bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generalized scale behavior and renormalization group for data analysis
Authors: Lahoche Vincent , Samary Dine Ousmane , Tamaazousti Mohamed 
Published: March 2022

Abstract
Some recent results showed that the renormalization group (RG) can be considered as a promising framework to address open issues in data analysis. In this work, we focus on one of these aspects, closely related to principal component analysis (PCA) for the case of large dimensional data sets with covariance having a nearly continuous spectrum. In this case, the distinction between ‘noise-like’ and ‘non-noise’ modes becomes arbitrary and an open challenge for standard methods. Observing that both RG and PCA search for simplification for systems involving many degrees of freedom, we aim to use the RG argument to clarify the turning point between noise and information modes. The analogy between coarse-graining renormalization and PCA has been investigated in Bradde and Bialek (2017 J. Stat. Phys.
167 462–75), from a perturbative framework, and the implementation with real sets of data by the same authors showed that the procedure may reflect more than a simple formal analogy. In particular, the separation of sampling noise modes may be controlled by a non-Gaussian fixed point, reminiscent of the behaviour of critical systems. In our analysis, we go beyond the perturbative framework using nonperturbative techniques to investigate non-Gaussian fixed points and propose a deeper formalism allowing us to go beyond power-law assumptions for explicit computations.
High-quality micro-shape fabrication of monocrystalline diamond by nanosecond pulsed laser and acid cleaning
Authors: Okamoto Yasuhiro , Okubo Tubasa , Kajitani Atsuya , Okada Akira 
Published: March 2022

Abstract
The flat plane of small surface roughness below 0.1 µm average roughness was obtained for monocrystalline diamond by nanosecond pulsed laser irradiation of 1060 nm and post-process acid cleaning, at a laser fluence around the material removal threshold value. The glossy and flat plane at the bottom of the micro-groove was parallel to the top surface of the specimen, although the round beam of Gaussian mode was irradiated in the direction perpendicular to the top surface of specimen. The square beam of top-hat mode produced a shallower micro-groove with a wider, flatter bottom compared with the round beam in Gaussian mode. The creation method of the flat plane with small surface roughness was discussed in the arrangement strategy of linear micro-grooving by the square beam of top-hat mode. Normal side-by-side repetition of linear micro-grooving did not create a flat plane with constant depth. Therefore, a two-step scanning method was proposed in order to overcome the problem in the normal side-by-side repetition of liner micro-grooving. Non-removal areas were partly retained between the processing lines in the first step, and the laser scanning was conducted on the retained area in the second step. The newly proposed two-step scanning method was practical and useful to create a widely flat plane with small surface roughness, and the two-step scanning method provided superior control over the micro-groove depth. This proposed method can reduce the surface roughness in addition to the shape creation of monocrystalline diamond, and it can be used as a high-quality micro-shape fabrication method of monocrystalline diamond.
Long-term physical activity participation trajectories were associated with subsequent cognitive decline, risk of dementia and all-cause mortality among adults aged ≥50 years: a population-based cohort study
Authors: Li Chenglong , Ma Yanjun , Hua Rong , Zheng Fanfan , Xie Wuxiang 
Published: March 2022

Abstract

Aim
to evaluate self-reported physical activity (PA) participation trajectories over a 6-year span and to assess associations with subsequent cognitive decline, incident dementia and all-cause mortality.

Methods
population-based cohort of 8,842 community-dwelling adults aged ≥50 years in England. Group-based trajectory modelling was used to identify 6-year trajectories of PA participation. Cognitive decline, incident dementia and all-cause mortality were outcomes.

Results
five trajectories were identified, including persistently low (N = 2,511), initially low then improving (1,651), initially high then declining (249), persistently moderate (2,422) and persistently high (2,009). Compared with persistently low, participants of initially low then improving and persistently high PA participation experienced decelerated global cognitive decline of 0.012 standard deviation (SD)/year (95% confidence interval [CI]: 0.004–0.021, P = 0.004) and 0.021 SD/year (95% CI: 0.013–0.029, P &lt; 0.001). They were also associated with lower dementia risk, with multivariate-adjusted hazard ratios (HRs) of 0.43 (95% CI: 0.31–0.60) and 0.35 (95% CI: 0.27–0.45). A similar pattern was observed for all-cause mortality, with HRs of 0.31 (95% CI: 0.13–0.74) and 0.25 (95% CI: 0.14–0.45). No significant differences were observed between persistently low and initially high then declining trajectories.

Conclusion
for middle-aged and older adults, both gradually improved and persistently active PA participation were associated with decelerated cognitive decline, lower risk of dementia and all-cause mortality. Strategies focusing on improving and maintaining PA participation could be of significance by attaining considerable neurocognitive and longevity benefits.
The white koji fungusAspergillus luchuensismut.kawachii
Authors: Futagami Taiki 
Published: March 2022

ABSTRACTThe white koji fungus, Aspergillus luchuensis mut. kawachii, is used in the production of shochu, a traditional Japanese distilled spirit. White koji fungus plays an important role in the shochu production process by supplying amylolytic enzymes such as α-amylase and glucoamylase. These enzymes convert starch contained in primary ingredients such as rice, barley, buckwheat, and sweet potato into glucose, which is subsequently utilized by the yeast Saccharomyces cerevisiae to produce ethanol. White koji fungus also secretes large amounts of citric acid, which lowers the pH of the shochu mash, thereby preventing the growth of undesired microbes and enabling stable production of shochu in relatively warm regions of Japan. This review describes the historical background, research tools, and recent advances in studies of the mechanism of citric acid production by white koji fungus.
Circ_0007611 stimulates IL-1 receptor accessory protein to inhibit trophoblast cell proliferation and induce cell apoptosis
Authors: Xing Haiyan , Ding Qing , Lu Hong , Li Qun 
Published: March 2022

Abstract
Preeclampsia (PE) is a common pregnancy disorder, and mounting evidence has revealed that circular RNA participates in PE development. However, the detailed molecular mechanism of circ_0007611 in PE progression remains unknown. RNA expressions of circ_0007611, microRNA-558 (miR-558), and IL-1 receptor accessory protein (IL1RAP) were detected by quantitative real-time polymerase chain reaction. Cell proliferation was investigated by clonogenicity, 5-Ethynyl-29-deoxyuridine, and DNA content quantitation assays. Cell apoptotic rate and angiogenesis were analyzed by cell apoptosis and tube formation assays, respectively. Protein expression was detected by western blot. The binding relationship between miR-558 and circ_0007611 or IL1RAP was identified by a dual-luciferase reporter or RNA immunoprecipitation assay. Circ_0007611 and IL1RAP expressions were significantly upregulated, while miR-558 was downregulated in the placental tissues of PE women in comparison with normal placental tissues. Functionally, circ_0007611 overexpression inhibited trophoblast cell proliferation and angiogenesis and induced cell apoptosis; however, circ_0007611 downregulation showed the opposite effects. Mechanistically, circ_0007611 acted as a miR-558 sponge, and miR-558 bound to IL1RAP. Besides, miR-558 overexpression or IL1RAP absence relieved circ_0007611-induced trophoblast cell dysfunction. Moreover, miR-558 contributed to cell proliferation and tube formation and inhibited cell apoptosis by reducing IL1RAP expression in trophoblast cells. Circ_0007611 aggravated trophoblast cell disorders by the miR-558/IL1RAP pathway in PE.
Discovery of efficacy biomarkers for non-small cell lung cancer with first-line anti-PD-1 immunotherapy by data-independent acquisition mass spectrometry
Authors: Chao Yencheng , Jiang Weipeng , Wang Xiaocen , Wang Xiaoyue , Song Juan , Chen Cuicui , Zhou Jian , Huang Qihong , Hu Jie , Song Yuanlin 
Published: March 2022

Abstract
First-line immune checkpoint inhibitors (ICIs) have greatly ameliorated outcomes in non-small cell lung cancer (NSCLC). However, approximately a quarter of patients receiving ICIs demonstrate long-term clinical benefit, and the true responders have not been fully clarified by the existing biomarkers. To discover potential biomarkers treatment-related outcome in plasma, mass spectrometry assay for data-independent acquisition was analyzed plasma samples collected before the anti-PD-1 treatment. From July 2019 to January 2020, 15 patients with EGFR/ALK-negative NSCLC receiving first-line anti-programmed cell death protein 1 (PD-1) inhibitors were enrolled, and six healthy individuals have collected the plasma samples as control. We explored plasma proteome profiles and conducted stratified analyses by anti-PD-1 responders and non-responders. To validate the target proteins by ELISA, we recruited 22 additional independent patients and 15 healthy individuals from April 2021 to August 2021. By identifying biomarkers to predict better efficacy, we performed differential expression analysis in 12 responders and three non-responders. Compared with healthy individuals, hierarchical cluster analysis revealed plasma proteome profiles of NSCLC were markedly changed in 170 differentially expressed proteins. Furthermore, we discovered that SAA1, SAA2, S100A8, and S100A9 were noticeably increased among non-responders than responders, which may serve as predictive biomarkers with unfavorable respond. The validated results from all samples via ELISA were confirmed this observation. Identified a set of plasma-derived protein biomarkers (SAA1, SAA2, S100A8, and S100A9) could potentially predict the efficacy in cohorts of patients with NSCLC treated with first-line anti-PD-1 inhibitors and deserves further prospective study.
A secondary motor area contributing to interlimb coordination during visually guided locomotion in the cat
Authors: Nakajima Toshi , Fortier-Lebel Nicolas , Drew Trevor 
Published: March 2022

Abstract
We investigated the contribution of cytoarchitectonic cortical area 4δc, in the caudal bank of the cruciate sulcus of the cat, to the control of visually guided locomotion. To do so, we recorded the activity of 114 neurons in 4δc while cats walked on a treadmill and stepped over an obstacle that advanced toward them. A total of 84/114 (74%) cells were task-related and 68/84 (81%) of these cells showed significant modulation of their discharge frequency when the contralateral limbs were the first to step over the obstacle. These latter cells included a substantial proportion (27/68 40%) that discharged between the passage of the contralateral forelimb and the contralateral hindlimb over the obstacle, suggesting a contribution of this area to interlimb coordination. We further compared the discharge in area 4δc with the activity patterns of cells in the rostral division of the same cytoarchitectonic area (4δr), which has been suggested to be a separate functional region. Despite some differences in the patterns of activity in the 2 subdivisions, we suggest that activity in each is compatible with a contribution to interlimb coordination and that they should be considered as a single functional area that contributes to both forelimb–forelimb and forelimb–hindlimb coordination.
Associations between neighborhood socioeconomic status, parental education, and executive system activation in youth
Authors: Murtha Kristin , Larsen Bart , Pines Adam , Parkes Linden , Moore Tyler M , Adebimpe Azeez , Bertolero Maxwell , Alexander-Bloch Aaron , Calkins Monica E , Davila Diego G , Lindquist Martin A , Mackey Allyson P , Roalf David R , Scott James C , Wolf Daniel H , Gur Ruben C , Gur Raquel E , Barzilay Ran , Satterthwaite Theodore D 
Published: March 2022

AbstractSocioeconomic status (SES) can impact cognitive performance, including working memory (WM). As executive systems that support WM undergo functional neurodevelopment during adolescence, environmental stressors at both individual and community levels may influence cognitive outcomes. Here, we sought to examine how SES at the neighborhood and family level impacts task-related activation of the executive system during adolescence and determine whether this effect mediates the relationship between SES and WM performance. To address these questions, we studied 1,150 youths (age 8–23) that completed a fractal n-back WM task during functional magnetic resonance imaging at 3T as part of the Philadelphia Neurodevelopmental Cohort. We found that both higher neighborhood SES and parental education were associated with greater activation of the executive system to WM load, including the bilateral dorsolateral prefrontal cortex, posterior parietal cortex, and precuneus. The association of neighborhood SES remained significant when controlling for task performance, or related factors like exposure to traumatic events. Furthermore, high-dimensional multivariate mediation analysis identified distinct patterns of brain activity within the executive system that significantly mediated the relationship between measures of SES and task performance. These findings underscore the importance of multilevel environmental factors in shaping executive system function and WM in youth.
Long-Term Health-Related Quality of Life in Non-Hospitalized Coronavirus Disease 2019 (COVID-19) Cases With Confirmed Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in England: Longitudinal Analysis and Cross-Sectional Comparison With Controls
Authors: Sandmann Frank G , Tessier Elise , Lacy Joanne , Kall Meaghan , Van Leeuwen Edwin , Charlett Andre , Eggo Rosalind M , Dabrera Gavin , Edmunds W John , Ramsay Mary , Campbell Helen , Amirthalingam Gayatri , Jit Mark 
Published: March 2022

Abstract

Background
We aimed to quantify the unknown losses in health-related quality of life of coronavirus disease 2019 (COVID-19) cases using quality-adjusted lifedays (QALDs) and the recommended EQ-5D instrument in England.

Methods
Prospective cohort study of nonhospitalized, polymerase chain reaction (PCR)-confirmed severe acute respiratory syndrome coronavirus 2–positive (SARS-CoV-2–positive) cases aged 12–85 years and followed up for 6 months from 1 December 2020, with cross-sectional comparison to SARS-CoV-2–negative controls. Main outcomes were QALD losses; physical symptoms; and COVID-19-related private expenditures. We analyzed results using multivariable regressions with post hoc weighting by age and sex, and conditional logistic regressions for the association of each symptom and EQ-5D limitation on cases and controls.

Results
Of 548 cases (mean age 41.1 years; 61.5% female), 16.8% reported physical symptoms at month 6 (most frequently extreme tiredness, headache, loss of taste and/or smell, and shortness of breath). Cases reported more limitations with doing usual activities than controls. Almost half of cases spent a mean of £18.1 on nonprescription drugs (median: £10.0), and 52.7% missed work or school for a mean of 12 days (median: 10). On average, all cases lost 13.7 (95% confidence interval [CI]: 9.7, 17.7) QALDs, whereas those reporting symptoms at month 6 lost 32.9 (95% CI: 24.5, 37.6) QALDs. Losses also increased with older age. Cumulatively, the health loss from morbidity contributes at least 18% of the total COVID-19-related disease burden in the England.

Conclusions
One in 6 cases report ongoing symptoms at 6 months, and 10% report prolonged loss of function compared to pre-COVID-19 baselines. A marked health burden was observed among older COVID-19 cases and those with persistent physical symptoms.
Altered Maternal Antibody Profiles in Women With Human Immunodeficiency Virus Drive Changes in Transplacental Antibody Transfer
Authors: Dolatshahi Sepideh , Butler Audrey L , Siedner Mark J , Ngonzi Joseph , Edlow Andrea G , Adong Julian , Jennewein Madeleine F , Atyeo Caroline , Bassett Ingrid V , Roberts Drucilla J , Lauffenburger Douglas A , Alter Galit , Bebell Lisa M 
Published: March 2022

Abstract

Background
Human immunodeficiency virus (HIV)–exposed, uninfected (HEU) children have a higher risk of severe infection, but the causes are poorly understood. Emerging data point to altered antibody transfer in women with HIV (WHIV); however, specific perturbations and the influence of antiretroviral therapy (ART) and HIV viremia remain unclear.

Methods
We evaluated antigen-specific transplacental antibody transfer across 14 antigens in paired maternal and umbilical cord plasma from 352 Ugandan women; 176 were WHIV taking ART. We measured antigen-specific immunoglobulin G (IgG) sub­class (IgG1, 2, 3, 4) levels and antibody Fcγ receptor (FcγRn, 2a, 2b, 3a, 3b) binding profiles. We used partial least squares discrimi­nant analysis to define antigen-specific transplacental antibody transfer features.

Results
Global antibody transfer patterns were similar by maternal HIV serostatus, pointing to effective placental function in WHIV. However, HEU umbilical cord antibody profiles were altered, driven by perturbed WHIV seroprofiles, with higher levels of herpesvirus antibodies (P &lt; .01 for Epstein-Barr virus, herpes simplex virus) and lower levels of classic vaccine-induced antibodies (P &lt; .01 for tetanus, polio, Haemophilus influenzae type b), suggesting that umbilical cord antibody profile differences arise from imbalanced WHIV immunity. Abnormal WHIV antibody profiles were associated with HIV viremia, lower CD4 count, and postconception ART initiation (P = .01).

Conclusions
Perturbed immune-dominance profiles in WHIV shift the balance of immunity delivered to neonates. Perturbed HIV-associated maternal antibody profiles are a key determinant of com­promised neonatal immunity. Maternal vaccination interventions may promote transfer of relevant, effective antibodies to protect HEU children against early-life infections.
Vaccine Effectiveness of 3 Versus 2 Doses of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) mRNA Vaccines in a High-Risk National Population
Authors: Butt Adeel A , Talisa Victor B , Yan Peng , Shaikh Obaid S , Omer Saad B , Mayr Florian B 
Published: March 2022

Abstract

Background
Knowledge of the vaccine effectiveness (VE) of a third or booster vaccine dose in preventing SARS-CoV-2 infection or its consequences is critical in developing recommendations for their use. We determined relative VE of 3 vs 2 doses of an mRNA vaccine in preventing symptomatic SARS-CoV-2 infection, hospitalization, and severe/critical disease.

Methods
Among veterans who had received 2 doses of an mRNA vaccine by 30 April 2021, we identified those who received a third dose of the same vaccine between 22 September and 24 November 2021 and 1:1 matched controls who had not received their third dose by then. Using Cox proportional hazards model, we calculated adjusted hazards ratios for symptomatic infection, hospitalization, and intensive care unit (ICU) admission or death after SARS-CoV-2–positive test.

Results
Among 2 321 366 veterans who received 2 doses of Pfizer BNT-162b2 or Moderna mRNA-1273 vaccine by 30 April 2021, we matched 395 686 persons who received a third dose of the same vaccine between 22 September and 24 November 2021 to controls who did not receive a third dose. Adjusted HRs (95% CI) were .15 (.11–.21) for symptomatic infection and .18 (.13–.26) for hospitalizations for 3 vs 2 doses, corresponding to relative VE of 85% and 82%. Five ICU admissions or deaths were observed (4 among recipients of 2 doses). There was no difference in VE between BNT162b2 versus mRNA-1273 recipients.

Conclusions
A third dose of a SARS-CoV-2 mRNA vaccine is associated with high VE against symptomatic infection, hospitalization, and critical disease in the pre-Omicron era.
Vascular dysfunction and increased cardiovascular risk in hypospadias
Authors: Lucas-Herald Angela K , Montezano Augusto C , Alves-Lopes Rheure , Haddow Laura , Alimussina Malika , O’Toole Stuart , Flett Martyn , Lee Boma , Amjad S Basith , Steven Mairi , Brooksbank Katriona , McCallum Linsay , Delles Christian , Padmanabhan Sandosh , Ahmed S Faisal , Touyz Rhian M 
Published: March 2022

Abstract

Aims
Hypogonadism is associated with cardiovascular disease. However, the cardiovascular impact of hypogonadism during development is unknown. Using hypospadias as a surrogate of hypogonadism, we investigated whether hypospadias is associated with vascular dysfunction and is a risk factor for cardiovascular disease.

Methods and results
Our human study spanned molecular mechanistic to epidemiological investigations. Clinical vascular phenotyping was performed in adolescents with hypospadias and controls. Small subcutaneous arteries from penile skin from boys undergoing hypospadias repair and controls were isolated and functional studies were assessed by myography. Vascular smooth muscle cells were used to assess: Rho kinase, reactive oxygen species (ROS), nitric oxide synthase/nitric oxide, and DNA damage. Systemic oxidative stress was assessed in plasma and urine. Hospital episode data compared men with a history of hypospadias vs. controls. In adolescents with hypospadias, systolic blood pressure (P = 0.005), pulse pressure (P = 0.03), and carotid intima-media thickness standard deviation scores (P = 0.01) were increased. Arteries from boys with hypospadias demonstrated increased U46619-induced vasoconstriction (P = 0.009) and reduced acetylcholine-induced endothelium-dependent (P &lt; 0.0001) and sodium nitroprusside-induced endothelium-independent vasorelaxation (P &lt; 0.0001). Men born with hypospadias were at increased risk of arrhythmia [odds ratio (OR) 2.8, 95% confidence interval (CI) 1.4–5.6, P = 0.003]; hypertension (OR 4.2, 95% CI 1.5–11.9, P = 0.04); and heart failure (OR 1.9, 95% CI 1.7–114.3, P = 0.02).

Conclusion
Hypospadias is associated with vascular dysfunction and predisposes to hypertension and cardiovascular disease in adulthood. Underlying mechanisms involve perturbed Rho kinase- and Nox5/ROS-dependent signalling. Our novel findings delineate molecular mechanisms of vascular injury in hypogonadism, and identify hypospadias as a cardiovascular risk factor in males.