bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performances of NIPT for copy number variations at different sequencing depths using the semiconductor sequencing platform
Authors: Yang Jiexia , Wu Jing , Peng Haishan , Hou Yaping , Guo Fangfang , Wang Dongmei , Ouyang Haoxin , Wang Yixia , Yin Aihua 
Published: July 2021

Abstract
Objective
To evaluate the performance of noninvasive prenatal testing (NIPT) and NIPT-PLUS for the detection of genome-wide microdeletion and microduplication syndromes (MMSs) at different sequencing depths. The NIPT sequencing depth was 0.15X, and the data volume was 3 million reads; the NIPT-PLUS sequencing depth was 0.4X, and the data volume was 8 million reads.

Methods
A cohort of 50,679 pregnancies was recruited. A total of 42,969 patients opted for NIPT, and 7710 patients opted for NIPT-PLUS. All high-risk cases were advised to undergo invasive prenatal diagnosis and were followed up.

Results
A total of 373 cases had a high risk of a copy number variation (CNV) as predicted by NIPT and NIPT-PLUS: NIPT predicted 250 high-risk CNVs and NIPT-PLUS predicted 123. NIPT-PLUS increased the detection rate by 1.02% (0.58% vs 1.60%, p < 0.001). A total of 291 cases accepted noninvasive prenatal diagnosis, with 197 cases of NIPT and 94 cases of NIPT-PLUS. The PPV of CNV > 10 Mb for NIPT-PLUS was significantly higher than that for NIPT (p = 0.02). The total PPV of NIPT-PLUS was 12.56% higher than that of NIPT (43.61% vs 30.96%, p = 0.03).

Conclusion
NIPT-PLUS had a better performance in detecting CNVs in terms of the total detection rate and total PPV. However, great care must be taken in presenting results and providing appropriate counseling to patients when deeper sequencing is performed in clinical practice.
Intestinal microbiota and active systemic lupus erythematosus: a systematic review
Authors: Vieira Juliana Rosa Pires , Rezende Andréa Toledo de Oliveira , Fernandes Marcos Rassi , da Silva Nilzio Antonio 
Published: July 2021

Abstract
Background
Systemic Lupus Erythematosus (SLE) is an autoimmune disease, characterized by being multi-systemic and, therefore, reaching various organs and affecting mainly young women. Its pathogenesis comprehends many factors, including the interaction between microbiota and immune system. This systematic review assessed the relationship between intestinal microbiota and SLE in activity, highlighting microbiota representative patterns regarding quantity and diversity.

Methods
This study considered researches carried out in patients with SLE, with no restriction of age or gender, which fulfilled the classification criteria of either Systemic Lupus International Collaborating Clinic (SLICC), American College of Rheumatology (ACR) or European League Against Rheumatism (EULAR) and used the Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) to classify disease in activity or remission were included. The search was carried out from October, 2020 to January, 2021 using the following databases: Medline via Pubmed, Scopus, and Embase. Five papers were included with a total of 288 participants with SLE.

Results
Regarding microbiota in patients with SLE in activity, there was significant increase in the following genera: Lactobacillus, Streptococcus, Megasphaera, Fusobacterium, Veillonella, Oribacterium, Odoribacter, Blautia, and Campylobacter. On the other hand, decrease in Faecalibacterium and Roseburia genera as well as Ruminococcus gnavus species was observed in remission cases, showing differences between the microbiota profile in SLE in activity and in remission.

Conclusions
Results suggest that dysbiosis may be involved in the disease activity process.

Trial registration
CRD42021229322.
Risk factors for the flare of systemic lupus erythematosus and its influence on prognosis: a single-center retrospective analysis
Authors: Zeng Xiaohong , Zheng Ling , Rui Hongbing , Kang Rihui , Chen Junmin , Chen Huaning , Liu Jizan 
Published: July 2021

Abstract
Objectives
To explore the risk factors for systemic lupus erythematosus (SLE) flare and their impact on prognosis.

Methods
The clinical characteristics, laboratory results, and treatment plans of 121 patients with SLE flare were retrospectively analyzed. Ninety-eight SLE outpatients with sustained remission during the same period were selected as controls. Logistic multivariate regression analysis was employed to screen for risk factors for SLE flare.

Results
Infection, thrombocytopenia, arthritis, anti-nucleosome antibodies positive, anti-β2-glycoprotein I (IgG) antibodies positive, and patient’s self-discontinuation of medicine maintenance therapy might be risk factors for SLE flare. Patients who discontinued medicine maintenance therapy by themselves had a significantly higher rate of severe SLE flare than patients with regular medicine maintenance therapy (P = 0.033). The incidence of anemia associated with SLE (P = 0.001), serositis (P = 0.005), and pulmonary hypertension (P = 0.003) in patients who discontinued medicine maintenance therapy were significantly higher than patients with regular medicine maintenance therapy. SLE patients with regular medicine maintenance therapy for less than 3 years had a higher risk of pulmonary hypertension than those with regular medicine maintenance therapy longer than 3 years (P = 0.034).

Conclusions
The accompanying thrombocytopenia, arthritis, anti-nucleosome antibodies positive and anti-β2-glycoprotein I (IgG) antibodies positive at the onset of SLE may affect the prognosis of SLE. Patient’s self-discontinuation of medicine maintenance therapy is the main cause of SLE flare, which may induce severe flare in SLE patients and lead to a significantly higher incidence of pulmonary hypertension.
Mathematical modeling of the impact of treatment on the dynamics of typhoid
Authors: Nyaberi Halson O. , Musaili Jane S. 
Published: July 2021

AbstractIn this paper, we propose a mathematical model for the transmission of typhoid which analyzes the impact of treatment of the infected individuals on the dynamics of the disease. The model consists of human population and pathogen population. The human population is subdivided into three compartments, namely susceptible individuals, infected individuals, and recovered individuals and pathogen population comprises one compartment. We derived the basic reproduction number $${\mathcal {R}}_0$$

R
0

, and analyzed the dynamical behaviors of both disease free equilibrium and endemic equilibrium by the theory of ordinary differential equations. Using MATLAB, we carried out numerical simulation and the findings indicate that effective treatment is adequate in eradicating typhoid fever.
FSH Level and Changes in Bone Mass and Body Composition in Older Women and Men
Authors: Wu Karin C , Ewing Susan K , Li Xiaojuan , Sigurðsson Sigurður , Guðnason Vilmundur , Kado Deborah M , Hue Trisha F , Woods Gina N , Veldhuis-Vlug Annegreet G , Vittinghoff Eric , Zaidi Mone , Rosen Clifford J , Lang Thomas , Kim Tiffany Y , Schwartz Ann V , Schafer Anne L 
Published: July 2021

Abstract

Context
FSH may have independent actions on bone remodeling and body fat regulation. Cross-sectionally, we have shown that serum FSH is associated with bone mineral density (BMD) and body fat in older postmenopausal women, but it remains unknown whether FSH predicts bone and fat changes.

Objective
We examined whether baseline FSH level is associated with subsequent bone loss or body composition changes in older adults.

Setting, Design, Participants
We studied 162 women and 158 men (mean age 82 ± 4 years) from the Age, Gene/Environment Susceptibility (AGES)-Bone Marrow Adiposity cohort, a substudy of the AGES-Reykjavik Study of community-dwelling older adults. Skeletal health and body composition were characterized at baseline and 3 years later.

Main Outcomes
Annualized change in BMD and body composition by dual-energy X-ray absorptiometry (DXA) and quantitative computed tomography (QCT). Models were adjusted for serum estradiol and testosterone levels.

Results
There was no evidence for an association between baseline FSH level and change in BMD or body composition by DXA or QCT. For femoral neck areal BMD, adjusted mean difference (95% CI) per SD increase in FSH was 1.3 (-0.7 to 3.3) mg/cm2/y in women, and -0.2 (-2.6 to 2.2) mg/cm2/y in men. For visceral fat, adjusted mean difference (95% CI) per SD increase in FSH was 1.80 (-0.03 to 3.62) cm2/y in women, and -0.33 (-3.73 to 3.06) cm2/y in men.

Conclusions
Although cross-sectional studies and studies in perimenopausal women have demonstrated associations between FSH and BMD and body composition, in older adults, FSH level is not associated with bone mass or body composition changes.
Interleukin-2 Transiently Inhibits Pulsatile Growth Hormone Secretion in Young but not Older Healthy Men
Authors: Roelfsema Ferdinand , Yang Rebecca , Veldhuis Johannes D 
Published: July 2021

AbstractContextInterleukin-2 (IL-2), a proinflammatory cytokine, has been used to treat malignancies. Increased cortisol and adrenocorticotropin (ACTH) were noted, but growth hormone (GH) secretion was not investigated in detail.ObjectiveWe quantified GH secretion after a single subcutaneous injection of IL-2 in 17 young and 18 older healthy men in relation to dose, age, and body composition.MethodsThis was a placebo-controlled, blinded, prospectively randomized, crossover study. At 20:00 hours IL-2 (3 or 6 million units/m2) or saline was injected subcutaneously. Lights were off between 23:00 and 07:00 hours. Blood was sampled at 10-minute intervals for 24 hours. Outcome measures included convolution analysis of GH secretion.ResultsGH profiles were pulsatile under both experimental conditions and lower in older than young volunteers. Since the effect of IL-2 might be time limited, GH analyses were performed on the complete 24-hour series and the 6 hours after IL-2 administration. Total and pulsatile 24-hour GH secretion decreased nonsignificantly. Pulsatile secretion fell over the first 6 hours after IL-2 (P = .03), with visceral fat as a covariate (P = .003), but not age (P = .10). Plots of cumulative 2-hour bins of GH pulse mass showed a distinction by treatment and age groups: A temporary GH decrease of 32% and 28% occurred in the first 2-hour bins after midnight (P = .02 and .04) in young participants, whereas in older individuals no differences were present at any time point.ConclusionThis study demonstrates that IL-2 temporarily diminishes GH secretion in young, but not older, men.
Type 2 Diabetes and Change in Total Hip Bone Area and Bone Mineral Density in Swedish Men and Women Older Than 55 Years
Authors: Mitchell Adam , Fall Tove , Melhus Håkan , Lind Lars , Michaëlsson Karl , Byberg Liisa 
Published: July 2021

Abstract

Context
In a cross-sectional study, we found an association between type 2 diabetes mellitus (T2DM) and smaller bone area together with greater bone mineral density (BMD) at the total hip.

Objective
This work aims to investigate these associations longitudinally, by studying T2DM status (no T2DM n = 1521, incident T2DM n = 119, or prevalent T2DM n = 106) in relation to changes in total hip bone area and BMD.

Methods
In 3 cohorts, the Swedish Mammography Cohort Clinical (SMCC; n = 1060), Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS; n = 483), and Uppsala Longitudinal Study of Adult Men (ULSAM; n = 203), with repeat assessment of T2DM status and dual energy x-ray absorptiometry (DXA) measurements of total hip bone area and BMD on average 8 years apart, a linear regression model was used to assess the effect of T2DM status on change in bone area and BMD at the total hip.

Results
After meta-analysis, the change in bone area at the total hip was 0.5% lower among those with incident T2DM compared to those without T2DM (–0.18 cm2; 95% CI, –0.30 to –0.06). The change in bone area was similar among those with prevalent T2DM compared to those without (0.00 cm2; 95% CI, –0.13 to 0.13). For BMD, the combined estimate was 0.004 g/cm2 (95% CI, –0.006 to 0.014) among those with incident T2DM and 0.010 g/cm2 (95% CI, –0.000 to 0.020) among those with prevalent T2DM, compared to those without T2DM.

Conclusion
Those with incident T2DM have a lower expansion in bone area at the total hip compared to those without T2DM.
Keratin 8 mutations in transgenic mice predispose to lung injury
Authors: Kim Sujin , Lim Younglan , Lee So-Young , Yoon Han-Na , Yi Hayan , Jang Kwi-Hoon , Ku Nam-On 
Published: July 2021

ABSTRACTKeratin 8 (K8) is the cytoskeletal intermediate filament protein of simple-type epithelia. Mutations in K8 predispose the affected individual and transgenic mouse to liver disease. However, the role of K8 in the lung has not been reported in mutant transgenic mouse models. Here, we investigated the susceptibility of two different transgenic mice expressing K8 Gly62–Cys (Gly62 replaced with Cys) or Ser74–Ala (Ser74 replaced with Ala) to lung injury. The mutant transgenic mice were highly susceptible to two independent acute and chronic lung injuries compared with control mice. Both K8 Gly62–Cys mice and K8 Ser74–Ala mice showed markedly increased mouse lethality (∼74% mutant mice versus ∼34% control mice) and more severe lung damage, with increased inflammation and apoptosis, under L-arginine-mediated acute lung injury. Moreover, the K8 Ser74–Ala mice had more severe lung damage, with extensive hemorrhage and prominent fibrosis, under bleomycin-induced chronic lung injury. Our study provides the first direct evidence that K8 mutations predispose to lung injury in transgenic mice.
TAPAS: Towards Automated Processing and Analysis of multi-dimensional bioimage data
Authors: Gilles Jean-François , Boudier Thomas 
Published: July 2021

Modern microscopy is based on reproducible quantitative analysis, image data should be batch-processed by a standardized system that can be shared and easily reused by others. Furthermore, such system should require none or minimal programming from the users. We developed TAPAS (Towards an Automated Processing and Analysis System). The goal is to design an easy system for describing and exchanging processing workflows. The protocols are simple text files comprising a linear list of commands used to process and analyse the images. An extensive set of 60 modules is already available, mostly based on the tools proposed in the 3D ImageJ Suite. We propose a wizard, called TAPAS menu, to help the user design the protocol by listing the available modules and the parameters associated. Most modules will have default parameters values for most common tasks. Once the user has designed the protocol, he/she can apply the protocol to a set of images, that can be either stored locally or on a OMERO database. An extensive documentation including the list of modules, various tutorials and link to the source code is available at https://imagej.net/TAPAS.
Pancreatic cancer incidence trends in the United States from 2000-2017: Analysis of Surveillance, Epidemiology and End Results (SEER) database
Authors: Ali Hassam , Pamarthy Rahul , Vallabhaneni Meghana , Sarfraz Shiza , Ali Hadiqa , Rafique Hamza 
Published: July 2021

Background: Recent incidence trends of pancreatic cancers were reviewed by demographics and histologic type to observe any new findings. Methods: Data was used from the Surveillance, Epidemiology, and End Results (SEER) registry 18 (2000-2017) and it underwent temporal trend analysis. Pancreatic cancer incidence rates were reported based on histological subtype and demographics. Results: The incidence rate of white males increased significantly during 2000-2017 (annual percent change (APC) = 3.5%) compared to previously reported APCs. The incidence of white females grew from an APC of 1.29% to 2.9%. Rates among black ethnicity increased with an APC of 4.2%. Rates among Hispanics and other ethnicities also showed increment. The rates for ductal adenocarcinoma showed a positive trend in all races, with the APC ≥ 6 % for females and APC ≥ 6.5 % for males. The rates of non-secretory endocrine tumors showed a decline in both genders of all five races in recent years after showing an initial positive trend till 2010. Rates for pancreatic adenocarcinoma continued to rise in all ethnicities from 2000-2017. Interestingly, there was a rise in carcinoid type pancreatic neuroendocrine tumors (PNETs) in all ethnicities. Cumulatively, males had a higher incidence than females; male to female Incidence Risk Ratio (IRRs) was 1.32. The IRR was > 1 for age groups ≥ 35 years. The male to female IRRs was less than 1 for cystic adenocarcinoma, secretory endocrine, and solid pseudopapillary carcinomas (IRR = 0.5, 0.9, and 0.2 respectively, confidence intervals 0.4–0.6 and 0.9-1.3, 0.2–0.3, respectively). Conclusion: Pancreatic cancer incidence continued to rise in the years 2000-2017. However, incidence differed by demographics and histologic type. Interestingly, recent years discerned a rise in PNETs (carcinoid type) which has not been reported previously.
Kidney Exchange: An Operations Perspective
Authors: Ashlagi Itai , Roth Alvin E. 
Published: July 2021

Many patients in need of a kidney transplant have a willing but incompatible (or poorly matched) living donor. Kidney exchange programs arrange exchanges among such patient-donor pairs, in cycles and chains of exchange, so that each patient receives a compatible kidney. Kidney exchange has become a standard form of transplantation in the United States and a few other countries, in large part because of continued attention to the operational details that arose as obstacles were overcome and new obstacles became relevant. We review some of the key operational issues in the design of successful kidney exchange programs. Kidney exchange has yet to reach its full potential, and the paper further describes some open questions that we hope will continue to attract attention from researchers interested in the operational aspects of dynamic exchange. This paper was accepted by David Simchi-Levi, Special Section of Management Science: 65th Anniversary.
Midwives' experiences of performing obstetric ultrasounds in maternity care: a systematic review
Authors: Bwanga Osward , Mwase Gabriel , Kaunda Happiness Chanda 
Published: July 2021

Background/aims Ultrasound scans, often performed by midwives, play a vital role in the management of pregnancy, but there is a lack of literature on midwives' experience of this task. This study aimed to systematically review the experiences of midwives when performing obstetrical ultrasounds in maternity care. Methods Online databases, journals and cited references were searched, with no date limit. Thematic analysis was used to synthesise the findings. Results A total of eight studies were included. The five themes identified were 1) the benefits of ultrasound in maternity care, 2) access to and performing an obstetric ultrasound, 3) the relationship between midwives and ultrasound experts, 4) ethical and legal issues and 5) education and training for midwives. Midwives' positive experiences were usually a result of access to obstetric ultrasound and adequate support from obstetricians and radiologists. Negative experiences were caused by ethical and legal complications, as well as a lack of ultrasound equipment and training. Conclusions There is a need to support midwives in performing basic obstetric ultrasounds, through education and training, to improve maternity care.
Wound prevalence survey in a regional integrated care organisation in the midwest of Ireland
Authors: Meagher Helen , Keane Niamh , Egan Siobhan , Sheikhi Ali , Moloney Michael A. , Kavanagh Eamon 
Published: July 2021

Background/aims: The aim of this clinical audit was to determine the point prevalence of wounds over a 1-week period during April 2019 in the midwest Regional Integrated Care Organisation (RICO), which has a population of 379 452. The RICO consists of six hospitals, a public health nursing service across three counties, community residential settings, nine older person's service sites, community health centres and one prison. Method: A peer-reviewed, purpose-designed data collection tool was used to gather demographic and wound data on each patient with a wound in the midwest RICO. Anonymised data were collected by the nurse undertaking routine wound care on one occasion during the 1-week study period. There were no exclusion criteria for this study; all patients with a wound were eligible for inclusion. Ethical approval was obtained. Results: Completed data collection forms were returned for 791 patients who had a combined total of 1164 wounds. Data were analysed using SPSS version 21 to produce descriptive statistics. A point prevalence of 0.2% of the total RICO population had a wound, with a mean of 1.47 wounds per patient. Some 51% of the cohort was female. The median age was 75 years (range 3–101 years, standard deviation=19.881). Leg ulcers were the most common wound type, with a prevalence of 0.07% (33.7% of the cohort). Conclusions: This clinical wound prevalence audit supports previous studies in relation to wound statistics in Ireland and will be useful for resource planning in an ageing population.
Resonant fiber optical gyroscope using the single-mode fiber ring resonator
Authors: Liu Lu , Liu Shuang , Qian Weiwen , Li Hanzhao , Ma Huilian 
Published: July 2021

This paper provides a scheme for realizing high-accuracy, low-cost resonant fiber optical gyroscopes (RFOGs) with single-mode (SM) fibers. The temperature-related polarization noise, which deteriorates the bias stability of the RFOG, has been suppressed thanks to a much longer birefringence beat length of SM fibers. It is also helpful to improve the theoretical sensitivity of the RFOG because of the very low loss of the SM fiber components. A transmissive 39-m-long SM fiber ring resonator (FRR) is fabricated. The measured finesse is 58.7, and its total loss is calculated to be less than 0.3 dB. Using this SM-FRR as the sensing element, an RFOG is then set up that achieves an angular random walk of

0.0039

∘

/

√

h

and a bias stability of 0.05°/h. The experimental results show that the SM-FRR scheme would be a good candidate for producing high-accuracy and low-cost RFOGs.
Miniaturized spectroscopy with tunable and sensitive plasmonic structures
Authors: Liang Li , Zheng Qilin , Wen Long , Cumming David R. S. , Chen Qin 
Published: July 2021

A broad linewidth and a lack of spectral analysis limit the applications of plasmonic sensors. In this Letter, a plasmonic sensor with a large sensitivity in the terahertz (THz) range is proposed based on high-quality factor (

>

1000

) surface lattice resonance in subwavelength near-flat metallic gratings. Moreover, such a highly selective spectral manipulating scheme, plus the greatly localized plasmonic resonance, enables miniaturized spectroscopy based on a single detector by integrating an electro-optical material with the gratings. A spectral resolution of 0.1 GHz at a center frequency of 1.1 THz is predicted showing a four times improvement of measuring efficiency. This technique shows promising potential in on-site matter inspection and point-of-care testing.