n=15). The EC group was provided with 3 months (3M) of MC at no charge, while the DC group received standard oncology care without MC for the first 3M. Patients met with licensed pharmacists at one of two MC manufacturers to determine optimal MC dosing, formulation, and route. Patients completed monthly pain logs, opioid/MC logs, and validated Patient-Reported Symptom Monitoring surveys. Results: A higher proportion of EC patients achieved a reduction in opioid use and improved pain control. On average over a 3M window, EC patients did not require opioid dose escalation, had lower mean pain, and had similar QOL compared to DC patients. Estimated mean daily THC and CBD dose at 3M was 76 mg (range 5-186 mg) and 36 mg (range <1-516 mg), respectively. Mean perceived benefit of MC was 5.1 and mean perceived negative impact was 2.7 (1 = no benefit/negative effects, 7 = a great deal of benefit/negative effects). 33% of patients died during the anticipated 6-month study period and patient compliance with study logs limited analysis. Conclusions: Randomized studies of MC in the oncology setting are feasible, but rigorous data collection is challenging. The addition of MC to standard oncology care in patients with AC was well-tolerated and may lead to improved pain control and lower opioid requirements. [Table: see text]
Acute care and hydration due to chemotherapy-induced nausea and vomiting (CINV) among patients receiving NEPA prophylaxis for anthracycline + cyclophosphamide (AC).
Authors: Roeland Eric , Navari Rudolph M. , Ruddy Kathryn Jean , LeBlanc Thomas William , Clark-Snow Rebecca Anne , Wickham Rita S. , Binder Gary , Bailey William L. , Schwartzberg Lee S. 
Published: November 2019

112 Background: In the US, the CMS OP-35 oncology outcome measure deems 30-day post-chemotherapy acute care involving nausea and emesis (NV) or 8 other toxicities as avoidable, with studies showing 15% of > 2500 patients receiving anthracycline + cyclophosphamide (AC)-based chemotherapy had avoidable acute care, of which 32% involved NV. Our aim was to evaluate resource use (emergency department [ED] visits, inpatient admissions [IP], or hydration) in a prospective trial of women with breast cancer who received combination netupitant/palonosetron (NEPA) + dexamethasone (DEX) for CINV prophylaxis for AC-based chemotherapy. Methods: Women initiating AC received oral or IV NEPA + DEX. Pre-specified endpoints included safety, complete response, acute care (ED/IP), unplanned IV hydrations (as determined by investigator), days of CINV, and ≥3 days of CINV. We defined CINV as emesis or rescue drug use up to 5 days after AC, and defined concomitant ED/IP or hydrations in the same period as CINV-related. We limited our analysis to the first 2 cycles, the median duration in the NEPA study. Results: 402 patients received ≥1 cycle of AC and 391 completed 2 cycles. Nine patients had IP (none CINV-related), and 5 patients had a total of 6 ED visits (1 CINV-related). Three patients had a CINV-related unplanned hydration. Patients had ≥1 day of CINV in 172 of 793 cycles (21.7%); of these, the majority had symptom duration for 1-2 days, while 78 (9.8%) had ≥3 days of CINV in a cycle. Conclusions: In this prospective CINV prophylaxis study in women receiving AC chemotherapy, < 1% of women receiving NEPA + DEX required acute care for CINV and < 1% required unplanned hydrations for CINV. These rates are below previously reported CINV-related acute care rates for AC suggesting NEPA may help avoid CINV-related acute care. Clinical trial information: NCT03403712.
A clinical model to predict one-year mortality for patients with advanced cancer.
Authors: Owusuaa Catherine , Van Der Padt - Pruijsten Annemieke , Nieboer Daan , van der Heide Agnes , Van Der Rijt Carin C. D. 
Published: November 2019

132 Background: Advance care planning is necessary for cancer patients who are in their last year of life. We developed a clinical model to predict 1-year mortality for patients with advanced cancer. Methods: Patients with advanced cancer and no curatively aimed treatment options were included in a prospective multicenter observational study involving six hospitals in the Netherlands (June-November 2017). Using cox regression, a model was developed with candidate predictors as identified in literature: surprise question (SQ), clinical characteristics (age, sex, primary tumor, metastases, WHO performance status, food intake, weight loss, pain, comorbidity, dyspnea, and fatigue), and laboratory values (serum albumin, hemoglobin, and C-reactive protein). The primary outcome was all-cause 1-year mortality. Discriminative ability was measured using the c-statistic and assessed using internal-external validation by study hospital. Results: Of 867 patients (median age 66 years, male 47%), 362 (42%) died within 1-year follow-up. Three models were developed: model 1: SQ; model 2: SQ + clinical characteristics; model 3: SQ + clinical characteristics + laboratory values. Predictors included in the most expansive model 3 were: SQ ‘no’ (ref: ‘yes’; HR 3.43, 95% CI 2.57-4.58), age per 10 years (HR 1.07, 95% CI 0.97-1.18), primary tumor-site (ref: prostate, breast, or thyroid; HR 1.35, 95% CI 1.01-1.82), visceral metastases (HR 1.32, 95% CI 1.05-1.65), brain metastases (HR 1.54, 95% CI 1.07-2.22), WHO performance status 1 (ref: 0; HR 1.03, 95% CI 0.76-1.41), WHO performance status 2+ (ref: 0; HR 1.50, 95% CI 1.04-2.15), any weight loss (ref: none; HR 1.09, 95% CI 0.86-1.38), pain score (HR 1.03, 95% CI 0.98-1.09); dyspnea grade 1 (ref: 0; HR 1.20, 95% CI 0.94-1.54), dyspnea grade 2+ (ref: 0; HR 1.33, 95% CI 0.93-1.91), C-reactive protein (HR 1.15, 95% CI 1.04-1.27), and serum albumin (HR 0.97, 95% CI 0.95-1.00). The pooled c-statistic at internal-external validation was 0.69 for model 1, 0.76 for model 2, and 0.78 for model 3. Conclusions: A model that combines the SQ with easily available clinical characteristics (with or without laboratory values) is more accurate in predicting 1-year mortality in patients with advanced cancer than the SQ alone.
Distress screening in cancer survivorship.
Authors: Brockway-Marchello Julia P. , Theroux Haley Hines , Piccolino Sophia Tsesmelis , Yang Qiuchen , Smith Cardinale B. 
Published: November 2019

138 Background: Cancer survivors have varied physical, psychosocial, emotional and financial needs that may differ from needs of active cancer treatment patients. Distress screening identifies and monitors the needs of patients and is mandated for certain accreditations. There is a paucity of data on the application of distress screening among survivors. We used a validated distress screening tool to conduct a needs assessment of cancer survivors in solid oncology. Methods: The Cancer Support Source Distress Screening tool is an 18-item survey given on the 2nd and every 3-month clinic visit to assess depression and distress. The first analysis, merged patient data (patients completing ≥ 2) with cancer registry to identify solid cancer survivors from July 2015 to October 2018. A descriptive analysis of these patients was performed. The second analysis was cross-sectional with a larger data set of all solid tumor patients completing a survey at any time pre, during, or post treatment. We compared distress and depression scores using analysis of variance. A bivariate and multivariate analysis evaluating change in depression and distress scores over time is ongoing. Results: In analysis one, 92 patients were identified. Depression scores improved for most cancer types; distress scores improved for all cancers. Emotional, communication, provider relationship, system of care, body image and social support were associated with significant changes in survivorship concern. In the expanded dataset, 908 patients were identified. The distribution of depression and distress scores are shown in the table. There was a significant decrease for depression scores (p<.001) and distress scores (p<.001). Multivariate analysis to evaluate change in depression and distress scores across the survivorship trajectory is ongoing. Conclusions: A distress screening survey may be a useful tool in assessing the unmet needs of cancer survivors. Identifying prevalent domains of survivorship issues can highlight areas of greatest perceived need and can guide quality improvement initiatives within a cancer program. [Table: see text]
Precision lung cancer survivorship care: Accrual to the Kentucky LEADS Collaborative Lung Cancer Survivorship Care Program.
Authors: Studts Jamie L ,   The Kentucky LEADS Collaborative Lung Cancer Survivorship Care Program Team
Published: November 2019

144 Background: Recent innovations in lung cancer care create an urgent need to generate survivorship care interventions that target lung cancer survivors and tailor content and services to this unique community. In addition to suffering significant distress and symptom burden, individuals diagnosed with lung cancer suffer the additional burden of stigma and bias and may not receive optimal social support. The Kentucky LEADS Collaborative Lung Cancer Survivorship Care Program adopts a precision survivorship approach by combining shared decision making and motivational interviewing to address specific threats to quality of life experienced by an individual facing lung cancer. Methods: A single-arm trial was conducted at nine cancer care facilities across Kentucky to assess intervention feasibility, acceptability, and preliminary efficacy. Eligible participants included individuals diagnosed with lung cancer who did not evince acute psychiatric or substance abuse issues. Upon consent, participants completed a baseline survey (T1) and medical data was extracted from the electronic record. Participants also completed the survey following intervention completion (T2) and six months post-baseline (T3). Analyses evaluate accrual and completion rates as well as participant demographics. Results: Over an approximately 12-month accrual period, nine sites accrued 142 participants. Three sites exceeded the accrual goal of 20. Of the participants accrued, 138 (97%) completed T1, 84 (58%) completed T2, 74 (52%) completed T3, and 70 (49%) provided complete data. The majority of participants were female (64%), the mean age was 63.4 (9.3) years, and nearly all participants were white/non-Hispanic (96%). Most participants had a high school degree or less (52%), described household incomes of $35K or less, but nearly all reported carrying health insurance (98%). Conclusions: The Kentucky LEADS program offers an intriguing approach to engaging lung cancer survivors by incorporating precision care strategies that may circumvent some of the more common challenges to reaching individuals diagnosed with lung cancer. Clinical trial information: NCT02989974.
Associations of caregiver-oncologist discordance in prognostic understanding with caregiver-reported therapeutic alliance and anxiety.
Authors: Loh Kah Poh , Xu Huiwen , Epstein Ronald M. , Mohile Supriya Gupta , Prigerson Holly Gwen , Plumb Sandy , Ladwig Susan , Wong Melisa L. , Kadambi Sindhuja M , McHugh Colin , An Amy W. , Trevino Kelly Marie , Saeed Fahad , Duberstein Paul 
Published: November 2019

15 Background: Discordance in prognostic understanding between caregivers of adults with cancer and the patient’s oncologist is common. However, the relationship between caregiver-oncologist discordance and caregiver bereavement outcomes is unknown. We evaluated the associations of caregiver-oncologist discordance in beliefs about the patient’s curability and life expectancy with caregiver-reported therapeutic alliance and anxiety. Methods: This is a secondary analysis of a multicenter study that assessed the effect of a communication intervention among patients with advanced cancer and their caregivers. Prior to intervention exposure, caregivers and oncologists were asked about their belief in the patient’s chances for cure and living ≥2 years: 100%, about 90%, about 75%, about 50/50, about 25%, about 10%, and 0%. Discordance was defined as a difference by 2 response levels on each prognostic understanding item. Outcomes at 7 months after patient death included caregiver-reported therapeutic alliance [modified 5-item Human Connection (THC) scale] and anxiety (Generalized Anxiety Disorder-7). We used multivariable linear regression models to assess the independent associations of discordance with therapeutic alliance and anxiety. Results: We included 97 caregivers (mean age 63, range 22-83). Approximately 40% of caregiver-oncologist dyads had discordant beliefs about curability (caregivers were more optimistic in 100% of dyads) and 63% had discordant beliefs about life expectancy (caregivers were more optimistic in 94% of dyads). On multivariate analysis, discordance in beliefs about prognostic estimates was associated with lower THC score (b = -6.94, SE 3.17, p = 0.03). Discordance in beliefs about curability was associated with lower anxiety levels (b = -1.79, SE 0.90, p = 0.05). Conclusions: Caregiver-oncologist discordance may decrease caregiver-reported therapeutic alliance and anxiety, both of which may shape how caregivers interact with the healthcare system. A better understanding the role of caregivers’ prognostic understanding will guide interventions to improve caregiver-oncologist therapeutic alliance and caregiver anxiety. Clinical trial information: NCT01485627.
Balanced framing in prognostic discussions among patients with advanced cancer.
Authors: An Amy W. , McHugh Colin , Nicholls Lauren Elizabeth , Epstein Ronald M. , Tejani Mohamedtaki Abdulaziz 
Published: November 2019

22 Background: Prognostic awareness, which incorporates understanding of treatment goals, curability, life-expectancy, and anticipated course of illness, is critical to informed decision-making. In this qualitative study, we explored how balanced framing is utilized during prognostic discussions in oncology office visits. Methods: We (2 oncologists, 3 palliative care physicians) performed a secondary analysis of transcripts of audio-recorded visits between oncologists, caregivers, and patients with advanced cancer obtained as part of a large NIH-funded study. Transcripts were from one study site and included a variety of oncologists, cancer sites, and levels of patient prognostic awareness, as defined by concordance with the oncologist. For analysis, we chose transcripts with some discussion relating to prognosis (eg. treatment goals, etc.). We met regularly to identify themes contributing to prognostic awareness. Differences were reconciled via group discussion. This process continued iteratively until saturation was achieved (n = 24). Results: Prognosis content was reviewed during discussion of treatment goals (n = 15), life-expectancy (n = 14), and future planning (n = 18). In 8 examples of balanced framing of treatment options, oncologists acknowledged the uncertain benefit of treatment and considered patient quality of life; in 7 that did not, oncologists presented treatment as default and emphasized positive outcomes. In 8 examples of balanced framing in estimating life-expectancy, oncologists presented patient-specific ranges and acknowledged exceptionally long and short survival possibilities; in 6 that did not, oncologists provided broad ranges or focused on unusually long survival. In 6 examples of balanced framing in future planning, oncologists acknowledged best supportive care as an alternative to treatment; of 12 that did not, only the next line in treatment or clinical trial was discussed. Conclusions: Although prior research suggests that balanced framing is uncommon, we have identified occasions in which it occurs and characterized how it can be accomplished in prognostic discussions. Further study is needed to better understand the effect of balanced framing on patient prognostic awareness.
Prevalence of prognostic uncertainty and impact on prognostic discussions in thoracic oncology.
Authors: Habib Anand , Zhang Zilu , Tanasijevic Anna , Chen Richard , Awad Mark M. , Odejide Oreofe Olukemi , Abel Gregory A. 
Published: November 2019

33 Background: Recent advances for late-stage lung cancer may have led to a shift from therapeutic ‘nihilism’ to ‘optimism’ (Temel, JCO 2016). It is not known whether this shift has increased prognostic uncertainty nor whether oncologists’ tolerance of uncertainty affects their prognostic discussion practices. Methods: In October 2018, we sent a 34-item survey by FedEx to a random sample of thoracic oncologists (n=444) listed in the publicly-available ASCO directory. The survey assessed professional training, perceptions of prognostic uncertainty for advanced lung cancer, prognostic discussion practices, uncertainty tolerance using an adapted Physicians’ Reactions to Uncertainty (PRU) scale (Gerrity , Motivation and Emotion 1995), and presented a clinical vignette. Results: We received 178 completed surveys from thoracic oncologists in 36 states (response rate: 40.4%). Median duration of practice was 29 years, and 56.7% endorsed an academic affiliation. 52.3% agreed that “there is more prognostic uncertainty in the management of lung cancer now than there was 10 years ago,” and 36.4% noted difficulty “staying up-to-date on the most recent science” in lung cancer management. Surprisingly, only 78.4% reported discussing prognosis with the vast majority (>95%) of their patients. In univariable logistic regression analyses, respondents had lower odds of reporting discussing prognosis with >95% of their patients if they scored highly on the PRU ‘anxious due to uncertainty’ subscale (OR=0.39 [0.18,0.83]), the PRU’s ‘reluctant to disclose uncertainty’ subscale (OR=0.43 [0.20,0.93]) or were male (OR=0.28 [0.08,0.97). Those with higher reluctant to disclose uncertainty scores were also less likely to agree that they would discuss life expectancy when first meeting a patient with stage IV NSCLC presented in the vignette (p=0.014). Conclusions: Data from this geographically diverse cohort of lung cancer oncologists suggest there is increasing prognostic uncertainty within thoracic oncology, and that many find it challenging to stay current with practice changes. Moreover, oncologists’ personal characteristics including gender and uncertainty tolerance may affect their propensity to discuss prognosis.