bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D spheroid-microvasculature-on-a-chip for tumor-endothelium mechanobiology interplay
Authors: Zhang Yingqi , Jiang Fengtao , Zhao Yunduo Charles , Cho Ann-Na , Fang Guocheng , Cox Charles D , Zreiqat Hala , Lu Zu Fu , Lu Hongxu , Ju Lining Arnold 
Published: July 2023

Abstract
During the final stage of cancer metastasis, tumor cells embed themselves in distant capillary beds, from where they extravasate and establish secondary tumors. Recent findings underscore the pivotal roles of blood/lymphatic flow and shear stress in this intricate tumor extravasation process. Despite the increasing evidence, there is a dearth of systematic and biomechanical methodologies that accurately mimic intricate 3D microtissue interactions within a controlled hydrodynamic microenvironment. Addressing this gap, we introduce an easy-to-operate 3D spheroid-microvasculature-on-a-chip (SMAC) model. Operating under both static and regulated flow conditions, the SMAC model facilitates the replication of the biomechanical interplay between heterogeneous tumor spheroids and endothelium in a quantitative manner. Serving as an in vitro model for metastasis mechanobiology, our model unveils the phenomena of 3D spheroid-induced endothelial compression and cell-cell junction degradation during tumor migration and expansion. Furthermore, we investigated the influence of shear stress on endothelial orientation, polarization, and tumor spheroid expansion. Collectively, our SMAC model provides a compact, cost-efficient, and adaptable platform for probing the mechanobiology of metastasis.
A combined fuzzy backtracking search optimization algorithm to localize retinal blood vessels for diabetic retinopathy
Authors: Neelapala Anil Kumar , Swarnadh Satapathi Gnane , Borra Vamsi , Mahapatra Ranjan Kumar , Shanbhag Pavitra 
Published: July 2023

Abstract
For diabetic retinopathy (DR) surgery, localization of retinal blood vessels is of paramount importance. Fundus images which are often used for DR diagnosis suffer from poor contrast (between the retinal background and the blood vessels, due to its size) limits the diagnosis. In addition to this, various pathological changes in retinal blood vessels may also be observed for different diseases such as glaucoma and diabetes. To alleviate, in this paper, an automated unsupervised retinal blood vessel segmentation technique, based on backtracking search optimization algorithm (BSA), is proposed. The BSA method is used to optimize the local search of fuzzy c-means clustering (FCM) algorithm to find micro-diameter sized vessels along with coarse vessels. The proposed technique is tested on two publicly available retinal datasets (i.e., STARE and DRIVE) and verified using the dataset collected from various hospitals in Bangalore and Mangalore, India. The results show that the performance of the proposed method is comparable to the conventional techniques in terms of sensitivity, specificity, and accuracy.
Factors associated with discharge against medical advice in alcohol withdrawal patients
Authors: Coleman Rachel , Coulton Simon , Phillips Thomas 
Published: July 2023

Abstract
This study aimed to examine characteristics associated with discharge against medical advice from the hospital in alcohol withdrawal patients, supporting the work of hospital staff and Alcohol Care Teams and identifying characteristics that may help target patients most likely to discharge against medical advice. We used Hospital Episode Statistics Data to identify demographic and clinical variables and compare these in alcohol withdrawal patients who discharged against medical advice from hospital, compared with those who were discharged by the clinical team. Factors significantly associated with alcohol withdrawal patients discharging against medical advice from hospital were: being admitted as an emergency; discharged on a weekend; living with no fixed abode; being male; being younger and having a shorter length of stay. This study identifies characteristics that can be used to support acute hospitals and Alcohol Care Teams, particularly in the allocation of resources to reduce discharges against medical advice and subsequent readmissions to the hospital. Particular consideration should be given to clinical provision in hospitals in emergency departments and on weekends, and also those patients who are admitted and are of no fixed abode.
Measuring the relative contribution to predictive power of modern nucleotide substitution modeling approaches
Authors: Bujaki Thomas , Van Looyen Katharine , Rodrigue Nicolas 
Published: July 2023

SummaryTraditional approaches to probabilistic phylogenetic inference have relied on information-theoretic criteria to select among a relatively small set of substitution models. These model selection criteria have recently been called into question when applied to richer models, including models that invoke mixtures of nucleotide frequency profiles. At the nucleotide level, we are therefore left without a clear picture of mixture models’ contribution to overall predictive power relative to other modeling approaches. Here, we utilize a Bayesian cross-validation method to directly measure the predictive performance of a wide range of nucleotide substitution models. We compare the relative contributions of free nucleotide exchangeability parameters, gamma-distributed rates across sites, and mixtures of nucleotide frequencies with both finite and infinite mixture frameworks. We find that the most important contributor to a model’s predictive power is the use of a sufficiently rich mixture of nucleotide frequencies. These results suggest that mixture models should be given greater consideration in nucleotide-level phylogenetic inference.
CNAsim: improved simulation of single-cell copy number profiles and DNA-seq data from tumors
Authors: Weiner Samson , Bansal Mukul S 
Published: July 2023

Abstract

Summary
CNAsim is a software package for improved simulation of single-cell copy number alteration (CNA) data from tumors. CNAsim can be used to efficiently generate single-cell copy number profiles for thousands of simulated tumor cells under a more realistic error model and a broader range of possible CNA mechanisms compared with existing simulators. The error model implemented in CNAsim accounts for the specific biases of single-cell sequencing that leads to read count fluctuation and poor resolution of CNA detection. For improved realism over existing simulators, CNAsim can (i) generate WGD, whole-chromosomal CNAs, and chromosome-arm CNAs, (ii) simulate subclonal population structure defined by the accumulation of chromosomal CNAs, and (iii) dilute the sampled cell population with both normal diploid cells and pseudo-diploid cells. The software can also generate DNA-seq data for sampled cells.

Availability and implementation
CNAsim is written in Python and is freely available open-source from https://github.com/samsonweiner/CNAsim.
Ludic cybermilitias: shadow play and computational propaganda in the Indonesian predatory state
Authors: Rasidi Pradipa P 
Published: July 2023

Abstract
This article ties the studies of computational propaganda to studies of the state in the Global South by examining “political buzzers”—actors of Indonesian computational propaganda. Rather than an extension of state propaganda, I argue that buzzers are a “twilight institution” straddling the boundaries between state and society. As cybermilitias, they are rooted in the historical conjuncture of Indonesian state practices in deploying privatized violence for extractive capitalist accumulation, exhibited by two cases in this article: the reclamation of Benoa Bay in Bali and the Ciliwung forced evictions in Jakarta. Informed by ethnographic fieldwork, I delve into buzzers’ experience of computational propaganda as an avenue for political agency. They conceive their clandestine labor into a play, conjuring the political metaphor of dalang (master puppeteers) pulling strings from behind the scenes. These shadow play theatrics constitute the ludic aspect of buzzers as ludic cybermilitias. By exploring how computational propaganda is shaped by and shapes state power in Indonesia, I problematize the notion that political buzzers signify “democratic regression” or “digital authoritarianism.” Instead, I propose that buzzers represent the latest manifestation of privatized violence within the predatory logic of post-authoritarian states in the Global South.
Oral glucocorticoids with intravenous cyclophosphamide or oral glucocorticoids alone in the treatment of IgA nephropathy present with nephrotic syndrome and mesangioproliferative glomerulonephritis
Authors: Du Wen , Chen Zijin , Fang Zhengyin , Li Junru , Weng Qinjie , Zheng Qimin , Xie Lin , Yu Hanlan , Gu Xiangchen , Shi Hao , Wang Zhaohui , Ren Hong , Wang Weiming , Ouyang Yan , Xie Jingyuan 
Published: July 2023

ABSTRACT

Background
Few studies have evaluated the treatment of immunoglobulin A nephropathy (IgAN) patients with nephrotic syndrome (NS) and mesangioproliferative glomerulonephritis (MPGN). The aim of this study was to compare the therapeutic effects of oral glucocorticoids (GCS) combined with intravenous cyclophosphamide (CTX) and oral GCS alone in the treatment of the MPGN-IgAN patients with NS.

Methods
Biopsy-proven primary IgAN patients who were aged ≥14 years at diagnosis, had coexistent NS and MPGN and estimated glomerular filtration rate (eGFR) ≥15 mL/min/1.73 m2, and were treated by oral GCS combined with intravenous CTX or oral GCS alone for 6–12 months were retrospectively included. The patients in the GCS + CTX (prednisone 0.6–0.8 mg/kg/day and intravenous CTX 0.6–1.0 g monthly) or GCS (prednisone 0.8–1 mg/kg/day) group were rather matched at a 1:1 ratio on key characteristics by propensity score matching. The primary outcome was defined as either complete remission or partial remission at Month 24. The secondary outcome was a composite renal endpoint defined as a 50% decline in eGFR, doubling of serum creatinine or progression to end-stage kidney disease.

Results
Among the 146 IgAN patients who met the inclusion criteria, 42 patients were enrolled in the GCS + CTX group, and 42 patients were enrolled in the GCS group after propensity score matching. The clinical and histological parameters were similar between the two groups. Remission occurred more frequently in the GCS + CTX group at Month 6 (88.1% vs 52.4%, P &lt; 0.001), Month 12 (88.1% vs 56.1%, P = 0.001) and Month 24 (85.0% vs 47.5%, P &lt; 0.001) than in the GCS group. Moreover, subgroup analysis revealed that the higher response rate at Month 24 in the GCS + CTX group than in the GCS group was also present in different subgroups defined by sex, age, eGFR or Oxford MEST-C. Notably, we found that eGFR decreased at a lower rate in patients from the GCS + CTX group than in patients from the GCS group [eGFR slope: 0.05(–3.09, 3.67) vs –2.56 (–11.30, 0.86) mL/min/1.73 m2/year, P = 0.03]. Based on multivariate Cox regression analysis, GCS + CTX treatment was found to be independently associated with a decrease in risk for the composite endpoint after adjusted by the International Risk Prediction Score with race (hazard ratio = 0.17, 95% confidence interval 0.04–0.83, P = .03). There was no significant difference in adverse events (50.0% vs 42.9%, P = 0.51) or serious adverse events (7.1% vs 11.9%, P = .71) between the two groups.

Conclusions
Oral GCS combined with intravenous CTX is superior to GCS alone in treating MPGN-IgAN patients combined with NS. As the retrospective design and small sample size, our findings need to be validated by a prospective study.
Feasibility of Targeted Next-Generation DNA Sequencing for Expanding Population Newborn Screening
Authors: Shum Bennett Oh Vic , Pretorius Carel Jacobus , Sng Letitia Min Fen , Henner Ilya , Barahona Paulette , Basar Emre , McGill Jim , Wilgen Urs , Zournazi Anna , Downie Lilian , Taylor Natalie , Cheney Liam , Wu Sylvania , Twine Natalie Angela , Bauer Denis Carolin , Watts Gerald Francis , Navilebasappa Akash , Kumar Kishore Rajagopal , Ungerer Jacobus Petrus Johannes , Bennett Glenn 
Published: July 2023

Abstract

Background
Newborn screening (NBS) is an effective public health intervention that reduces death and disability from treatable genetic diseases, but many conditions are not screened due to a lack of a suitable assay. Whole genome and whole exome sequencing can potentially expand NBS but there remain many technical challenges preventing their use in population NBS. We investigated if targeted gene sequencing (TGS) is a feasible methodology for expanding NBS.

Methods
We constructed a TGS panel of 164 genes which screens for a broad range of inherited conditions. We designed a high-volume, low-turnaround laboratory and bioinformatics workflow that avoids the technical and data interpretation challenges associated with whole genome and whole exome sequencing. A methods-based analytical validation of the assay was completed and test performance in 2552 newborns examined. We calculated annual birth estimates for each condition to assess cost-effectiveness.

Results
Assay analytical sensitivity was &gt;99% and specificity was 100%. Of the newborns screened, 1.3% tested positive for a condition. On average, each individual had 225 variants to interpret and 1.8% were variants of uncertain significance (VUS). The turnaround time was 7 to 10 days. Maximum batch size was 1536 samples.

Conclusions
We demonstrate that a TGS assay could be incorporated into an NBS program soon to increase the number of conditions screened. Additionally, we conclude that NBS using TGS may be cost-effective.
A Feminist Act of Defiance: ‘Iphigenia says no’ by Katerina Anghelaki-Rooke
Authors: Giannakopoulou Liana 
Published: July 2023

AbstractIn ‘Iphigenia says no’, Anghelaki-Rooke provides a critique of the myth of Iphigenia’s sacrifice that gives the story a distinctively feminine poetic voice designed to subvert the unchallenged authority of myth. Her poem is an impassioned plea for a feminist poetics that gives women a voice and agency, rejecting any form of control or authority over the female mind and body. The choice of Euripides’ tragedy Iphigenia at Aulis and an emphasis on the chorus are central to the anti-war message of the poem, but other contextual factors also frame the poet’s choice of myth and determine the direction of her rewriting: these are a feminist anti-war stance that is distinct from the anti-war stance of male poets like Seferis; the peace movements of the Cold War period and their political reverberations in Greece in the early 1960s; archaeological excavations and the renewed interest in the play that these inspired; classical reworkings in popular films of the years immediately prior to the writing of the poem; and the national curriculum and its underlying ideology.
Use of Standardized Inflammatory Bowel Disease Endoscopy Scores in Clinical Practice
Authors: Gaidos Jill K J , Al Bawardy Badr , Farraye Francis A , Regueiro Miguel 
Published: July 2023

Abstract

Background
Inflammatory bowel disease (IBD) treatment targets include mucosal healing based on standardized endoscopic scoring systems. The rates and ease of use of these scoring systems in practice have not been well described. We aimed to assess the rates and factors associated with the use of IBD endoscopic scoring systems in practice from IBD LIVE attendees.

Methods
IBD Live is an international case-based conference focusing on the management of patients with IBD. We created a web-based survey consisting of 38 questions on the frequency and ease of use of various IBD endoscopic scores. This survey was emailed to the IBD Live listserv in March 2022 with a second email sent 14 days later. We included only respondents who are currently performing endoscopy. Continuous variables were analyzed using an unpaired student’s t-test. Categorical variables were analyzed using Pearson’s chi-square test.

Results
There were 65 responses out of 170 (38.2% response rate) regular attendees. Eleven responses were excluded (4 with no response on the use of endoscopy scores, and 7 were not performing endoscopy). Of the respondents, 72.2% are from the United States, 70.4% are adult gastroenterologists, 53.9% in academic practice, and 40.7% in practice for ≥15 years. Of the endoscopy scores used ≥50% of the time, 74.1% were using the Mayo Endoscopic Subscore (MES), 72.3% using the Rutgeerts Score, 61.2% using the Simple Endoscopic Score for Crohn’s Disease, and 28.6% using the Pouchitis Disease Activity Index. Attending IBD LIVE ≥ monthly (P = .028), attending an IBD conference at least every 2 years (P = .020), and having the scoring system incorporated into the endoscopy documentation software (P = .002) were associated with more consistent use of the MES. Attending IBD Live at least monthly (P = .026), having an IBD volume of ≥50% (P = .011), and attending an IBD conference at least every 2 years (P = .004) was associated with more frequent use of the Rutgeerts score. There were no factors that increased the use of other endoscopic scores.

Conclusions
The MES and the Rutgeerts score are more commonly used with much lower rates of use of endoscopic scores for Crohn’s disease and pouchitis. The use of these endoscopy scores is more common among those who regularly attend IBD conferences, have higher volume IBD practices, and have these scoring systems incorporated into endoscopy software. Further evaluation of barriers to use and ways to improve utilization of endoscopic scoring for Crohn’s disease and pouchitis is needed.
Niche differentiation among facultative filter feeders: Insights from invasive Ponto-Caspian mysids
Authors: Borza Péter , Rani Varsha , Vad Csaba F 
Published: July 2023

Abstract
The degree of dietary specialization has a fundamental impact on the ecological function and interactions of suspension feeders. While niche differentiation by food particle size is common among obligate suspension feeders, its role is not evident in facultative ones. In this study, we aimed at providing new insights on the matter by focusing on sympatric mysid species. As mysids use different mechanisms for raptorial and filter-feeding, they represent a more adequate model system than for example, the more extensively studied copepods. We made morphological measurements on the 4 coexisting invasive Ponto-Caspian mysid species to determine the areas and mesh sizes of their filters. We also quantified their clearance rates on the microalga Cryptomonas sp. in a laboratory experiment to reveal how morphological differences manifest in their overall filtering capacity. We found relatively small but consistent differences in the primary filter area among the species, indicating that morphological constraints due to the enclosed position of the setae might limit the possibility for differentiation. The primary filter mesh sizes were small in all 4 species (0.69–2.73 μm) with moderate but consistent intraspecific differences, suggesting that the benefit of being able to capture small particles might outweigh the pressure for differentiation. The observed clearance rates were in accordance with the morphological characteristics of the species, highlighting that auxiliary filters (present in one of the species, Limnomysis benedeni) are needed to increase filtering capacity considerably. Our study confirmed that food particle size can contribute to the niche differentiation of facultative filter feeders, but also indicated that they can tolerate a higher overlap than obligate ones. The observed differences were related to the habitat preferences and predatory potentials of the species, suggesting that complementarity among the different niche axes might further facilitate their coexistence.
Vegetarian and vegan diets: benefits and drawbacks
Authors: Wang Tian , Masedunskas Andrius , Willett Walter C , Fontana Luigi 
Published: July 2023

Abstract
Plant-based diets have become increasingly popular thanks to their purported health benefits and more recently for their positive environmental impact. Prospective studies suggest that consuming vegetarian diets is associated with a reduced risk of developing cardiovascular disease (CVD), diabetes, hypertension, dementia, and cancer. Data from randomized clinical trials have confirmed a protective effect of vegetarian diets for the prevention of diabetes and reductions in weight, blood pressure, glycosylated haemoglobin and low-density lipoprotein cholesterol, but to date, no data are available for cardiovascular event rates and cognitive impairment, and there are very limited data for cancer. Moreover, not all plant-based foods are equally healthy. Unhealthy vegetarian diets poor in specific nutrients (vitamin B12, iron, zinc, and calcium) and/or rich in highly processed and refined foods increase morbidity and mortality. Further mechanistic studies are desirable to understand whether the advantages of healthy, minimally processed vegetarian diets represent an all-or-nothing phenomenon and whether consuming primarily plant-based diets containing small quantities of animal products (e.g. pesco-vegetarian or Mediterranean diets) has beneficial, detrimental, or neutral effects on cardiometabolic health outcomes. Further, mechanistic studies are warranted to enhance our understanding about healthy plant-based food patterns and the biological mechanisms linking dietary factors, CVD, and other metabolic diseases.
First molecular detection of Entamoeba gingivalis subtypes in individuals from Turkey
Authors: Örsten Serra , Şahin Cem , Yılmaz Engin , Akyön Yakut 
Published: July 2023

Abstract
Entamoeba gingivalis is a parasitic protozoan that colonizes the human oral cavity and there are two subtypes (ST1 and ST2) that have been identified to date. However, there are no reports on the molecular detection or characterization of E. gingivalis in Turkey. The objective of this study was to detect the presence of E. gingivalis in Turkish healthy individuals and those with periodontal disease and to subtype the isolates using molecular techniques. Samples from the oral cavity of 94 individuals were taken and the presence of E. gingivalis was determined by PCR using primers for SsrRNA and the amplicons were then confirmed by DNA sequencing. Each participant completed a questionnaire that included demographic data, habits and lifestyle, as well as health status. The presence of E. gingivalis was detected in a total of 19 samples (11 patients and eight healthy individuals). Molecular characterization determined that 12 samples belonged to ST1 and seven samples belonged to ST2. The presence of E. gingivalis was higher in patients with periodontal disease than in healthy individuals, and this association was statistically significant (P &lt; .05). This study constitutes the first report of molecular detection and subtyping of E. gingivalis in Turkey.
Safety and Monitoring of Inflammatory Bowel Disease Advanced Therapies
Authors: Bhat Shubha , Click Benjamin , Regueiro Miguel 
Published: July 2023

Abstract
The recent approval of new medications with novel mechanisms of action and emergence of updated safety information for existing therapies has changed the treatment landscape of inflammatory bowel disease (IBD). These advances led to unique adverse effect profiles and identification of new safety signals, resulting in the evolution of the safety, monitoring, and positioning of IBD therapies. In this updated review, we (1) examine the existing and updated safety data of monoclonal antibodies and small molecules for IBD, with a focus on recently Food and Drug Administration (FDA)-approved therapies, and (2) propose risk stratification and assessment considerations prior to and during IBD treatment.
Algebraic Automatic Continued Fractions in Characteristic 2
Authors: Hu Yining 
Published: July 2023

Abstract
We present two families of automatic sequences that define algebraic continued fractions in characteristic $2$. The period-doubling sequence belongs to the first family $\mathcal {P}$, and its sum modulo $2$, the Thue–Morse sequence, belongs to the second family $\mathcal {G}$. The family $\mathcal {G}$ contains all the iterated sums of sequences from the $\mathcal {P}$ and more.