bluuebunny/crossref_metadata_2025 huggingface dataset:
Effectiveness of immunotherapy given to cancer patients in the hospitalized setting.
Authors: Araoye Mojisola O , Byrne Brian J.
Published: October 2020

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Background: Immunotherapy is a type of cancer treatment that uses an individual’s immune system to fight cancer. Most clinical trials involving immunotherapy have been done on healthy patients, thus excluding many hospitalized patients. Many oncologists feel there are less significant toxicities to immunotherapy and thus may give them to sicker patients. This may delay discussions regarding goals of care and contribute to increased costs at end of life. This exploratory study focuses specifically on the use of immune checkpoint inhibitors in hospitalized patients to determine outcomes of patients treated in the inpatient setting. Methods: This is a retrospective chart-review study. Data on patients from the Hartford Healthcare system was extracted from EPIC. Patients were eligible if they had received at least one dose of a PD1 or PDL1 inhibitor (pembrolizumab, nivolumab, atezolizumab) during a hospital stay. The number of doses received in total, side effects, as well as discharge status was also recorded. Results: A total of 74 patients received at least one dose of a PD1 or PDL1 inhibitor during a hospital stay. 46% of the total patients treated either died in the hospital (16.2%) or were discharged to hospice (29.3%). 54 percent of patients were discharged with a plan to continue with therapy. For the subgroup of the 27 patients whose treatment was initiated in the hospital, 48% of them received only one cycle of treatment and 74% received less than 4 treatments total. The average number of cycles was 5.3. The percentage of patients who died in the hospital was 11.1% and the percentage of patients discharged to hospice was 33.3%. 55.5% were successfully discharged with a plan to continue with therapy. Conclusions: For patients who receive immunotherapy in the hospital setting there is a questionable benefit with more than 45% dying in the hospital or being discharged to hospice. Further evaluation can be done looking at increasing the cost, delaying palliative care, and patient/family satisfaction with their end of life care by giving immunotherapy in the hospital. A new quality measure looking at time from last immunotherapy to hospice enrollment or death may need to be followed in the future due to these poor outcomes in the hospitalized setting. [Table: see text]
Financial and employment toxicity related to breast reconstruction following mastectomy in a diverse population-based cohort.
Authors: Berlin Nicholas L. , Momoh Adeyiza O. , Abrahamse Paul , Katz Steven J. , Jagsi Reshma , Hawley Sarah T.
Published: October 2020

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Background: Despite mandated private insurance coverage for breast reconstruction following mastectomy, health care costs are increasingly passed onto women who seek these procedures through cost-sharing arrangements and high-deductible health plans. In this population-based study, we sought to characterize financial and employment toxicities related to pursuing breast reconstruction following mastectomy. Methods: Women (white, African American, and Latina-English and Spanish speaking) with early stage breast cancer (stages 0-II) diagnosed between July 2013 to September 2014 and who underwent mastectomy were identified through the Georgia and Los Angeles Surveillance, Epidemiology, and End Results (SEER) registries and surveyed. Primary outcome measures included patient-reported appraisal of financial toxicity and employment status following breast cancer treatment using previously developed measures. Multivariable models evaluated the association between breast reconstruction and self-reported financial and employment status. Results: Among 868 breast cancer patients who underwent mastectomy, 43.5% (n = 378) did not undergo breast reconstruction and 56.5% (n = 490) underwent reconstruction. 43.4% of the cohort reported being worse off financially since their diagnosis (49.4% with reconstruction vs. 35.0% without reconstruction, P< .001). Among women who were employed at time of breast cancer diagnosis (n = 535), 70.2% who underwent reconstruction reported being worse off regarding employment status compared to 51.1% who did not undergo reconstruction ( P< .001). Receipt of reconstruction was independently associated with a self-reported decline in financial status (Odds Ratio (OR) 2.1, 95% Confidence Interval (CI) 1.4-3.4, P= .001). Similarly, reports of being worse off regarding employment status were also higher in those who underwent reconstruction vs. not (OR 2.2, 95% CI 1.2-3.8, P= .006). Spanish-speaking Latina women more often reported being worse off regarding employment status (OR 4.3, 95% CI 2.1-9.0, P< .001) than white women. Conclusions: In this diverse cohort of women who underwent mastectomy for early stage breast cancer, women who elected to undergo reconstruction experienced more self-reported financial and employment toxicities. Patients should be counseled regarding the potential costs related to these procedures. Policy-makers should be aware of the financial barriers for women who undergo reconstruction despite mandatory insurance coverage in the United States.
Compliance with every 12-week zoledronic acid dosing guidelines for bone metastasis in breast cancer patients.
Authors: Kumar Monika , Dev Pallavi , Kainthla Radhika
Published: October 2020

81

Background:
Bisphosphonates, including zoledronic acid (Zometa), decrease skeletal-related events in breast cancer patients with bone metastasis but are also associated with side effects and utilization costs. Data from a randomized trial supporting 12-week versus 4-week dosing of Zometa was released in July 2016 and officially published in January 2017. We examined the practice pattern of Zometa dosing over time in our practice to determine compliance and develop interventions for improvement.
Methods:
We conducted a retrospective chart review on all breast cancer patients treated at Parkland Health and Hospital System oncology clinic to identify patients who were initiated on Zometa for bone metastasis between June 2015 and September 2019. The initially prescribed dosing frequencies were assessed for time periods before and after the Zometa dosing data was made available. The prescribing patterns were also compared between teaching and non-teaching clinics. An educational review of the guidelines was presented to providers in all clinics in March 2020 to improve compliance.
Results:
In the year prior to July 2016, of the 27 patients who started Zometa, only 1 (4%) was on every 12-week dosing. In the six months after release of the data, 29% (6/21 patients) were placed on 12-week Zometa dosing. Between January 2019 and September 2019, 52% of patients were started on the recommended 12-week dosing interval. These patterns were consistent between teaching and non-teaching clinics.
Conclusions:
We found that the variability in Zometa prescribing patterns persisted despite updated national guidelines and multiple studies supporting 12-week dosing intervals. In addition to educational interventions, we plan to implement electronic interventions to improve rates of compliance with the goal of 80% adherence by September 2020. Improved adherence will likely lead to a reduction in potential complications from treatment as well as infusion costs (estimated $482.81 saved per patient annually).
Disparities in the use of telehealth during the COVID-19 pandemic.
Authors: Smith Cardinale B. , Bhardwaj Aarti Sonia
Published: October 2020

87

Background: New York City was the epicenter of the COVID-19 pandemic. Public concern about exposure and policies to “flatten the curve” led to abrupt curtailment of health care service use, including cancer. Innovative strategies to mitigate the disruption, including telemedicine, was utilized. However, this may be less accessible to minority populations. We evaluated the differences in telehealth use among minorities and non-minorities with cancer. Methods: Our health system includes an NCI designated cancer center and 8 ambulatory sites across New York City. Utilizing the electronic medical record (EMR) we collected data on all cancer patients with an in-person or telehealth visit during the peak of the pandemic from March 1, 2020 to June 1, 2020. Race/ethnicity and visit type data was collected from the EMR. Telehealth includes video visits and telephone encounters. We used ANOVA and-chi square where appropriate to identify differences between the racial and ethnic groups in terms of use and type of telehealth and compared any differences to baseline cancer center demographics. Results: There were a total of 7,681 telehealth visits during 3/1/2020-6/1/2020; 76% were video visits. At baseline in 2019, < 1% of all patient visits were conducted via telehealth. Within our cancer center our demographic breakdown for patients seen in 2019 includes 42% patients were white, 23% Black, 14% Hispanic and 7% Asian. Among those patients utilizing video visits, 50% patients were white, 17% Black, 8% Asian, and 5% Hispanic. Among those patients utilizing phone encounters, 43% patients were white, 23% Black, 7% Hispanic and 6% Asian. Conclusions: During the COVID-19 pandemic our utilization of telehealth increased exponentially. There were significant disparities observed in the use of telehealth with Black, Hispanic and Asian patients having less utilization. These findings are important as telehealth use will now become more integrated into standard oncologic care, and it is likely that we will have a second or third wave of COVID-19 infections. Future work to understand the determinants of these disparities and interventions are needed. [Table: see text]
Factors associated with clinical trial participation for patients with prostate cancer.
Authors: Shinder Brian , Kim Sinae , Patel Hiren V. , Srivastava Arnav , Mayer Tina M. , Saraiya Biren , Singer Eric A.
Published: October 2020

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Background: Clinical trials are critical for the development of new treatment paradigms for Prostate Cancer (PCa). The primary aim of this study was to characterize the factors associated with clinical trial participation for patients with PCa. The secondary objective was to examine survival outcomes in the clinical trial and control cohorts. Methods: The National Cancer Database (NCDB) was queried for patients with PCa who were coded as having enrolled in a clinical trial. Trial patients were matched in a 1:8 ratio to controls based on clinical stage. Sociodemographic variables were compared between the two groups and univariate and multivariate logistic regression models evaluated factors associated with clinical trial participation. Kaplan-Meier product limit estimate was used to compare overall survival (OS) between the groups. Results: From 2004-2015, 495 patients enrolled in clinical trials were included for analysis. The mean age of trial patients was 63.2 compared to 66.4 in the matched cohort (p < 0.0001). More patients in the trial group had a Charlson-Deyo comorbidity score of 0 (89.3% vs. 82.1%, p = 0.0002). On multivariate analysis, patients who traveled between 50-250 miles (OR 1.59; 95%CI 1.15-2.19, p = 0.005) or came from a zip code where greater than 93% of the population has a high school degree (OR 4.97; 95%CI 2.89-8.54, p < 0.0001) were more likely to participate in a clinical trial. There was no association between race and insurance status on clinical trial participation. Median OS was not significantly different among clinical trial participants than the control cohort (120.9 months vs. not reached, p = 0.928). Conclusions: In this contemporary analysis of PCa patients from a national hospital registry database, we found that certain patient sociodemographic factors remain associated with clinical trial participation, though clinical trial participants do not seem to experience a difference in OS. Further work, both qualitative and quantitative, is necessary to identify clinical and non-clinical barriers to research participation in order to improve the validity of PCa trials.
The association between Medicare’s next generation sequencing (NGS), national coverage decision (NCD), and NGS utilization.
Authors: Wong William Bruce , Sheinson Daniel , Ogale Sarika , Flores Carlos , Gross Cary Philip
Published: October 2020

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Background: In 2018, Medicare released a NGS NCD memo which would facilitate reimbursement for NGS tests for patients (pts) with advanced or metastatic cancer who had not been previously tested using NGS for the same cancer and genetic content. We examined the association between the NCD and: a) NGS utilization trends in commercially-insured and Medicare pts and b) repeat NGS testing. Methods: We conducted a retrospective study of pts with advanced non-small cell lung cancer (aNSCLC), metastatic colorectal cancer (mCRC), metastatic breast cancer (mBC) or advanced melanoma (aM), diagnosed 2011 (2013 for mCRC) through Dec. 2019 using the Flatiron Health EHR-derived de-identified database, comprising data from over 280 (largely community based) cancer clinics (~800 sites of care). Pts were classified as Medicare or Commercially insured based on age and insurance type, and grouped into quarters based on their advanced or metastatic diagnosis date. NGS testing rates per quarter were based on evidence of first NGS test within 60 days from diagnosis. We used an interrupted time series analysis to assess NGS utilization trends pre- and post-NCD policy effective date (March 2018). The frequency of repeat NGS testing was assessed among those pts with only 1 primary cancer. Results: The utilization analysis included 70,290 pts while the repeat NGS testing analysis included 51,385 pts. Across the 4 tumors combined, the use of NGS was < 1% in 2011 (both insurance types) and increased to 41% in commercially-insured pts and 37% in Medicare in 2019. In each tumor, NGS utilization was < 6% in Q1 2014; however, the rate of increase varied by tumor, with aNSCLC increasing to 58% in commercial and 48% in Medicare, while mBC and aM remained < 20% in Q4 2019. Among pts with aNSCLC, mCRC, or mBC, the quarterly rate of increase in NGS testing was higher post-NCD compared to pre-NCD (p < 0.05 for pre-post difference in rate of NGS increase within each cancer type). The difference in trends pre- and post-NCD was not significantly different between commercial and Medicare in any of the tumors (p > 0.05 within each cancer type). Repeat NGS testing increased over time from 17.8% (in Q3 2014 to Q2 2016) to 29.6% (in Q2 2018 to Q4 2019). Conclusions: NGS utilization trends significantly changed post-NCD, however the rate of change was not significantly different by insurance, indicating private insurers may also be following the guidance of the NCD. We observed an increase in repeat NGS testing, despite the NCD not covering repeat testing with the same NGS test.
Effects of Intermittent Fasting or Calorie Restriction on Markers of Lipid Metabolism in Human Skeletal Muscle
Authors: Liu Bo , Hutchison Amy T , Thompson Campbell H , Lange Kylie , Wittert Gary A , Heilbronn Leonie K
Published: October 2020

Context

Impaired lipid metabolism is linked with obesity-associated insulin resistance, which may be reversed by caloric restriction (CR).

Objective

In a secondary analysis of a randomized controlled trial, we compared the effects of intermittent fasting (IF) and CR on markers of lipid metabolism in muscle.

Design

Seventy-six women (body mass index, 25-40 kg/m2) were randomly assigned to 1 of 3 diets for 8 weeks and provided foods at 70% (CR70 and IF70) or 100% (IF100) of energy requirements. IF groups ate breakfast prior to a 24-hour fast on 3 nonconsecutive days per week. On nonfasting days, IF70 ate at 100% and IF100 ate at 145% of energy requirements to achieve the prescribed target. Weight, body composition, insulin sensitivity by clamp, nonesterified fatty acids (NEFAs), β-hydroxybutyrate (BHB), and markers of lipid metabolism and oxidative stress in muscle by quantitative polymerase chain reaction were measured at baseline and week 8 following a 12-hour overnight fast (all groups) and 24-hour fast (IF groups).

Results

IF70 resulted in greater weight and fat loss and reduced NEFAs vs CR70 and IF100 after an overnight fast. IF70 and IF100 induced a greater reduction only in mRNA levels of antioxidant enzymes glutathione peroxidase 1 (GPX1), superoxide dismutase 1, soluble (SOD1), and SOD2 vs CR70. Fasting for 24 hours increased NEFAs and BHB in IF groups, but impaired insulin sensitivity and increased PLIN5 mRNA levels.

Conclusions

In comparison to CR, IF did not increase markers of lipid metabolism in muscle, but reduced expression of antioxidant enzymes. However, fasting-induced insulin resistance was detected, alongside increased PLIN5 expression, potentially reflecting transient lipid storage.
Blood Pressure Management by Anesthesia Professionals: Evaluating Clinician Skill From Electronic Medical Records
Authors: Sessler Daniel I. , Khan Mohammad Z. , Maheshwari Kamal , Liu Liu , Adegboye Janet , Saugel Bernd , Mascha Edward J.
Published: October 2020

BACKGROUND:

Avoiding intraoperative hypotension might serve as a measure of clinician skill. We, therefore, estimated the range of hypotension in patients of nurse anesthetists, and whether observed differences were associated with a composite of serious complications.

METHODS:

First, we developed a multivariable model to predict the amount of hypotension, defined as minutes of mean arterial pressure (MAP) <65 mm Hg, for noncardiac surgical cases from baseline characteristics excluding nurse anesthetist. Second, we compared observed and predicted amounts of hypotension for each case and summarized “excess” amounts across providers. Third, we estimated the extent to which hypotension on an individual case level was independently associated with a composite of serious complications. Finally, we assessed the range of actual and excess minutes of MAP <65 mm Hg on a provider level, and the extent to which these pressure exposures were associated with complications.

RESULTS:

We considered 110,391 hours of anesthesia by 99 nurse anesthetists. A total of 69% of 25,702 included cases had at least 1 minute of MAP <65 mm Hg, with a median (quartiles) of 4 (0–15) minutes on the case level. We were unable to explain much variance of intraoperative hypotension from baseline patient characteristics. However, cases in the highest 2 quartiles (>10 and >24 min/case more than predicted) were an estimated 27% (95% confidence interval [CI], 1.1–1.4) and 31% (95% CI, 1.2–1.5) more likely to experience complications compared to those with 0 excess minutes (both P < .001). There was little variation of the average excess minutes <65 mm Hg across the nurse anesthetists, with median (quartiles) of 1.6 (1.2–1.9) min/h. There was no association in confounder-adjusted models on the nurse anesthetist level between average excess hypotension and complications, either for continuous exposure (P = .09) or as quintiles (P = .30).

CONCLUSIONS:

Hypotension is associated with complications on a case basis. But the average amount of hypotension for nurse anesthetists over hundreds of cases differed only slightly and was insufficient to explain meaningful differences in complications. Avoiding hypotension is a worthy clinical goal, but does not appear to be a useful metric of performance because the range of average amounts per clinician is not meaningfully associated with patient outcomes, at least among nurse anesthetists in 1 tertiary center.
Critical Theory in Times of Crisis
Authors: Spillers Hortense
Published: October 2020

This essay looks at the relationship between political movements in the streets and critical theory in the academy. It asks whether today the lack of innovation in critical theory we see in some disciplines occasions, if not reflects, the muting of political dissent outside of the university. Contemporary critical theory now seems split into two separate fields, “criticism” and “theory,” revealing a configuration quite unlike what we saw in the earlier Frankfurt School, where these two terms were merged in the name of “critical theory,” which was practiced with attention to social crisis. We’re up to the neck in crises now. How will critical theory respond?
Judgment and Social Being
Authors: Blanton C. D.
Published: October 2020

A notion of ideology relies necessarily on deeper assumptions about a consciousness subject to misapprehension and error. But in their inversions of Hegel, the mature Marx’s account of the commodity and general formula of capital dethrone consciousness altogether, assigning faculties of judgment and knowledge to the commodity instead. This essay turns to the late work of Georg Lukács to trace an alternative power of judgment formed by labor as such, in the problem of “teleological positing.”
Drosophila sperm development and intercellular cytoplasm sharing through ring canals do not require an intact fusome
Authors: Kaufman Ronit S. , Price Kari L. , Mannix Katelynn M. , Ayers Kathleen M. , Hudson Andrew M. , Cooley Lynn
Published: October 2020

Animal germ cells communicate directly with each other during gametogenesis through intercellular bridges, often called ring canals (RCs), that form as a consequence of incomplete cytokinesis during cell division. Developing germ cells in Drosophila have an additional specialized organelle connecting the cells called the fusome. Ring canals and the fusome are required for fertility in Drosophila females, but little is known about their roles during spermatogenesis. With live imaging, we directly observe the intercellular movement of GFP and a subset of endogenous proteins through RCs during spermatogenesis, from two-cell diploid spermatogonia to clusters of 64 post-meiotic haploid spermatids, demonstrating that RCs are stable and open to intercellular traffic throughout spermatogenesis. Disruption of the fusome, a large cytoplasmic structure that extends through RCs and is important during oogenesis, had no effect on spermatogenesis or male fertility under normal conditions. Our results reveal that male germline RCs allow the sharing of cytoplasmic information that might play a role in quality control surveillance during sperm development.
Mitchell-Riley syndrome iPSC exhibit reduced pancreatic endoderm differentiation due to an RFX6 mutation
Authors: Trott Jamie , Alpagu Yunus , Tan Ee Kim , Shboul Mohammad , Dawood Yousif , Elsy Michael , Wollmann Heike , Tano Vincent , Bonnard Carine , Eng Shermaine , Narayanan Gunaseelan , Junnarkar Seetanshu , Wearne Stephen , Strutt James , Kumar Aakash , Tomaz Lucian B. , Goy Pierre-Alexis , Mzoughi Slim , Jennings Rachel , Hagoort Jaco , Eskin Ascia , Lee Hane , Nelson Stanley F. , Al-Kazaleh Fawaz , El-Khateeb Mohammad , Fathallah Rajaa , Shah Harsha , Goeke Jonathan , Langley Sarah R. , Guccione Ernesto , Hanley Neil , De Bakker Bernadette S. , Reversade Bruno , Dunn N. Ray
Published: October 2020

Mitchell-riley syndrome (MRS) is caused by recessive mutations in the Regulatory Factor X, 6 (RFX6) gene and is characterised by pancreatic hypoplasia and neonatal diabetes. To determine why MRS patients specifically lack pancreatic endocrine cells, we micro-CT imaged a 12-week old foetus homozygous for the nonsense mutation RFX6 c.1129C>T, which revealed loss of the pancreas body and tail. From this foetus, we derived iPSC and show that differentiation of these cells in vitro proceeds normally until generation of pancreatic endoderm, which is significantly reduced. We additionally generated an RFX6HA reporter allele by gene targeting in wild-type H9 cells to precisely define RFX6 expression and in parallel performed in situ hybridization for RFX6 in the dorsal pancreatic bud of a Carnegie Stage 14 human embryo. Both in vitro and in vivo, we find that RFX6 specifically labels a subset of PDX1-expressing pancreatic endoderm. In summary, RFX6 is essential for efficient differentiation of pancreatic endoderm, and its absence in MRS patients specifically impairs formation of endocrine cells of the pancreas head and tail.
Do Particles Interact Electronically? —Proof of Interparticle Charge-transfer Excitation between Adjoined Anatase and Rutile Particles
Authors: Shen Yang , Nitta Akio , Takashima Mai , Ohtani Bunsho
Published: October 2020

Here, we report experimental evidence of interparticle spatial overlapping of orbitals to result in interparticle charge-transfer excitation (ICTE) at an anatase-rutile interface which is expected to be applicable to clarify the relative band position of metal-oxides and mixture homogeneity of mixture samples measured by reversed double-beam photoacoustic spectroscopy.
The Psychological Burden of Retirement from Sport
Authors: Esopenko Carrie , Coury Josephine R. , Pieroth Elizabeth M. , Noble James M. , Trofa David P. , Bottiglieri Thomas S.
Published: October 2020

Participation in sport is associated with numerous physical and psychological health benefits, but also can have negative consequences, such as career ending injuries, which may have long-term effects on mental health. Recent research suggests that involuntary retirement, due to injury, illness, or being cut from a sport, can be particularly detrimental. As such, this review focuses on the impact athletic retirement has on the psychological well-being of collegiate athletes. We provide an algorithm to inform clinical decision making regarding involuntary retirement, as well as recommendations for the development of support programs and educational resources for athletes struggling with career transition. Our aim is that in developing retirement algorithms, support programs, and educational resources for athletes who are retired from sport, we can intervene early thus reducing the potential long-term psychological burden they may experience.
Cooking with biomass fuel and cardiovascular disease: a cross-sectional study among rural villagers in Phitsanulok, Thailand
Authors: Juntarawijit Chudchawal , Juntarawijit Yuwayong
Published: October 2020

Background: Burning biomass fuel is a major source of indoor air pollution; about 40% of Thai people still use biomass for cooking. There is increasing evidence of the association between biomass smoke exposure and serious health effects including cardiovascular disease. The object of this cross-sectional study was to investigate the association between biomass use for household cooking and cardiovascular outcome, including coronary heart disease, hypertension, high cholesterol, diabetes mellitus, and stroke among rural villagers in Phitsanulok, Thailand. 

Methods: Data from 1078 households were collected using a face-to-face interview questionnaire. In each household, data on cardiovascular disease, cooking practices, and cooking fuel, types of fuel they normally used for cooking, were collected.

Results: After being adjusted for gender, age, cigarette smoke, secondhand smoke, and exposure to other sources of air pollution, it was found that the family members of cooks using biomass fuel were at risk of coronary heart disease (CHD; OR=4.35; 95%CI 0.10–18.97), hypertension (OR=1.61; 95%CI 1.10–2.35), high cholesterol (HC; OR=2.74; 95%CI 1.66–4.53), and diabetes (OR=1.88; 95%CI 1.03–3.46). Compared to LPG use, using wood was associated with stroke (OR=7.64; 95%CI 1.18–49.61), and using charcoal was associated with HC (OR=1.52; 95%CI 1.04–2.24). Compared to never user, household cooks who sometimes use charcoal had an increased risk of hypertension (OR=2.04; 95%CI 1.32–3.15), HC (OR=2.61; 95%CI 1.63–4.18), and diabetes (OR=2.09; 95%CI 1.17–3.73); and cooks who often use charcoal had an elevated risk of stroke (OR=3.17; 95%CI 1.04–9.71), and HC (OR=1.52; 95%CI 1.02–2.27) to their family members.

Conclusions: The study results were consistent with those found in studies from other parts of the world, and supports that exposure to biomass smoke increase cardiovascular diseases. The issue should receive more attention, and promotion of clean fuel use is a prominent action.
Annotation and curation of human genomic variations: an ELIXIR Implementation Study
Authors: David Alessia , Barbié Valérie , Attimonelli Marcella , Preste Roberto , Makkonen Enni , Marjonen Heidi , Lindstedt Mats , Kristiansson Kati , Hunt Sarah E. , Cunningham Fiona , Lappalainen Ilkka , Sternberg Michael J.E.
Published: October 2020

Background: ELIXIR is an intergovernmental organization, primarily based around European countries, established to host life science resources, including databases, software tools, training material and cloud storage for the scientific community under a single infrastructure.

Methods: In 2018, ELIXIR commissioned an international survey on the usage of databases and tools for annotating and curating human genomic variants with the aim of improving ELIXIR resources. The 27-question survey was made available on-line between September and December 2018 to rank the importance and explore the usage and limitations of a wide range of databases and tools for annotating and curating human genomic variants, including resources specific for next generation sequencing, research into mitochondria and protein structure.

Results: Eighteen countries participated in the survey and a total of 92 questionnaires were collected and analysed. Most respondents (89%, n=82) were from academia or a research environment. 51% (n=47) of respondents gave answers on behalf of a small research group (<10 people), 33% (n=30) in relation to individual work and 16% (n=15) on behalf of a large group (>10 people). The survey showed that the scientific community considers several resources supported by ELIXIR crucial or very important. Moreover, it showed that the work done by ELIXIR is greatly valued. In particular, most respondents acknowledged the importance of key features and benefits promoted by ELIXIR, such as the verified scientific quality and maintenance of ELIXIR-approved resources.

Conclusions ELIXIR is a “one-stop-shop” that helps researchers identify the most suitable, robust and well-maintained bioinformatics resources for delivering their research tasks.
First report on molecular identification of Fusarium species causing fruit rot of mandarin (Citrus reticulata) in Bangladesh
Authors: Hasan Mohammed Faruk , Islam Mohammed Asadul , Sikdar Biswanath
Published: October 2020

Background: Fusarium rot is a newly introduced, devastating disease of citrus fruits. The current investigation was undertaken to characterize the microbes responsible for fruit rot in Citrus reticulata.

Methods: Pathogens were isolated from infected citrus fruits using morphological and molecular approaches. For confirmation of the isolated fungi, polymerase chain reaction (PCR) amplification and internal transcribed spacer gene sequencing techniques were used.

Results: The isolated fungus was grown on potato dextrose agar for three days and it produced clamydospores, hyphae and macroconidia. PCR amplification of isolated fungal DNA gave a 650 bp product. The sequence obtained from isolated fungi had 99.42% similarity with the reference Fusarium concentricum sequence in NCBI GenBank. The obtained sequence was deposited in GenBank (Accession No. MT856371). Two isolates showed virulence capability on fresh guava, sweet orange and tomato fruits, which confirmed species identification and Koch’s postulates. Artificially inoculated fungal species grown on tested fruits showed typical Fusarium species symptoms.

Conclusions: Outcomes of the present study are beneficial for the detection of this detrimental disease in postharvest Citrus reticulata fruits. Further research is needed for the control of this economically important disease. This is the first study of fruit rot in Citrus reticulata caused by Fusarium in Bangladesh.
Prenatal lead exposure: associations with growth and anthropometry in early childhood in a UK observational birth cohort study
Authors: Taylor Caroline M. , Golding Jean , Kordas Katarzyna
Published: October 2020

Background:Lead is a neurotoxic metal that crosses the placenta freely. It has adverse effects on a range of birth outcomes. The few studies reporting on the associations of prenatal exposure to lead and child growth have had conflicting results. This study aimed to examine the effect of low-level prenatal exposure to lead on children’s growth from 4 to 61 months old.

Methods:Pregnant women were enrolled in the UK Avon Longitudinal Study of Parents and Children (ALSPAC). Whole blood samples for pregnancies with a live birth were analysed for lead (n=4140). A 10% subsample of the offspring cohort (Children in Focus) were invited to clinics at 10 time points (4–61 months) at which anthropometric measurements were carried out; z-scores for height, weight and BMI were calculated using the 1990 British Growth Reference Standards. Associations between prenatal log10-lead concentrations and z-scores and other anthropometric measures were modelled using adjusted linear regression models in an imputed dataset for children who attended at least one clinic (n=574).

Results:The mean prenatal blood lead concentration was 3.59±1.50 (range 1.22–14.70) µg/dl. There was no evidence for any associations of low-level prenatal lead exposure with z-scores for BMI, height or weight in adjusted models from age 4 to 61 months. There were no associations for other anthropometric measures including mid-upper arm circumference, head circumference and waist circumference. There was some evidence for a weakly positive effect of prenatal lead exposure on head circumference in girls at age 43 and 61 months (at 61 months unstandardised B coefficient 1.59 (95% CI 0.12, 3.16) cm, p=0.048) but not at other ages.

Conclusions:There was no consistent evidence of associations between prenatal exposure to lead and measures of growth and anthropometry from age 4 to 61 months in this cohort of children in the UK.
Data-Driven Preference Learning Methods for Value-Driven Multiple Criteria Sorting with Interacting Criteria
Authors: Liu Jiapeng , Kadziński Miłosz , Liao Xiuwu , Mao Xiaoxin
Published: October 2020

The learning of predictive models for data-driven decision support has been a prevalent topic in many fields. However, construction of models that would capture interactions among input variables is a challenging task. In this paper, we present a new preference learning approach for multiple criteria sorting with potentially interacting criteria. It employs an additive piecewise-linear value function as the basic preference model, which is augmented with components for handling the interactions. To construct such a model from a given set of assignment examples concerning reference alternatives, we develop a convex quadratic programming model. Because its complexity does not depend on the number of training samples, the proposed approach is capable for dealing with data-intensive tasks. To improve the generalization of the constructed model on new instances and to overcome the problem of overfitting, we employ the regularization techniques. We also propose a few novel methods for classifying nonreference alternatives in order to enhance the applicability of our approach to different data sets. The practical usefulness of the proposed approach is demonstrated on a problem of parametric evaluation of research units, whereas its predictive performance is studied on several monotone classification problems. The experimental results indicate that our approach compares favourably with the classical UTilités Additives DIScriminantes (UTADIS) method and the Choquet integral-based sorting model.

Summary of Contribution. The paper tackles vital challenges at the intersections of multiple criteria decision analysis and machine learning, showing how computationally advanced techniques can be used for faithfully representing human preferences and dealing with complex decision problems. Specifically, we propose a novel preference learning method for multiple criteria sorting problems. The introduced approach incorporates convex quadratic programming to construct a value-based preference model based on large sets of preference statements. In this way, we extend the applicability of decision analysis methods to preferences derived from historical data or observation of users' behavior in addition to the preference judgments explicitly revealed by the decision-makers. The method's practical usefulness is illustrated on a variety of real-world datasets from fields such as higher education, medicine, human resources, and housing market. Its potential for supporting better decision-making is enhanced by both an interpretable form of the assumed model handling interactions between criteria as well as a high predictive performance demonstrated in the extensive computational experiments.
On the Solution of ℓ0-Constrained Sparse Inverse Covariance Estimation Problems
Authors: Phan Dzung T. , Menickelly Matt
Published: October 2020

The sparse inverse covariance matrix is used to model conditional dependencies between variables in a graphical model to fit a multivariate Gaussian distribution. Estimating the matrix from data are well known to be computationally expensive for large-scale problems. Sparsity is employed to handle noise in the data and to promote interpretability of a learning model. Although the use of a convex ℓ1 regularizer to encourage sparsity is common practice, the combinatorial ℓ0 penalty often has more favorable statistical properties. In this paper, we directly constrain sparsity by specifying a maximally allowable number of nonzeros, in other words, by imposing an ℓ0 constraint. We introduce an efficient approximate Newton algorithm using warm starts for solving the nonconvex ℓ0-constrained inverse covariance learning problem. Numerical experiments on standard data sets show that the performance of the proposed algorithm is competitive with state-of-the-art methods.

Summary of Contribution: The inverse covariance estimation problem underpins many domains, including statistics, operations research, and machine learning. We propose a scalable optimization algorithm for solving the nonconvex ℓ0-constrained problem.
Surge Pricing and Its Spatial Supply Response
Authors: Besbes Omar , Castro Francisco , Lobel Ilan
Published: October 2020

We consider the pricing problem faced by a revenue-maximizing platform matching price-sensitive customers to flexible supply units within a geographic area. This can be interpreted as the problem faced in the short term by a ride-hailing platform. We propose a two-dimensional framework in which a platform selects prices for different locations and drivers respond by choosing where to relocate, in equilibrium, based on prices, travel costs, and driver congestion levels. The platform’s problem is an infinite-dimensional optimization problem with equilibrium constraints. We elucidate structural properties of supply equilibria and the corresponding utilities that emerge and establish a form of spatial decomposition, which allows us to localize the analysis to regions of movement. In turn, uncovering an appropriate knapsack structure to the platform’s problem, we establish a crisp local characterization of the optimal prices and the corresponding supply response. In the optimal solution, the platform applies different treatments to different locations. In some locations, prices are set so that supply and demand are perfectly matched; overcongestion is induced in other locations, and some less profitable locations are indirectly priced out. To obtain insights on the global structure of an optimal solution, we derive in quasi-closed form the optimal solution for a family of models characterized by a demand shock. The optimal solution, although better balancing supply and demand around the shock, quite interestingly also ends up inducing movement away from it.

This paper was accepted by David Simchi-Levi, optimization.
Social Influence Undermines the Wisdom of the Crowd in Sequential Decision Making
Authors: Frey Vincenz , van de Rijt Arnout
Published: October 2020

Teams, juries, electorates, and committees must often select from various alternative courses of action what they judge to be the best option. The phenomenon that the central tendency of many independent estimates is often quite accurate—“the wisdom of the crowd”—suggests that group decisions based on plurality voting can be surprisingly wise. Recent experimental studies demonstrate that the wisdom of the crowd is further enhanced if individuals have the opportunity to revise their votes in response to the independent votes of others. We argue that this positive effect of social information turns negative if group members do not first contribute an independent vote but instead cast their votes sequentially such that early mistakes can cascade across strings of decision makers. Results from a laboratory experiment confirm that when subjects sequentially state which of two answers they deem correct, majorities are more often wrong when subjects can see how often the two answers have been chosen by previous subjects than when they cannot. As predicted by our theoretical model, this happens even though subjects’ use of social information improves the accuracy of their individual votes. A second experiment conducted over the internet involving larger groups indicates that although early mistakes on easy tasks are eventually corrected in long enough choice sequences, for difficult tasks wrong majorities perpetuate themselves, showing no tendency to self-correct.

This paper was accepted by Yuval Rottenstreich, decision analysis.
The Impact of Work Method on Musculoskeletal Disorders Complaints in Pharmacy Unit
Authors: Nasution Achmad Delianur , Mahyuni Eka Lestari
Published: October 2020

Background: Musculoskeletal disorders (MSDs) are complaints on parts of skeletal muscle which is perceived by someone ranging from mild to severe. These complaints often occur in the manual process, heavy workload, and work environment interactions that may lead to a non-ergonomic work posture. This study aims to analyze the impact of the work method to MSDs complaints at the pharmacy unit of The University of Sumatera Utara Hospital. Method: This study is an observational survey using a cross-sectional design. The population was all workers in the pharmacy unit of the University of Sumatera Utara Hospital numbered 27 people. Samples were taken from the total population. Data were collected using camera media and direct observation of the work process that took place in the pharmacy unit of USU Hospital. Musculoskeletal complaints were obtained by mapping the pain using Nordic Body Map (NBM). The data obtained were analyzed using a simple logistic regression test to see the impact of the working methods of the pharmacy unit workers on their complaints of musculoskeletal disorders. Results: There was a significant association between work methods in the Pharmacy unit and the MSDs complaints with p-value = 0,001. This was supported by the mean of the work patterns in the pharmacy unit which have a heavy workload and the interaction with the layout according to anthropometry. There was a significant association between the work method causing musculoskeletal complaints when the drug compounding process (p = 0.000). It was evidenced from the result of NBM questionnaire that the three most prevalent complaints of MSDs were pain around the neck, back, and right shoulder. Conclusion: It can be concluded that the static working methods with a heavy workload must be accompanied by a relaxation to avoid burn out and fatigue.
The Views of Thai Buddhist Monks on a Good Death
Authors: Sangchart Bumpenchit , Ngamgam Suksan Promdee , Ekwuttiwongsa Rawat , Sangruangake Monthida
Published: October 2020

Background:When Buddhist monks were sick, they had to take care of themselves, or they will be taken care of by other monks. The care may be provided until they recover from the illness or throughout life. The monks who are the caregivers go through near-death and death experiences. The purpose of this phenomenological study was to investigate the meanings of a good death based on the experience of 13 Thai Buddhist monks that providing care for the sick monks until the sick monks passed away. Method:Purposeful sampling was used to select participants who voluntarily participated in the study. In-depth interviews were the main methods of data gathering. Established trustworthiness of a qualitative inquiry based on quality criteria of Lincoln and Guba. The methodological interpretations of Diekelmann and Allen established the thematic analysis of this study. Results:Six main themes and six subthemes of a good death emerged from participants which formed the basis of the findings reported: (a) free from suffering, consisting of 1) death without life's restraints, 2) peaceful death, and 3) death as a sleeping person (but not awake); (b) natural death with good deeds; (c) awareness of death, composed of (1) accepting death, (2) preparation before death, and (3) letting things go; (d) last spirituality becoming a mental charity; (e) resting in peace; and (f) nirvana.  Conclusion: The results of the present study could fulfill and extend the meanings of good death to a wider and deeper which are different from the previous studies.
Use of upper-limb compression garments in the management of lipoedema
Authors: Elwell Rebecca , Rich Anna
Published: October 2020

Compression hosiery is commonly used for the management of lymphoedema as well as lipoedema, but it is more commonly indicated for the lower limbs than for the upper limbs. The effects of compression hosiery on upper-limb lipoedema are poorly understood and researched. It is known that compression hosiery works in conjunction with activity or movement when standing or walking, which produces anti-inflammatory and oxygenating effects in the tissues. This effect is naturally difficult to realise in the upper limbs. Lymphoedema practitioners who treat those with lipoedema should bear in mind that compression treatment might not produce the same effects in upper-limb lipoedema as it does in lower-limb lipoedema. In these times of an overstretched health service, pragmatic resource use is essential.
The Professional Midwifery Advocate in non-NHS organisations
Authors: Ecclestone Lorraine
Published: October 2020

A professional midwifery advocate supports midwives, allowing for clinical supervision, education and development. The impact of this role in non-NHS organisations has not been well-researched
The pandemic surveillance state: an enduring legacy of COVID-19
Authors: Kampmark Binoy
Published: October 2020

Containing the spread of pandemic transmission tends to go hand in hand with a surveillance regime that tracks movement, transmission and those who contract the virus or disease. An enduring legacy of the COVID-19 crisis will be the incremental development of surveillance technologies, ostensibly purposed to identify the threat and spread of a pandemic, giving birth to what amounts to the pandemic surveillance state. Whether this is seen as an undesirable outcome depends very much on the field of expertise and the relevant slant. Health professionals and epidemiologists favor more surveillance; privacy and data security advocates fear a further denuding of protections. This paper examines the dangers of such technologies and efforts to seek a middle ground on app technologies designed to protect privacy. Such designs may, in time, seem more hopeful than actual.
An adaptation of The Narrow Corridor
Authors: Fenske James
Published: October 2020

Blithering idiot. You agreed to write an article-length review on the new book by Acemoglu and Robinson. Acemoglu has published more in the last five years than you have in your whole career. You’re pretty sure Robinson was one of your letter writers. Hither have you come? What if you make a fool of yourself? What if you say something that upsets them? … You have to do this. Manoel Bittencourt flew you to Johannesburg. You drank his scotch while making him listen to the latest Soen album. You owe him. It’s just a book review. You can do this.