bluuebunny/crossref_metadata_2025_split huggingface dataset:
Propensity score matching enables batch-effect-corrected imputation in single-cell RNA-seq analysis
Authors: Xu Xinyi , Yu Xiaokang , Hu Gang , Wang Kui , Zhang Jingxiao , Li Xiangjie 
Published: July 2022

Abstract
Developments of single-cell RNA sequencing (scRNA-seq) technologies have enabled biological discoveries at the single-cell resolution with high throughput. However, large scRNA-seq datasets always suffer from massive technical noises, including batch effects and dropouts, and the dropout is often shown to be batch-dependent. Most existing methods only address one of the problems, and we show that the popularly used methods failed in trading off batch effect correction and dropout imputation. Here, inspired by the idea of causal inference, we propose a novel propensity score matching method for scRNA-seq data (scPSM) by borrowing information and taking the weighted average from similar cells in the deep sequenced batch, which simultaneously removes the batch effect, imputes dropout and denoises data in the entire gene expression space. The proposed method is testified on two simulation datasets and a variety of real scRNA-seq datasets, and the results show that scPSM is superior to other state-of-the-art methods. First, scPSM improves clustering accuracy and mixes cells of the same type, suggesting its ability to keep cell type separation while correcting for batch. Besides, using the scPSM-integrated data as input yields results free of batch effects or dropouts in the differential expression analysis. Moreover, scPSM not only achieves ideal denoising but also preserves real biological structure for downstream gene-based analyses. Furthermore, scPSM is robust to hyperparameters and small datasets with a few cells but enormous genes. Comprehensive evaluations demonstrate that scPSM jointly provides desirable batch effect correction, imputation and denoising for recovering the biologically meaningful expression in scRNA-seq data.
A Multi-Analyte LC–MS/MS Method for Determination and Quantification of Six Nitrosamine Impurities in Sartans like Azilsartan, Valsartan, Telmisartan, Olmesartan, Losartan and Irbesartan
Authors: Gopireddy Ramana Reddy , Maruthapillai Arthanareeswari , Mahapatra Sudarshan 
Published: July 2022

Abstract
A sensitive and robust method for determination and quantification of potential genotoxic impurities in sartans has been developed. These impurities need to be controlled at trace levels during quantification in drug substances and drug products for safe consumption. Recent regulatory requirements also suggested the need to have highly sensitive analytical method for trace level quantification of nitrosamine impurities. In this paper, we have described a simple, rapid and sensitive liquid chromatography-mass spectrometry method for six potential genotoxic nitrosamine impurities: N-Nitroso dimethyl amine (NDMA), N-Nitroso diethyl amine (NDEA), N-Nitroso Ethyl Iso propylamine (NIPEA), N-Nitroso-Nmethyl-4-aminobutyric acid (NMBA) N-Nitroso diisopropylamino (NDIPA) and N-Nitroso dibutyl amine (NDBA) in Azilsartan (AZL), Valsartan (VAL), Telmisartan (TEL), Olmesartan (OLM), Losartan (LOS) and Irbesartan (IRB) with a limit of quantification of less than 0.003 ppm. Chromatographic separation is achieved using Poroshell HPH- C18, 150 × 4.6 mm, 2.7 μm column with 0.1% formic acid in water as mobile phase A and 0.1% formic acid in methanol as mobile phase B at a flow rate of 0.5 mL/min using gradient mode of elution at a total run time of 20 min. Six nitrosamine impurities are ionized and quantified in positive mode of atmospheric pressure chemical ionization using multiple reaction monitoring. As per ICH guidelines, method validation is performed and evaluated the limit of quantification and detection and found to give good S/N ratios with good linearity range of 0.003–0.045 ppm with regression coefficient &gt; 0.999 for all the six nitrosamine impurities. Method recoveries are also established using three-step sample preparation and are found to be satisfactory within 80–120%. The single method can be used routinely applied for the detection of nitrosamines in AZL, VAL, TEL, OLM, LOS and IRB.
Efficacy and safety of triamcinolone acetonide in the prevention of esophageal stricture after endoscopic submucosal dissection: a meta-analysis
Authors: Jia Yuting , Guo Bin , Zhang Wenbin , Li Erfeng , Zhang Quanmao 
Published: July 2022

Abstract

Aim
The role of triamcinolone acetonide (TA) in the prevention of esophageal stricture is not well established. This meta-analysis aimed to evaluate its safety and efficacy for the prevention of esophageal stricture after endoscopic submucosal dissection (ESD).

Methods
A comprehensive search was performed in electronic databases including PubMed, the Cochrane Library, Embase for possible controlled studies. The primary outcomes were stenosis rate and endoscopic balloon dilatation (EBD) sessions required, and secondary outcome included complications. Random effects were used to calculate the pooled outcome. Sensitivity analysis and publication bias were conducted to verify the robustness and reliability of the results. Results: Ten studies containing 499 patients were obtained. In the pooled analysis, statistical significance was found in triamcinolone acetonide injection reduced the incidence of stenosis (OR = 0.29, 95% CI [0.11, 0.80], P &lt; 0.05) and the number of endoscopic balloon dilation (MD = −3.33, 95% CI [−4.15, −2.50], P &lt; 0.0001) compared with control. Triamcinolone acetonide injection therapy did not increase the risk of complications (OR = −0.77%, CI [−1.62, 0.09], P = 0.08). Subgroup analysis indicated that the single injection of triamcinolone acetonide after endoscopic submucosal dissection significantly reduced the incidence of stenosis compared with without any prophylaxis. Different concentrations and single session volume of triamcinolone acetonide reduced the incidence of stenosis. It also showed that the dose according to the size of the lesion was more effective than the fixed dose in preventing esophageal stricture. Conclusion: Triamcinolone acetonide injection can reduce the incidence of stricture formation as well as the need for EBD sessions without increasing complications.
Association of Proinflammatory Diet With Frailty Onset Among Adults With and Without Depressive Symptoms: Results From the Framingham Offspring Study
Authors: Millar Courtney L , Dufour Alyssa B , Hebert James R , Shivappa Nitin , Okereke Olivia I , Kiel Douglas P , Hannan Marian T , Sahni Shivani 
Published: July 2022

AbstractBackgroundDietary inflammation is associated with increased risk of frailty. Those with depressive symptoms may be at higher risk of frailty onset because they typically have higher levels of inflammation. The study objective was to determine the association between a proinflammatory diet and frailty onset in those with and without clinically relevant depressive symptoms.MethodsThis prospective study included 1 701 nonfrail individuals with self-reported baseline (1998–2001) data available for the evaluation of energy-adjusted dietary inflammatory index (E-DIITM; calculated from food frequency questionnaires), depressive symptoms (from the Center for Epidemiologic Studies Depression; CES-D), and follow-up frailty measurements (2011–2014). Frailty was defined as fulfilling ≥3 Fried frailty criteria (i.e., slow gait, weak grip strength, unintentional weightloss, low physical activity, and self-reported exhaustion). Results are presented by baseline CES-D scores &lt;16 or ≥16 points, which denotes the absence or presence of clinically relevant depressive symptoms, respectively. Logistic regression estimated odds ratios (OR) and 95% confidence intervals (95% CI) between E-DII and frailty onset, adjusting for confounders.ResultsIn all study participants, mean (SD) age was 58(8) years and E-DII was −1.95 (2.20; range: −6.71 to +5.40, higher scores denote a more proinflammatory diet), and 45% were male. In those without clinically relevant depressive symptoms, 1-unit higher E-DII score was associated with 14% increased odds (95% CI: 1.05–1.24) of frailty. In those with depressive symptoms, 1-unit higher E-DII score was associated with 55% increased odds of frailty (95% CI: 1.13–2.13).ConclusionsThe association between inflammatory diet and increased odds of frailty appeared somewhat stronger among those with depressive symptoms. This preliminary finding warrants further investigation.
African Penguins and Localized Fisheries Management: Response to Butterworth and Ross-Gillespie
Authors: Sydeman W J , Hunt G L , Pikitch E K , Parrish J K , Piatt J F , Boersma P D , Kaufman L , Anderson D W , Thompson S A , Sherley R B 
Published: July 2022

Abstract
We present a response to Butterworth and Ross-Gillespie's (2022) comment on our perspectives on how forage fish fisheries are impacting the endangered African penguin (Sphenicus demersus), and corresponding management options. Butterworth and Ross-Gillespie overstate model uncertainties and downplay the clear ecological and conservation significance of the fisheries closure experiment. We demonstrate that their criticism of “pseudo-replication” is weak, and not in line with their own analyses nor with the interpretations of many international scientific review panels commissioned by the government of South Africa to evaluate experimental results. Their comment does not alter our fundamental conclusions that forage fisheries operating near penguin breeding colonies compete with the birds for food resources, are detrimental to the penguin's population health, and are impeding recovery. Given that sardines are depleted (DFFE, 2021) and the African penguin is approaching a conservation crisis, we reiterate our position that continuing the precautionary approach of closures at the local scale of central-place foraging penguins is warranted to facilitate their population growth under fisheries management goals to conserve and maintain ecosystem functions.
Mapping habitat loss in the deep-sea using current and past presences of Isidella elongata (Cnidaria: Alcyonacea)
Authors: González-Irusta José Manuel , Cartes Joan E , Punzón Antonio , Díaz David , de Sola Luis Gil , Serrano Alberto 
Published: July 2022

Abstract
The bamboo coral Isidella elongata is an engineering species that forms a characteristic biogenic habitat in the bathyal mud of the Mediterranean Sea. This habitat has been severely reduced in recent decades due to trawling impacts, and there is a growing concern about its conservation status. In this work, the habitat loss of I. elongata was computed using a novel approach that combines the realized niche of the species with the estimation of its past distribution (before trawling) to delineate potential areas of habitat loss with different levels of uncertainty. The realized niche of the species was modelled using only live colonies and including trawling effort as explanatory variable whereas the past distribution was estimated also using the leftovers of dead colonies as presences. Trawling effort had a statistically significant negative effect on the extent of the realized niche of I. elongata, confirming previous results on the impact of this pressure on its distribution. The novel approach used in this work has allowed us to map for the first time several areas of potential habitat loss for I. elongata in the studied area, opening new opportunities to provide this essential information for future management and restoration actions of vulnerable marine ecosystems worldwide.
Effects of calcium salts of palm oil inclusion and ad libitum feeding regimen on growth performance, carcass characteristics, and plasma glucose-dependent insulinotropic polypeptide concentration of feedlot steers
Authors: Pittaluga Alejandro M , Ortiz-Fraguada Mairim Y , Parker Anthony Joseph , Relling Alejandro E 
Published: July 2022

Abstract
Sixty Angus × SimAngus-crossbred steers (body weight [BW] 279 ± 16 kg) were used to evaluate the effect of calcium salts of palm oil inclusion (CPO) and the amount of feed offered (AFO) on plasma glucose-dependent insulinotropic polypeptide (GIP) concentration and its association with energy metabolism and marbling score (MS) in feedlot steers. Steers were blocked by BW and gain to feed (G:F) and randomly assigned to individual feedlot pens. Treatments (2 × 2 factorial) consisted of ad libitum-fed steers without (ANF) or with (AWF) the inclusion of CPO or restricted-fed steers (85% of the ad libitum intake of ANF) without (RNF) or with the inclusion of CPO (RWF). After weaning, steers were adapted to individual pens and fed a corn silage-based diet for 30 d and subsequently placed in a ground corn (GC)–based diet. Diets were given ad libitum or at 85% of the ANF intake and with or without CPO. After 59 d on the finishing diet, all steers had ad libitum access to the finishing diet until harvest. Measurements of CO2 emission and O2 consumption to estimate respiratory quotient (RQ) were taken (n = 9/treatment). Correlations between plasma GIP and insulin concentrations and RQ were analyzed. A linear regression was performed to evaluate the association of plasma GIP and MS. All data were analyzed using the PROC MIXED procedure of SAS. During the first 103 d of the trial, there were AFO × CPO interactions (P ≤ 0.01) for BW, dry matter intake (DMI), average daily gain (ADG), and net energy for maintenance (NEm) intake. Ad libitum-fed steers without CPO presented the greatest DMI among dietary treatments and had greater BW and ADG compared with steers in the RWF and RNF treatments. After all steers had ad libitum access to dietary treatments, steers that were previously restricted showed a 30% and 19% increase (P ≤ 0.01) in ADG and G:F, respectively. There was a three-way interaction time × CPO × AFO (P = 0.04) for plasma GIP concentration. There was no correlation (P = 0.96) of GIP with RQ, whereas insulin demonstrated marginal significance for a positive (P = 0.07) and negative (P = 0.08) correlation with plasma GIP and RQ, respectively. There was no association (P = 0.30) between GIP and MS. These data indicate that GIP secretion results from an interaction between CPO and energy intake depending on the time relative to feed intake that GIP might indirectly regulate energy metabolism through insulin secretion, and that GIP does not appear to be associated with MS.
Identifying and Assisting Burn Patients and Their Families With Needs Through Administration of an Assessment Tool on Admission
Authors: Fassel Mikenzy , Ong Jia Ern , Galet Colette , Wibbenmeyer Lucy 
Published: July 2022

Abstract
Using a modified Safe Environment for Every Kid Questionnaire (Needs Survey), we previously showed a significant correlation between adverse childhood experiences (ACEs) and family needs. Herein, we retrospectively assessed whether patients’ and their families’ needs identified using the Needs Survey were addressed prior to discharge. We hypothesized that, without the knowledge gained by administering this tool, many basic needs may not have been fully addressed. Seventy-nine burn patients and families previously enrolled in our ACE studies were included. Answers to the Needs Surveys were reviewed to identify families with needs. Medical records were reviewed to determine if a social worker assessment (SWA) was completed per standard of care and if their needs were addressed prior to discharge. Of the 79 burn patients who received inpatient care and completed the Needs Survey, family needs were identified in 67 (84.8%); 42 (62.7%) received an SWA, and 25 (37.3%) did not. Those who did not receive a SWA had a shorter hospitalization and suffered less severe burns. Demographics, socioeconomics, ACEs, and identified needs were similar between the groups. Our study showed that SWA was performed on many patients with basic needs. However, with the focus of SWAs being on discharge arrangements, not all needs were addressed, and individualized resources were often not provided. Administering the Needs Survey on admission may help our social workers streamline and expedite this process to help support successful recovery for our burn patients and their families.
Inadvertent Radiation Exposures in Combat Zones: Risk of Contamination and Radiobiologic Consequences
Authors: Jensen Kirk , Vasko Vasyl 
Published: July 2022

ABSTRACT
On February 24, 2022, Russia began a military invasion of Ukraine. Missile and air strikes were reported throughout the country, shortly followed by a large ground invasion from multiple directions. Four major theaters developed: the Kyiv offensive, the Northeastern Ukraine offensive, the Eastern Ukraine offensive, and the Southern Ukraine offensive, with continued missile and air strikes far into Western Ukraine. Advancing Russian military units launched an attack and captured the Chernobyl nuclear station. Russian troops dug trenches into the area commonly known as the “Red Forest,” violating the established radiation safety measures and threatening security within the Chernobyl Exclusion Zone. The placement of military units in such close proximity to the station also sparked concerns of possible damage occurring to the containment vessel constructed around the station’s wrecked fourth reactor. There are 15 operating nuclear reactors in Ukraine. Each is vulnerable to an attack or sabotage that could precipitate a malfunction and possible release of radioactive isotopes. In this short commentary, we will discuss radiobiologic data obtained after the analysis of historical nuclear power plant (NPP) accidents and emphasize new challenges for nuclear security when NPPs are found and are possible targets within a conflict zone.
A search for monochromatic light towards the Galactic Centre
Authors: Marcy Geoffrey W , Tellis Nathaniel K , Wishnow Edward H 
Published: July 2022

ABSTRACT
A region 140 square degrees towards the Galactic Centre was searched for monochromatic optical light, both pulses shorter than 1 s and continuous emission. A novel instrument was constructed that obtains optical spectra of every point within 6 square deg every second, able to distinguish lasers from astrophysical sources. The system consists of a modified Schmidt telescope, a wedge prism over the 0.28-m aperture, and a fast CMOS camera with 9500 × 6300 pixels. During 2021, a total of 34 800 exposures were obtained and analysed for monochromatic sources, both subsecond pulses and continuous in time. No monochromatic light was found. A benchmark laser with a 10-m aperture and located 100 light years (ly) away would be detected if it had a power more than ∼60 megawatt (MW) during 1 s, and from 1000 ly away, 6000 MW is required. This non-detection of optical lasers adds to previous optical SETI non-detections from more than 5000 nearby stars of all masses, from the Solar gravitational lens focal points of Alpha Centauri, and from all-sky searches for broadband optical pulses. These non-detections, along with those of broadband pulses, constitute a growing SETI desert in the optical domain.
Reoperation in adult patients with recurrent glioblastoma: A matched cohort analysis
Authors: Yang Kaiyun , Ellenbogen Yosef , Martyniuk Amanda , Sourour Michel , Takroni Radwan , Somji Mohamed , Gardiner Emily , Hui Katrina , Odedra Devang , Larrazabal Ramiro , Algird Almunder , Kachur Edward , Reddy Kesava , Murty Naresh , Farrokhyar Forough , Singh Sheila K 
Published: July 2022

Abstract

Background
Despite maximal safe cytoreductive surgery and postoperative adjuvant therapies, glioblastoma (GBM) inevitably recurs and leads to deterioration of neurological status and eventual death. There is no consensus regarding the benefit of repeat resection for enhancing survival or quality of life in patients with recurrent GBM. We aimed to examine if reoperation for GBM recurrence incurs a survival benefit as well as examine its complication profile.

Methods
We performed a single-center retrospective chart review on all adult patients who underwent resection of supratentorial GBM between January 1, 2008 and December 1, 2013 at our center. Patients with repeat resection were manually matched for age, sex, tumor location, and Karnofsky Performance Status (KPS) with patients who underwent single resection to compare overall survival (OS), and postoperative morbidity.

Results
Of 237 patients operated with GBM, 204 underwent single resection and 33 were selected for repeat surgical resections. In a matched analysis there was no difference in the OS between groups (17.8 ± 17.6 months vs 17 ± 13.5 months, P = .221). In addition, repeat surgical resection had a higher rate of postoperative neurological complications compared to the initial surgery.

Conclusions
When compared with matched patients who underwent a single surgical resection, patients undergoing repeat surgical resection did not show significant increase in OS and may have incurred more neurological complications related to the repeat resection. Further studies are required to assess which patients would benefit from repeat surgical resection and optimize timing of the repeat resection in selected patients.
Warm glow and consumers’ valuation of ethically certified products
Authors: Iweala Sarah , Spiller Achim , Nayga Rodolfo M , Lemken Dominic 
Published: July 2022

Abstract
A number of self-beneficial motives can trigger pro-environmental and prosocial behavior of individuals. We focus on the role of the warm glow of giving—the personal benefit people experience when doing good irrespective of the consequences—in the valuation of ethically certified food products. Our data is based on an online experimental auction with more than 800 consumers in Germany. Participants bid on tea and chocolate advertised with prosocial and pro-environmental certifications after being randomly exposed to affectively and informatively framed messages. We also measured the experienced warm glow of participants. Our main results are (1) that the experienced warm glow is only linked to a higher willingness-to-pay of older and higher income respondents; (2) that the experienced warm glow does not differ between prosocial and pro-environmental causes; and (3) that treatment effects do not differ according to the participants’ warm glow level but according to the certification itself.