bluuebunny/crossref_metadata_2025 huggingface dataset:
The biological responses and mechanisms of endothelial cells to magnesium alloy
Authors: Hou Zhe , Xiang Maolong , Chen Nuoya , Cai Xiao , Zhang Bo , Luo Rifang , Yang Li , Ma Xiaoyi , Zhou Lifeng , He Fugui , Yu Hongchi , Wang Yunbing
Published: May 2021

Due to its good biocompatibility and degradability, magnesium alloy (Mg alloy) has shown great promise in cardiovascular stent applications. Rapid stent re-endothelialization is derived from migrated and adhered endothelial cells (ECs), which is an effective way to reduce late thrombosis and inhibit hyperplasia. However, fundamental questions regarding Mg alloy affecting migration and adhesion of ECs are not fully understood. Here, we evaluated the effects of Mg alloy on the ECs proliferation, adhesion and migration. A global gene expression profiling of ECs co-culturing with Mg alloy was conducted, and the adhesion- and migration-related genes were examined. We found that Mg alloy had no adverse effects on ECs viability but significantly affected ECs migration and adhesion. Co-cultured with Mg alloy extract, ECs showed contractive adhesion morphology and decreased motility, which was supported by the down-regulation of adhesion-related genes (Paxillin and Vinculin) and migration-related genes (RAC 1, Rho A and CDC 42). Accordingly, the re-endothelialization of Mg alloy stent was inhibited in vivo. Our results may provide new inspiration for improving the broad application of Mg alloy stents.
Journal citation reports and the definition of a predatory journal: The case of the Multidisciplinary Digital Publishing Institute (MDPI)
Authors: Oviedo-García M Ángeles
Published: May 2021

The extent to which predatory journals can harm scientific practice increases as the numbers of such journals expand, in so far as they undermine scientific integrity, quality, and credibility, especially if those journals leak into prestigious databases. Clarivate's Journal Citation Reports (JCR), a reference for the assessment of researchers and for grant-making decisions, is used as a standard whitelist, in so far as the selectivity of a JCR-indexed journal adds a legitimacy of sorts to the articles that the journal publishes. The Multidisciplinary Digital Publishing Institute (MDPI) had 53 journals ranked in the 2018 JCRs annual report. These journals are analysed, not only to contrast the formal criteria for the identification of predatory journals, but taking a step further, their background is also analysed with regard to self-citations and the source of those self-citations in 2018 and 2019. The results showed that the self-citation rates increased and was very much higher than those of the leading journals in the JCR category. Besides, an increasingly high rate of citations from other MDPI-journals was observed. The formal criteria together with the analysis of the citation patterns of the 53 journals under analysis all suggest they may be predatory journals. Hence, specific recommendations are given to researchers, educational institutions and prestigious databases advising them to review their working relations with those sorts of journals.
Society of Behavioral Medicine (SBM) Position Statement: increase access to mental health services due to COVID-19-related parent and family stress
Authors: Bean Melanie K , Adams Elizabeth L , Buscemi Joanna , Ford Sabrina , Wischenka Danielle , Behrman Pam , Wilson Dawn K , Gladstone Tracy R G , Fitzgibbon Marian L
Published: May 2021

COVID-19 has caused drastic increases in family stress contributing to deleterious social and emotional ramifications. Before COVID-19, millions of Americans lacked access to mental health resources, and now in the midst of a global pandemic, resources are more limited in times of greater need. In March 2020, the Coronavirus Aid, Relief, and Economic Security (CARES) Act provided funding for mental health reforms; yet many barriers remained to receiving sufficient care. In February 2021, the Society of Behavioral Medicine recommended federal legislators expand Community Behavioral Healthcare Centers, increase funding for Federally Qualified Healthcare Centers and School Based Health Centers, incentivize providers to accept Medicaid, and institute more statewide licensing flexibilities to expand the reach of mental health care. In March 2021, the American Rescue Plan was signed into law and provided an additional ~$4 billion in funding for community mental health services, implementing substance abuse prevention and treatment programs, increasing the behavioral health workforce, promoting behavioral telehealth within primary care, increasing school-based mental health services, implementing suicide prevention programs, and improving services for traumatized families. This significant investment in parents and children’s mental health is a tremendous step in the right direction and provides reassurance that relief is underway. Ongoing surveillance of the programmatic and clinical outcomes that result from these new policy reforms will be important for identifying areas that may need continual support as our nation recovers from COVID-19.
Return to Work After Coronavirus Disease 2019 Acute Respiratory Distress Syndrome and Intensive Care Admission: Prospective, Case Series at 6 Months From Hospital Discharge*
Authors: Carenzo Luca , Dalla Corte Francesca , Haines Ryan W. , Palandri Chiara , Milani Angelo , Aghemo Alessio , Pini Daniela , Protti Alessandro , Cecconi Maurizio
Published: May 2021

OBJECTIVES:

Joblessness is common in survivors from critical care. Our aim was to describe rates of return to work versus unemployment following coronavirus disease 2019 acute respiratory distress syndrome requiring intensive care admission.

DESIGN:

Single-center, prospective case series.

SETTING:

Critical Care Follow-Up Clinic, Humanitas Clinical and Research Center—IRCCS, Rozzano, Italy.

PATIENTS:

One hundred and one consecutive laboratory-confirmed coronavirus disease 2019 patients were discharged from our hospital following an ICU stay between March 1, 2020, and June 30, 2020. Twenty-five died in the ICU. Seventy-six were discharged alive from hospital. Two patients refused participation, while three were unreachable. The remaining 71 were alive at 6 months and interviewed.

INTERVENTIONS:

Baseline and outcome healthcare data were extracted from the electronic patient records. Employment data were collected using a previously published structured interview instrument that included current and previous employment status, hours worked per week, and timing of return to work. Health-related quality of life status was assessed using the Italian EQ-5D-5L questionnaire.

MEASUREMENTS AND MAIN RESULTS:

Of the 71 interviewed patients, 45 (63%) were employed prior to coronavirus disease 2019, of which 40 (89%) of them worked full-time. Thirty-three (73%) of the previously employed survivors had returned to work by 6 months, 10 (22%) were unemployed, and 2 (5%) were newly retired. Among those who returned to work, 20 (85%) of them reported reduced effectiveness at work. Those who did not return to work were either still on sick leave or lost their job as a consequence of coronavirus disease 2019. Reported quality of life of survivors not returning to work was worse than of those returning to work.

CONCLUSIONS:

The majority of coronavirus disease 2019 survivors following ICU in our cohort had returned to work by 6 months of follow-up. However, most of them reported reduced work effectiveness. Prolonged sick leave and unemployment were common findings in those not returning.
The Impact of Stress Within and Across Generations: Neuroscientific and Epigenetic Considerations
Authors: Miller Christopher W. T.
Published: May 2021

The impact of stress and trauma on biological systems in humans can be substantial. They can result in epigenetic changes, accelerated brain development and sexual maturation, and predisposition to psychopathology. Such modifications may be accompanied by behavioral, emotional, and cognitive overtones during one’s lifetime. Exposure during sensitive periods of neural development may lead to long-lasting effects that may not be affected by subsequent environmental interventions. The cumulative effects of life stressors in an individual may affect offspring’s methylome makeup and epigenetic clocks, neurohormonal modulation and stress reactivity, and physiological and reproductive development. While offspring may suffer deleterious effects from parental stress and their own early-life adversity, these factors may also confer traits that prove beneficial and enhance fitness to their own environment. This article synthesizes the data on how stress shapes biological and behavioral dimensions, drawing from preclinical and human models. Advances in this field of knowledge should potentially allow for an improved understanding of how interventions may be increasingly tailored according to individual biomarkers and developmental history.
Rates of Diplopia in Ahmed FP7, Baerveldt 250, and 350 Glaucoma Patients Compared With Medical Controls
Authors: Kilgore Khin P. , Wang Feng , Stern Nicole C. , Sabbagh Nouran , Jamali Sepideh , White Launia J. , Sit Arthur J. , Bitrian Elena , Roddy Gavin W. , Mohney Brian G. , Khanna Cheryl L.
Published: May 2021

Precis:

Diplopia was present in ~20% of patients with Ahmed FP7 (FP7) or Baerveldt 350 (B350), compared with 5% to 6% in those with Baerveldt 250 (B250) or controls, suggesting risk of diplopia should be included in preoperative counseling.

Purpose:

The purpose of this study was to examine the prevalence of diplopia and strabismus in patients with B250, B350, or FP7 glaucoma drainage devices (GDD).

Materials and Methods:

In this cohort study, glaucoma patients 18 years and above who had received, or would be receiving, a B250, B350, or FP7 GDD, and medically treated controls were consecutively enrolled from August 8, 2017, through July 31, 2019. The Diplopia Questionnaire was administered ≥30 days postoperatively, and upon enrollment to the controls. All diplopic patients underwent orthoptic measurements, which were reviewed by a strabismus specialist. Patients with GDDs in quadrants other than superotemporal, multiple GDDs, or scleral buckles were excluded. Bonferroni correction was applied for pairwise comparisons.

Results:

Diplopia was reported in 23/129 (17.8%) GDD patients and 5/99 (5.1%) control patients (P=0.003): 8/35 (22.9%) FP7, 2/32 (6.3%) B250, and 13/62 (21.0%) B350, with significant differences between FP7 versus controls (P=0.014) and B350 versus controls (P=0.011). Diplopia was attributable to GDD in 2 FP7 (5.9%, 95% confidence interval: 0.7-19.2), 0 B250, and 4 B350 (6.5%, 95% confidence interval: 1.7-15.2) patients, without significant differences between the GDDs.

Conclusions:

Patients with the larger (B350) or the higher profile plate (FP7) GDDs were more likely to experience diplopia than controls, and diplopia was attributable to the GDD in ~6% of patients with either a FP7 or a B350 GDD. Since diplopia can affect patients’ quality of life, preoperative counseling for GDD surgery, particularly B350 and FP7, should include a discussion of the risk of diplopia.
Assessing the Reliability of Intraocular Pressure Measurements Using Rebound Tonometry
Authors: Realini Tony , McMillan Brian , Gross Ronald L. , Devience Eva , Balasubramani Goundappa K.
Published: May 2021

Precis:

In a trio of prospective studies, the iCare rebound tonometer demonstrated significantly lower test-retest variability than Goldmann tonometry with good interoperator and interdevice reproducibility, supporting its value in monitoring intraocular pressure (IOP) changes over time.

Purpose:

The purpose of this study was to characterize intraoperator and interoperator and interdevice reliability of IOP measurements with rebound tonometry (RT, ic100).

Methods:

Three prospective cross-sectional studies were conducted in distinct sample of adult patients with established glaucoma, suspected glaucoma, or no glaucoma at the West Virginia University Eye Institute. Participants in study 1 underwent 5 RT measurements in one randomly selected eye and 5 Goldmann tonometry measurements in the fellow eye by 1 operator; intraoperator variability was compared using the F test. In study 2, 3 operators each obtained 3 RT measurements in participants in randomized operator order. In study 3, a single operator collected 3 measurements each with 3 RTs in randomized device order. Between-operator and between-device reproducibility were characterized using intraclass correlation coefficients (ICCs).

Results:

Overall, 28, 19, and 25 subjects participated in the 3 respective studies. Within-subject variance across subjects was 0.757 in RT measurements and 2.471 in Goldmann measurements (P=0.0035). Interoperator reproducibility of RT measurements was good in both eyes [ICC for right eyes 0.78, 95% confidence interval (CI): 0.60-0.85; ICC for left eyes 0.75, 95% CI: 0.50-0.83]. Interdevice reproducibility of RT measurements was good approaching excellent (ICC for right eyes 0.87, 95% CI: 0.83-0.90; ICC for left eyes 0.89, 95% CI: 0.86-0.91).

Conclusions:

The RT’s lower measurement variability and good interoperator and interdevice reproducibility suggest that it can characterize IOP changes over time more robustly than Goldmann tonometry, aiding clinicians in assessing the effectiveness of glaucoma therapy and the consistency of IOP control.
Idiopathic intracranial hypertension with initial presentation of optic disc edema
Authors: Zhao Qing , Du Xueli , Yang Ye , Zhou Yali , Zhao Xinxin , Zhang Meng
Published: May 2021

Introduction:

Idiopathic intracranial hypertension (IIH) is a disorder of elevated intracranial pressure in young women of childbearing age. The typical symptom is headache, and the symptom of visual obscuration tends to be overlooked. So, the patients usually visit the department of neurology for headache management. Here, we report a patient with IIH who first presented with ophthalmic symptoms.

Patient concerns:

A 28-year-old overweight female complained of intermittent darkened vision in both eyes lasting for 2 months. She was diagnosed with papilledema at another hospital and received local and systemic application administration of neurotrophic drugs and glucocorticoids 1 month before. Because of the poor outcomes, she visited our ophthalmology clinic for further management. She had no other medical history.

Diagnosis:

On ophthalmic examination, bilateral optic disc edema with blurred boundary was observed. The cranial magnetic resonance imaging and blood examination showed no obvious abnormality. A lumbar puncture was performed by a neurologist, which demonstrated an opening pressure of 30 cm of water. The cerebrospinal fluid biochemistry and bacteriology results were normal. A diagnosis of IIH was made based on the above findings.

Outcomes:

Oral acetazolamide, weight loss therapy and local corticosteroid treatment were initiated. At 7-week follow-up, the darkened vision and optic disc edema was obviously alleviated.

Conclusion:

IIH is a neurologic disease, but patients with this disease may first present to ophthalmology department because of the visual symptoms, such as blurred or darkened vision, visual loss, and even diplopia. As ophthalmologists, we should screen for this disease in a timely manner when we encounter similar patients with bilateral optic edema.
Study of the impact of cultivation conditions and peg surface modification on the in vitro biofilm formation of Staphylococcus aureus and Staphylococcus epidermidis in a system analogous to the Calgary biofilm device
Authors: Diepoltová Adéla , Konečná Klára , Janďourek Ondřej , Nachtigal Petr
Published: May 2021

Introduction.

Staphylococcus aureus

(SA) and

Staphylococcus epidermidis

(SE) are the most common pathogens from the genus

Staphylococcus

causing biofilm-associated infections. Generally, biofilm-associated infections represent a clinical challenge. Bacteria in biofilms are difficult to eradicate due to their resistance and serve as a reservoir for recurring persistent infections.

Gap Statement. A variety of protocols for in vitro drug activity testing against staphylococcal biofilms have been introduced. However, there are often fundamental differences. All these differences in methodical approaches can then be reflected in the form of discrepancies between results.

Aim. In this study, we aimed to develop optimal conditions for staphylococcal biofilm formation on pegs. The impact of peg surface modification was also studied.

Methodology. The impact of tryptic soy broth alone or supplemented with foetal bovine serum (FBS) or human plasma (HP), together with the impact of the inoculum density of bacterial suspensions and the shaking versus the static mode of cultivation, on total biofilm biomass production in SA and SE reference strains was studied. The surface of pegs was modified with FBS, HP, or poly-l-lysine (PLL). The impact on total biofilm biomass was evaluated using the crystal violet staining method and statistical data analysis.

Results. Tryptic soy broth supplemented with HP together with the shaking mode led to crucial potentiation of biofilm formation on pegs in SA strains. The SE strain did not produce biofilm biomass under the same conditions on pegs. Preconditioning of peg surfaces with FBS and HP led to a statistically significant increase in biofilm biomass formation in the SE strain.

Conclusion. Optimal cultivation conditions for robust staphylococcal biofilm formation in vitro might differ among different bacterial strains and methodical approaches. The shaking mode and supplementation of cultivation medium with HP was beneficial for biofilm formation on pegs for SA (ATCC 29213) and methicillin-resistant SA (ATCC 43300). Peg conditioning with HP and PLL had no impact on biofilm formation in either of these strains. Peg coating with FBS showed an adverse effect on the biofilm formation of these strains. By contrast, there was a statistically significant increase in biofilm biomass production on pegs coated with FBS and HP for SE (ATCC 35983).
Mortality audit of cancer patients with SARS-CoV-2 positivity or COVID-19
Authors: Kakati Kaberi , Rahman Tashnin , Barman Debabrata , Bhattacharyya Mouchumee , Borthakur Bibhuti Bhusan , Barman Rashmisnata , Kalita Apurba , Kataki Amal Chandra , Krishnatreya Manigreeva
Published: May 2021

Coronavirus disease-2019 (COVID-19) has disrupted cancer care services globally. The present review of cause of deaths was conducted in a tertiary care cancer center in the North East India. In our institute, all cancer patients requiring admission for surgery, chemotherapy, and other daycare procedures require testing for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). From 09 July 2020 to 16 May 2021, 119 cancer patients with SARS-CoV-2 positive report or COVID-19 have been admitted at our institute Covid ward. A total of 19 cancer patients with COVID-19 succumbed. Of 19 deaths, 13 (68.4%) patients were men and 6 (31.6%) patients were women. The age range from 27 years to 74 years (median =55 years). Vomiting alone or with diarrhea was the most common symptom requiring admission after testing (4/19, 21.0%), followed by bleeding from primary tumour site (3/19, 15.7%). The antecedent and underlying cause of deaths in 19 (100%) patients was cancer. SARS-CoV-2 infection should not be a hindrance for cancer treatment and management.
Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens
Authors: Stromberg Zachary R. , Theiler James , Foley Brian T. , y Gutiérrez Adán Myers , Hollander Attelia , Courtney Samantha J. , Gans Jason , Deshpande Alina , Martinez-Finley Ebany J. , Mitchell Jason , Mukundan Harshini , Yusim Karina , Kubicek-Sutherland Jessica Z.
Published: May 2021

Viral pathogen can rapidly evolve, adapt to novel hosts and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a novel computational approach called FEVER (Fast Evaluation of Viral Emerging Risks) to design assays that simultaneously accomplish: 1) broad-coverage biosurveillance of an entire class of viruses, 2) accurate diagnosis of an outbreak strain, and 3) mutation typing to detect variants of public health importance. We demonstrate the application of FEVER to generate assays to simultaneously 1) detect sarbecoviruses for biosurveillance; 2) diagnose infections specifically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and 3) perform rapid mutation typing of the D614G SARS-CoV-2 spike variant associated with increased pathogen transmissibility. These FEVER assays had a high in silico recall (predicted positive) up to 99.7% of 525,708 SARS-CoV-2 sequences analyzed and displayed sensitivities and specificities as high as 92.4% and 100% respectively when validated in 100 clinical samples. The D614G SARS-CoV-2 spike mutation PCR test was able to identify the single nucleotide identity at position 23,403 in the viral genome of 96.6% SARS-CoV-2 positive samples without the need for sequencing. This study demonstrates the utility of FEVER to design assays for biosurveillance, diagnostics, and mutation typing to rapidly detect, track, and mitigate future outbreaks and pandemics caused by emerging viruses.
Regulation of CHK1 inhibitor resistance by a c-Rel and USP1 dependent pathway
Authors: Hunter Jill E. , Campbell Amy E. , Hannaway Nicola L. , Kerridge Scott , Luli Saimir , Butterworth Jacqueline A. , Sellier Helene , Mukherjee Reshmi , Thomas Huw D. , Brownridge Philip J. , Coxhead Johnathon , Taylor Leigh , Leary Peter , Hasoon Megan S.R. , Collins Ian , Garrett Michelle D. , Eyers Claire E. , Perkins Neil D.
Published: May 2021

We previously discovered that deletion of c-Rel in the Eμ-Myc mouse model of lymphoma results in earlier onset of disease, a finding that contrasted with the expected function of this NF-κB subunit in B-cell malignancies. Here we report that c-rel -/- Eµ-Myc cells have an unexpected and major defect in the CHK1 pathway, with almost undetectable levels of CHK1 and CLSPN protein leading to therapeutic resistance to the highly specific CHK1 inhibitor (CHK1i) CCT244747. Similar downregulation of CHK1 levels was also seen in CCT244747 resistant U20S osteosarcoma cells. Further investigation revealed that downregulation of the deubiquitinase USP1 is responsible, at least in part, for these effects. Importantly, we demonstrate that c-rel -/- Eµ-Myc lymphoma cells survive though upregulation of compensatory PI3K/AKT pathway activity. Moreover, targeting this pathway with Pictilisib (GDC-0941) effectively killed c-rel -/- Eµ-Myc in vivo, while having no effect on wild type Eμ-Myc cells. This data reveals an NF-κB regulated pathway controlling CHK1 activity in cancer cells and identifies a potential mechanism for both acquiring and overcoming CHK1i resistance in cancer patients.
How effective are frogs in regulating crop pest population in a natural multi-trophic system??
Authors: Ghosh Deyatima , Chatterjee Sabyasachi , Basu Parthiba
Published: May 2021

Potential of frogs as important natural pest control agents has been highlighted earlier. But the effectiveness of frogs in regulating the pest load in intensive agricultural landscape in a multi-trophic system is not clear. We performed controlled field experiment in paddy field with a varying density (observed in high and low agricultural intensity (AI) areas) of a commonly found frog species and compared the pest and pest predator build-up. The consumption rate of the model amphibian was studied using enclosure experiment. The consequent trophic cascade effect of frogs on both crop pest and other arthropod pest predator was analyzed using mathematical population growth models. Although frogs consumed pests, they could not reduce crop pest abundance. although a lesser frog density found in high AI areas significantly affected the pest predator abundance. Based on the functional response result, mathematical growth models demonstrated that with a constant harvesting factor (Holling’s Type II) frogs will always have a negative impact on the beneficial natural enemy population due to intraguild predation thereby limiting its potential as a pest regulator. Our study challenges the notion of frogs as an effective pest control agent and argues that increasing habitat diversity might improve overall biological pest suppression.
Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions
Authors: Wang Jing , Li Jianguang , Li Zaiyuan , Liu Bo , Zhang Lili , Guo Dongliang , Huang Shilian , Qian Wanqiang , Guo Li
Published: May 2021

Longan (Dimocarpus longan) is a subtropical fruit best known for its nutritious fruit and regarded as a precious tonic and traditional medicine since ancient times. High-quality chromosome-scale genome assembly is valuable for functional genomic study and genetic improvement of longan. Here, we report a chromosome-level reference genome sequence for longan cultivar JDB with an assembled genome of 455.5 Mb in size anchored to fifteen chromosomes, representing a significant improvement of contiguity (contig N50=12.1 Mb, scaffold N50= 29.5 Mb) over a previous draft assembly. A total of 40,420 protein-coding genes were predicted in D. longan genome. Synteny analysis suggests longan shares the widespread gamma event with core eudicots, but has no other whole genome duplications. Comparative genomics showed that D. longan genome experienced significant expansions of gene families related to phenylpropanoid biosynthesis and UDP-glucosyltransferase. Deep genome sequencing analysis of longan cultivars identified longan biogeography as a major contributing factor for genetic diversity, and revealed a clear population admixture and introgression among cultivars of different geographic origins, postulating a likely migration trajectory of longan overall confirmed by existing historical records. Finally, genome-wide association studies (GWAS) of longan cultivars identified quantitative trait loci (QTL) for six different fruit quality traits and revealed a shared QTL containing three genes for total soluble solid and seed weight. The chromosome-level reference genome assembly, annotation and population genetic resource for D. longan will facilitate the molecular studies and breeding of desirable longan cultivars in the future.
The stiffness-sensitive transcriptome of human tendon stromal cells
Authors: Hussien Amro A. , Niederöst Barbara , Bollhalder Maja , Goedecke Nils , Snedeker Jess G.
Published: May 2021

Matrix stiffness and its effects on tensional homeostasis act as major regulators of cellular states in health and disease. Stiffness-sensing studies are typically performed using cells that have acquired “mechanical memory” through prolonged propagation in rigid mechanical environments, e.g. tissue culture plastic (TCP). This may potentially mask the full extent of the stiffness-driven mechanosensing programs. To address this, we developed a biomaterial system composed of two-dimensional mechano-variant silicone substrates that is permissive to large-scale cell culture expansion processes. We broadly mapped the stiffness-mediated mechano-responses by performing RNA sequencing on human tendon-derived stromal cells. We find that matrix rigidities approximating tendon microscale stiffness range (E.~35 kPa) distinctly favor programs related to chromatin remodeling and Hippo signaling; whereas more compliant stiffnesses (E.2 kPa) were enriched in responses related to pluripotency, synapse assembly and angiogenesis. We also find that tendon stromal cells undergo dramatic phenotypic drift on conventional TCP, with near-complete suppression of tendon-related genes and emergence of expression signatures skewed towards fibro-inflammatory and metabolic activation. Strikingly, mechano-variant substrates abrogate fibroblasts activation, with tenogenic stiffnesses inducing a transcriptional program that strongly correlate with established tendon tissue-specific signatures. Computational inference predicted that AKT1 and ERK1/2 are major signaling hubs mediating stiffness-sensing in tendon cells. Together, our findings highlight how the underlying biophysical cues may dictate the transcriptional identity of resident cells, and how matrix mechano-reciprocity regulates diverse sets of previously underappreciated mechanosensitive processes in tendon stromal fibroblasts.
A machine learning approach for MRI-based classification of individuals with mild cognitive impairment
Authors: Tibon Roni
Published: May 2021

Diagnosis criteria for Mild Cognitive Impairment (MCI) rely on cognitive symptoms and do not require specific biomarker evidence of pathology. Nevertheless, patients may still have subtle brain changes that are identifiable with neuroimaging. To classify MCI patients vs. healthy age-matched controls, two algorithms—Multilayer Perceptron (MLP) and Support Vector Machine (SVM)—were applied to structural MRI data from the OASIS-1 cohort (https://www.oasis-brains.org/). Despite their comparable performance in some measures, the MLP algorithm was preferable due to superior recall of MCI cases.
Elevated colonic microbiota-associated paucimannosidic and truncated N-glycans in pediatric ulcerative colitis
Authors: Li Henghui , Zhang Xu , Chen Rui , Cheng Kai , Ning Zhibin , Li Jianjun , Twine Susan , Stintzi Alain , Mack David , Figeys Daniel
Published: May 2021

Pediatric ulcerative colitis (UC) is a distinct type of inflammatory bowel disease with severe disease activity and rapid progression, which can lead to detrimental life-long consequences. The pathogenesis of pediatric UC remains unclear, although dysbiosis of the gut microbiota has been considered an important factor. In this study, we used mass spectrometry-based glycomic approaches to examine the N-glycans that were associated with the intestinal mucosal-luminal interface microbiota cells of treatment-naïve pediatric UC or control patients. We observed abundant paucimannosidic and other truncated N-glycans that were associated with the microbiota and found that the pediatric UC microbiota samples contained significantly higher levels of these atypical N-glycans compared to those of controls. This study indicates that intestinal N-glycans may be used as novel UC biomarker candidates and the aberrant metabolism of glycans by gut microbiota may be involved in the pathogenesis of UC in children.
Robust Segmentation of Cellular Ultrastructure on Sparsely Labeled 3D Electron Microscopy Images using Deep Learning
Authors: Machireddy Archana , Thibault Guillaume , Loftis Kevin G. , Stoltz Kevin , Bueno Cecilia E. , Smith Hannah R. , Riesterer Jessica L. , Gray Joe W. , Song Xubo
Published: May 2021

A deeper understanding of the cellular and subcellular organization of tumor cells and their interactions with the tumor microenvironment will shed light on how cancer evolves and guide effective therapy choices. Electron microscopy (EM) images can provide detailed view of the cellular ultrastructure and are being generated at an ever-increasing rate. However, the bottleneck in their analysis is the delineation of the cellular structures to enable interpretable rendering. We have mitigated this limitation by using deep learning, specifically, the ResUNet architecture, to segment cells and subcellular ultrastructure. Our initial prototype focuses on segmenting nuclei and nucleoli in 3D FIB-SEM images of tumor biopsies obtained from patients with metastatic breast and pancreatic cancers. Trained with sparse manual labels, our method results in accurate segmentation of nuclei and nucleoli with best Dice score of 0.99 and 0.98 respectively. This method can be extended to other cellular structures, enabling deeper analysis of inter- and intracellular state and interactions.
Investigation of precision, accuracy and confidence of X-ray diffraction for determining crystallite size in nanopowders
Authors: Moore Alexander P. , Nemer Martin B. , Rodriguez Mark A. , Roberts Christine C. , Fleig Patrick F. , Papenguth Hans W.
Published: May 2021

X-ray diffraction (XRD) is often utilized as a method of determining bulk sample crystallite size in powder characterization. While it is generally accepted that XRD peak broadening allows for qualitative crystallite size comparisons, its use for quantitative information is still debated. This study investigates the quantitative capability of XRD for determining the crystallite sizes of magnesium oxide nanocrystals by examining the precision, accuracy and uncertainty using the whole pattern (WP) weighted least-squares and Williamson–Hall (WH) methods. The precision of the methods was investigated by re-preparing, re-running and re-analysing identical samples. Both methods were found to be precise within 2 nm. The accuracy of the methods was investigated by comparing them against independent crystallite size analyses using visual particle identification from scanning electron microscopy micrographs and from indirect calculations using Brunauer–Emmett–Teller (BET) adsorption-determined surface areas. The WP method was found to be more accurate than the WH method, which consistently underpredicted the crystallite size. Finally, the confidence of the methods was investigated using a Bayesian inference statistical inversion method. The WP method was found to have a narrower confidence distribution in its crystallite size determination than the WH method. The broad WH confidence indicates that reliable quantitative single-measurement crystallite size determinations are not feasible using the WH technique. However, the WP method demonstrated precision, accuracy and confidence, allowing quantitative crystallite size determinations to be made.
Photon-counting MCP/Timepix detectors for soft X-ray imaging and spectroscopic applications
Authors: Tremsin Anton S. , Vallerga John V. , Siegmund Oswald H. W. , Woods Justin , De Long Lance E. , Hastings Jeffrey T. , Koch Roland J. , Morley Sophie A. , Chuang Yi-De , Roy Sujoy
Published: May 2021

Detectors with microchannel plates (MCPs) provide unique capabilities to detect single photons with high spatial (<10 µm) and timing (<25 ps) resolution. Although this detection technology was originally developed for applications with low event rates, recent progress in readout electronics has enabled their operation at substantially higher rates by simultaneous detection of multiple particles. In this study, the potential use of MCP detectors with Timepix readout for soft X-ray imaging and spectroscopic applications where the position and time of each photon needs to be recorded is investigated. The proof-of-principle experiments conducted at the Advanced Light Source demonstrate the capabilities of MCP/Timepix detectors to operate at relatively high input counting rates, paving the way for the application of these detectors in resonance inelastic X-ray scattering and X-ray photon correlation spectroscopy (XPCS) applications. Local count rate saturation was investigated for the MCP/Timepix detector, which requires optimization of acquisition parameters for a specific scattering pattern. A single photon cluster analysis algorithm was developed to eliminate the charge spreading effects in the detector and increase the spatial resolution to subpixel values. Results of these experiments will guide the ongoing development of future MCP devices optimized for soft X-ray photon-counting applications, which should enable XPCS dynamics measurements down to sub-microsecond timescales.
XANES reflects coordination change and underlying surface disorder of zinc adsorbed to silica
Authors: Nelson Joey
Published: May 2021

Zinc K-edge X-ray absorption near-edge structure (XANES) spectroscopy of Zn adsorbed to silica and Zn-bearing minerals, salts and solutions was conducted to explore how XANES spectra reflect coordination environment and disorder in the surface to which a metal ion is sorbed. Specifically, XANES spectra for five distinct Zn adsorption complexes (Znads) on quartz and amorphous silica [SiO2(am)] are presented from the Zn–water–silica surface system: outer-sphere octahedral Znads on quartz, inner-sphere octahedral Znads on quartz, inner-sphere tetrahedral Znads on quartz, inner-sphere octahedral Znads on SiO2(am) and inner-sphere tetrahedral Znads on SiO2(am). XANES spectral analysis of these complexes on quartz versus SiO2(am) reveals that normalized peak absorbance and K-edge energy position generally decrease with increasing surface disorder and decreasing Zn–O coordination. On quartz, the absorption-edge energy of Znads ranges from 9663.0 to 9664.1 eV for samples dominated by tetrahedrally versus octahedrally coordinated species, respectively. On SiO2(am), the absorption-edge energy of Znads ranges from 9662.3 to 9663.4 eV for samples dominated by tetrahedrally versus octahedrally coordinated species, respectively. On both silica substrates, octahedral Znads presents a single K-edge peak feature, whereas tetrahedral Znads presents two absorbance features. The energy space between the two absorbance peak features of the XANES K-edge of tetrahedral Znads is 2.4 eV for Zn on quartz and 3.2 eV for Zn on SiO2(am). Linear combination fitting of samples with a mixture of Znads complex types demonstrates that the XANES spectra of octahedral and tetrahedral Znads on silica are distinct enough for quantitative identification. These results suggest caution when deciphering Zn speciation in natural samples via linear combination approaches using a single Znads standard to represent sorption on a particular mineral surface. Correlation between XANES spectral features and prior extended X-ray absorption fine structure (EXAFS) derived coordination environments for these Znads on silica samples provides insight into Zn speciation in natural systems with XANES compatible Zn concentrations too low for EXAFS analysis.
Tetrakis[μ2-1,1,1,3,3,3-hexafluoro-2-(trifluoromethyl)propan-2-olato]tetrakis(μ3-2-methylpropan-2-olato)octacopper(I)
Authors: Purdy Andrew P. , Butcher Ray J.
Published: May 2021

The title compound, [Cu8(C4H9O)4(C4F9O)4], crystallizes in the monoclinic space group, P21/n and contains a self-assembly of two C16H18Cu4F18O4 units linked by bridging tert-butyl groups [Cu—O bonds of length 2.3779 (15) and 2.4248 (15) Å], generating a centrosymmetric dimer. The asymmetrical unit, C16H18Cu4F18O4, contains an almost square-planar arrangement of the four Cu atoms linked by bridging tert-butyl and perfluorinated tert-butyl groups with Cu—Cu distances ranging from 2.7108 (4) to 2.7612 (4) Å and Cu —Cu—Cu angle values close to 90° [ranging from 89.459 (10)° to 90.025 (11)°]. These dimers are further linked by weak C—H...F and F...F interactions. As is commonly encountered in perfluorinated tert-butyl groups, one of the CF3 groups is disordered and was refined with two equivalent conformations with occupancies of 0.74 (3) and 0.26 (3).
Crystal structure and molecular docking study of (E)-2-{[(E)-2-hydroxy-5-methylbenzylidene]hydrazinylidene}-1,2-diphenylethan-1-one
Authors: Kansiz Sevgi , Tatlidil Digdem , Dege Necmi , Aktas Feyzi Alkim , Al-Asbahy Samir Osman Mohammed , Alaman Agar Aysen
Published: May 2021

The title compound, C22H18N2O2, is a Schiff base that exists in the phenol–imine tautomeric form and adopts anEconfiguration with respect to the C=N bond. The molecular structure is stabilized by an O—H...N hydrogen bond, forming anS(6) ring motif. In the crystal, pairs of C—H...O hydrogen bonds link the molecules to form inversion dimers. Weak π–π stacking interactions along thea-axis direction provide additional stabilization of the crystal structure. The molecule is non-planar, the aromatic ring of the benzaldehyde residue being nearly perpendicular to the phenyl and 4-methylphenol rings with dihedral angles of 88.78 (13) and 82.26 (14)°, respectively. A molecular docking study between the title molecule and the COVID-19 main protease (PDB ID: 6LU7) was performed, showing that it is a potential agent because of its affinity and ability to adhere to the active sites of the protein.
Crystal structure and Hirshfeld surface analysis of 1-[(E)-2-(5-chloro-2-hydroxyphenyl)hydrazin-1-ylidene]naphthalen-2(1H)-one
Authors: Bougueria Hassiba , Chetioui Souheyla , Bensegueni Mohammed Abdellatif , Djukic Jean-Pierre , Benarous Nesrine
Published: May 2021

The title compound, C16H11ClN2O2, was obtained by diazotization of 2-amino-4-chlorophenol followed by a coupling reaction with β-naphthol. There are two molecules (AandB) in the asymmetric unit. The crystal structure features only one type of intermolecular interaction, that is strong hydrogen bonds involving the hydroxyl group. The naphthol and phenol fragments attached to the C=N—N— moiety exhibit ans-transconformation. In addition, those fragments are almost coplanar, subtending a dihedral angle of 13.11 (2)° in moleculeAand 10.35 (2)° in moleculeB. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H...H (32.1%), C...H/H...C (23.1%), Cl...H/H...Cl (15.2%), O...H/H...O (12.8%) and C...C (9%) contacts.
Designing food experiences for well-being: a framework advancing design thinking research from a customer experience perspective
Authors: Batat Wided , Addis Michela
Published: May 2021

Purpose

Literature from across design studies and innovation management, as well as food marketing research evidence, is examined to highlight the interdisciplinary and experiential research approaches to food consumption and well-being. This conceptual paper aims to address the need to expand the food industry’s goals by considering its contributions to the consumer’s overall food well-being. Food experience design (FED) seeks to understand how food professionals can design healthy and pleasurable food experiences aimed at enhancing people’s food well-being. FED does so by proposing a holistic and integrative framework.

Design/methodology/approach

This approach examines design thinking by conducting an analysis of the multidisciplinary literature. This paper addresses the gap in the literature by advancing the theoretical and empirical understanding of food design thinking through the lenses of experiential theory and consumer well-being.

Findings

This review paper clarifies the scope of FED scholarship and offers a call for collective efforts to establish a focused body of knowledge that leads food marketing professionals and scholars to adopt an experiential perspective to food consumption and production focused on experiential pleasure of food as a driving force for consumer’s well-being.

Research limitations/implications

The review paper addresses the need to expand the food industry’s goals by considering its contributions to the consumer’s overall food well-being. FED seeks to understand how food professionals can design healthy and pleasurable food experiences aimed at enhancing people’s food well-being. FED does so by proposing a holistic and integrative framework.

Practical implications

This research provides designers with the operative tools to create innovative food experiences and increase the food well-being of consumers. Toward that end, designers need to extend their skills and evolve their language and competencies to create valuable dialogues with other stakeholders involved. Collaboration requires many other premises. This paper contributes to the discussion by identifying and clarifying them.

Originality/value

This research highlights the imperative to take multidisciplinary, transformative and experiential approaches to researching food innovation strategies from a consumer’s well-being perspective.
Challenges in combatting female genital mutilation: narratives of black Sub-Saharan African (BSSA) women in the English west Midlands region
Authors: Nyashanu Mathew , Mguni Maureen
Published: May 2021

Purpose

It is believed that more than 120 million women have undergone female genital mutilation (FGM) and more than 2 million young girls are at risk of undergoing FGM. FGM is practiced in different parts of the world. With globalisation and the increased movement of people across the globe, FGM is now a global problem. While ending FGM remains a priority, the approaches and strategies being used have generated contested views across the social divide. The purpose of this study is to explore the challenges in combatting FGM as experienced by Black Sub-Saharan African (BSSA) women in Diaspora.

Design/methodology/approach

This qualitative study used a phenomenological approach. Narratives were collected from 40 BSSA women from 20 Sub-Saharan African countries living in the English West Midlands region. A thematic approach underpinned by the four phases of data analysis in the Silences Framework were used to analyse the data.

Findings

The research study found that stigmatisation of survivors, utilisation of graphic images in FGM awareness, exclusion of practising communities’ gatekeepers in FGM interventions, conflation of religion and FGM practice and obsession with securing a conviction were obstacles in combating FGM. Diaspora community-driven studies exploring FGM and contested notions in addressing it from women perspectives are scarce.

Originality/value

This study pulls together the experiences of BSSA women and their perspectives on contested notions in combating FGM in the UK. The debate asserts the growing need to consider gender sensitive radical interventions, which involves educating perpetrators and gatekeepers among FGM practising communities.
Response measures to COVID-19 in prisons and other detention centers
Authors: Alves da Costa Filipa , Neufeld Maria , Hamad Mohamed , Carlin Eric , Ferreira-Borges Carina
Published: May 2021

Purpose

The purpose of this paper is to summarize activities being undertaken by the World Health Organization (WHO) Regional Office for Europe to prevent and control COVID-19 in and beyond prisons, activities specifically designed to increase information sharing and to support Member States, to comment on potential impacts of these initiatives at country-level responses and to underline the need for a rights-based approach to managing the pandemic, including the right to vaccination.

Design/methodology/approach

The Health in Prisons Programme (HIPP) of the WHO Regional Office for Europe worked with partner organizations to review regularly the evidence on best practices in prison health and use it to inform policy recommendations at the global level. HIPP issued overarching guidance and specific tools to support implementation of measures to prevent and control the spread of COVID-19 in prisons and other custodial settings. Moreover, to monitor the emergence of outbreaks, the HIPP developed a minimum data set for countries voluntarily to report COVID-19 cases and identify situations in need of direct support.

Findings

Since May 2020, the WHO has periodically received data from Member States, leading to the development of country-specific bulletins to support countries and, whenever appropriate, to organize virtual missions to further support ministries and public health bodies responsible for managing COVID-19 in prisons.

Originality/value

The development of a specific set of indicators for prisons enables exploring data in a disaggregated manner. Monitoring response measures developed in prison enables judging their appropriateness to minimize the spread of SARS-CoV2 in prisons and alignment with guidance issued by the WHO.