bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collagen orientation probed by polarized Raman spectra can serve as differential diagnosis indicator between different grades of meniscus degeneration
Authors: Prokopi Nikoletta , Andrikopoulos Konstantinos S. , Beobide Amaia Soto , Voyiatzis George A. , Papachristou Dionysios J. 
Published: October 2021

AbstractThe purpose of the present study was to analyze normal and degenerated menisci with Raman methodology on thin sections of formalin fixed paraffin embedding tissues and to correlate the Raman findings with the grade of meniscus degeneration. Menisci (n = 27) were removed from human knee joints after total knee replacement or meniscectomy. Following routine histopathological analysis to determine the grade of meniscal lesions obtained from healthy and degenerated formaline fixed paraffin embedded (FFPE) meniscal sections, Raman polarization approach was applied to evaluate the orientation of collagen fibrils in different levels of the same 5 μm thick FFPE meniscal tissue sections, used for histopathological assessment. We collected Raman spectra in two different polarization geometries, v-HH and v-VV, and calculated the mean value of the v-HH/v-VV intensity ratio of two Raman bands, sensitive and non-sensitive to the molecular orientation. The collagen specific amide I band at 1665 cm−1, has the higher sensitivity dependence on the Raman polarization. The mean values of ratio v-HH/v-VV of the 1665 cm−1peak intensity was significantly higher in healthy, mean ± SD: 2.56 ± 0.46, compared to degenerated menisci, mean ± SD: 1.85 ± 0.42 (p = 0.0014). The mean values of v-HH/v-VV intensity ratio were 2.18 and 1.50 for low and high degenerated menisci, respectively (p < 0.0001). The difference of peak intensities in the two laser polarizations is decreased in the degenerated meniscus; this difference is diminishing as the degeneration increases. The v-HH/v-VV ratio was also of significant difference in low as compared to control and high grade meniscus lesions (p = 0.036 and p < 0.0001, respectively) offering valuable information for the approach of its biology and function. In the present study we showed that the 5 μm thick sections can be used for Raman analysis of meniscal tissue with great reliability, in terms of sensitivity, specificity, false-negative and false-positive results. Our data introduce the interesting hypothesis that compact portable Raman microscopy on tissue sections can be used intra-operatively for fast diagnosis and hence, accurate procedure design in the operating room.
Deep learning on fundus images detects glaucoma beyond the optic disc
Authors: Hemelings Ruben , Elen Bart , Barbosa-Breda João , Blaschko Matthew B. , De Boever Patrick , Stalmans Ingeborg 
Published: October 2021

AbstractAlthough unprecedented sensitivity and specificity values are reported, recent glaucoma detection deep learning models lack in decision transparency. Here, we propose a methodology that advances explainable deep learning in the field of glaucoma detection and vertical cup-disc ratio (VCDR), an important risk factor. We trained and evaluated deep learning models using fundus images that underwent a certain cropping policy. We defined the crop radius as a percentage of image size, centered on the optic nerve head (ONH), with an equidistant spaced range from 10–60% (ONH crop policy). The inverse of the cropping mask was also applied (periphery crop policy). Trained models using original images resulted in an area under the curve (AUC) of 0.94 [95% CI 0.92–0.96] for glaucoma detection, and a coefficient of determination (R2) equal to 77% [95% CI 0.77–0.79] for VCDR estimation. Models that were trained on images with absence of the ONH are still able to obtain significant performance (0.88 [95% CI 0.85–0.90] AUC for glaucoma detection and 37% [95% CI 0.35–0.40] R2 score for VCDR estimation in the most extreme setup of 60% ONH crop). Our findings provide the first irrefutable evidence that deep learning can detect glaucoma from fundus image regions outside the ONH.
Oral administration of E-type prostanoid (EP) 1 receptor antagonist suppresses carcinogenesis and development of prostate cancer via upregulation of apoptosis in an animal model
Authors: Masato Masahito , Miyata Yasuyoshi , Kurata Hiroki , Ito Hidenori , Mitsunari Kensuke , Asai Akihiro , Nakamura Yuichiro , Araki Kyohei , Mukae Yuta , Matsuda Tsuyoshi , Harada Junki , Matsuo Tomohiro , Ohba Kojiro , Sakai Hideki 
Published: October 2021

AbstractProstaglandin E2 plays an important role in carcinogenesis and malignant potential of prostate cancer (PC) cells by binding to its specific receptors, E-type prostanoid (EP) receptors. However, anti-carcinogenic effects of the EP receptor antagonist are unclear. In this study, we used a mouse model of PC. The mice were provided standard feed (control) or feed containing the EP1 receptor antagonist and were sacrificed at 10, 15, 30, and 52 weeks of age. Apoptosis was evaluated by immunohistochemical analysis using a cleaved caspase-3 assay. The incidence of cancer in the experimental group was significantly lower than that in the control group at 15, 30, and 52 weeks of age. The percentage of poorly differentiated PC cells was significantly lower in the experimental group than in the control group at 30 and 52 weeks of age. The percentage of apoptotic cells in the experimental group was significantly higher than that in the control group at 15, 30, and 52 weeks of age. These findings indicate that feeding with the addition of EP1 receptor antagonist delayed PC progression via the upregulation of apoptosis. We suggest that the EP1 receptor antagonist may be a novel chemopreventive agent for PC.
Cerebrospinal fluid markers for synaptic function and Alzheimer type changes in late life depression
Authors: Siafarikas Nikias , Kirsebom Bjørn-Eivind , Srivastava Deepak P. , Eriksson Cecilia M. , Auning Eirik , Hessen Erik , Selbaek Geir , Blennow Kaj , Aarsland Dag , Fladby Tormod 
Published: October 2021

AbstractTo explore markers for synaptic function and Alzheimer disease (AD) pathology in late life depression (LLD), predementia AD and normal controls (NC). A cross-sectional study to compare cerebrospinal fluid (CSF) levels of neurogranin (Ng), Beta-site amyloid-precursor-protein cleaving enzyme1 (BACE1), Ng/BACE1 ratio and Amyloid-β 42/40 ratio, phosphorylated-tau and total-tau in LLD with (LLD AD) or without (LLD NoAD) AD pathology, predementia AD and normal controls (NC). We included 145 participants (NC = 41; predementia AD = 66 and LLD = 38). LLD comprised LLD AD (n = 16), LLD NoAD (n = 19), LLD with non-AD typical changes (n = 3, excluded). LLD AD (pADJ < 0.05) and predementia AD (pADJ < 0.0001) showed significantly higher Ng than NC. BACE1 and Ng/BACE1 ratio were altered similarly. Compared to LLD NoAD, LLD AD showed significantly higher Ng (pADJ < 0.001), BACE1 (pADJ < 0.05) and Ng/BACE1 ratio (pADJ < 0.01). All groups had significantly lower Aβ 42/40 ratio than NC (predementia AD and LLD AD, p < 0.0001; LLD NoAD, p < 0.05). Both LLD groups performed similarly on tests of memory and executive function, but significantly poorer than NC. Synaptic function in LLD depended on AD pathology. LLD showed an association to Amyloid dysmetabolism. The LLD groups performed poorer cognitively than NC. LLD AD may be conceptualized as “predementia AD with depression”.
Quantifying SARS-CoV-2 nucleocapsid antigen in oropharyngeal swabs using single molecule array technology
Authors: Olsen Dorte Aa. , Brasen Claus L. , Kahns Søren , Madsen Jeppe B. , Kierkegaard Helene , Christensen Henry , Jensen Anders , Sydenham Thomas V. , Møller Jens K. , Madsen Jonna S. , Brandslund Ivan 
Published: October 2021

AbstractThis study aimed to develop a highly sensitive SARS-CoV-2 nucleocapsid antigen assay using the single molecule array (Simoa) technology and compare it with real time RT-PCR as used in routine clinical practice with the ambition to achieve a comparative technical and clinical sensitivity. Samples were available from 148 SARS-CoV-2 real time RT-PCR positive and 73 SARS-CoV-2 real time RT-PCR negative oropharyngeal swabs. For determination of technical sensitivity SARS-CoV-2 virus culture material was used. The samples were treated with lysis buffer and analyzed using both an in-house and a pre-commercial SARS-CoV-2 nucleocapsid antigen assay on Simoa. Both nucleocapsid antigen assays have a technical sensitivity corresponding to around 100 SARS-CoV-2 RNA molecules/mL. Using a cut-off at 0.1 pg/mL the pre-commercial SARS-CoV-2 nucleocapsid antigen assay had a sensitivity of 96% (95% CI 91.4–98.5%) and specificity of 100% (95% CI 95.1–100%). In comparison the in-house nucleocapsid antigen assay had sensitivity of 95% (95% CI 89.3–98.1%) and a specificity of 100% (95% CI 95.1–100%) using a cut-off at 0.01 pg/mL. The two SARS-CoV-2 nucleocapsid antigen assays correlated with r = 0.91 (P < 0.0001). The in-house and the pre-commercial SARS-CoV-2 nucleocapsid antigen assay demonstrated technical and clinical sensitivity comparable to real-time RT-PCR methods for identifying SARS-CoV-2 infected patients and thus can be used clinically as well as serve as a reference method for antigen Point of Care Testing.
The network interplay of interferon and Toll-like receptor signaling pathways in the anti-Candida immune response
Authors: Salgado Ranieri Coelho , Fonseca Dennyson Leandro M. , Marques Alexandre H. C. , da Silva Napoleao Sarah Maria , França Tábata Takahashi , Akashi Karen Tiemi , de Souza Prado Caroline Aliane , Baiocchi Gabriela Crispim , Plaça Desirée Rodrigues , Jansen-Marques Gabriel , Filgueiras Igor Salerno , De Vito Roberta , Freire Paula Paccielli , de Miranda Gustavo Cabral , Camara Niels Olsen Saraiva , Calich Vera Lúcia Garcia , Ochs Hans D. , Schimke Lena F. , Jurisica Igor , Condino-Neto Antonio , Cabral-Marques Otavio 
Published: October 2021

AbstractFungal infections represent a major global health problem affecting over a billion people that kills more than 1.5 million annually. In this study, we employed an integrative approach to reveal the landscape of the human immune responses toCandidaspp.through meta-analysis of microarray, bulk, and single-cell RNA sequencing (scRNA-seq) data for the blood transcriptome. We identified across these different studies a consistent interconnected network interplay of signaling molecules involved in both Toll-like receptor (TLR) and interferon (IFN) signaling cascades that is activated in response to differentCandidaspecies (C. albicans,C. auris,C. glabrata,C. parapsilosis, andC. tropicalis). Among these molecules are several types I IFN, indicating an overlap with antiviral immune responses. scRNA-seq data confirmed that genes commonly identified by the three transcriptomic methods show cell type-specific expression patterns in various innate and adaptive immune cells. These findings shed new light on the anti-Candidaimmune response, providing putative molecular pathways for therapeutic intervention.
Phosphorus availability and leaching losses in annual and perennial cropping systems in an upper US Midwest landscape
Authors: Hussain Mir Zaman , Hamilton Stephen K. , Robertson G. Philip , Basso Bruno 
Published: October 2021

AbstractExcessive phosphorus (P) applications to croplands can contribute to eutrophication of surface waters through surface runoff and subsurface (leaching) losses. We analyzed leaching losses of total dissolved P (TDP) from no-till corn, hybrid poplar (Populus nigra X P. maximowiczii), switchgrass (Panicum virgatum), miscanthus (Miscanthus giganteus), native grasses, and restored prairie, all planted in 2008 on former cropland in Michigan, USA. All crops except corn (13 kg P ha−1 year−1) were grown without P fertilization. Biomass was harvested at the end of each growing season except for poplar. Soil water at 1.2 m depth was sampled weekly to biweekly for TDP determination during March–November 2009–2016 using tension lysimeters. Soil test P (0–25 cm depth) was measured every autumn. Soil water TDP concentrations were usually below levels where eutrophication of surface waters is frequently observed (> 0.02 mg L−1) but often higher than in deep groundwater or nearby streams and lakes. Rates of P leaching, estimated from measured concentrations and modeled drainage, did not differ statistically among cropping systems across years; 7-year cropping system means ranged from 0.035 to 0.072 kg P ha−1 year−1 with large interannual variation. Leached P was positively related to STP, which decreased over the 7 years in all systems. These results indicate that both P-fertilized and unfertilized cropping systems may leach legacy P from past cropland management.
Contamination of multi dose eyedrops in the intra and perioperative context
Authors: Daehn Tristan , Schneider Andreas , Knobloch Johannes , Hellwinkel Olaf J. C. , Spitzer Martin Stephan , Kromer Robert 
Published: October 2021

AbstractIn this study, we examined the rate of contamination of multi-dose ophthalmic solutions in the operating theatre and the underlying risk for infection by examining the microbiological load on the tips of the dispenser bottles. A total of 245 samples of eye drop bottles were collected and analysed between June 2018 and January 2019. All were collected in the operating theatre of the University Eye Hospital Hamburg-Eppendorf. Contamination of the dropper tip occurred in 2% of the samples. Although the prevalence of contamination was low, the results of this study reveal the possibility of contamination of multi-dose eyedrops even when used by health care professionals in the controlled environment of an operating theatre. Following these results, we recommend the use of single-dose eyedrops in the pre- and intraoperative context.
Influence of the Atlantic meridional overturning circulation on the U.S. extreme cold weather
Authors: Yin Jianjun , Zhao Ming 
Published: October 2021

AbstractDue to its large northward heat transport, the Atlantic meridional overturning circulation influences both weather and climate at the mid-latitude Northern Hemisphere. Here we use a state-of-the-art global weather/climate modeling system with high resolution (GFDL CM4C192) to quantify this influence focusing on the U.S. extreme cold weather during winter. We perform a control simulation and the water-hosing experiment to obtain two climate states with and without a vigorous Atlantic meridional overturning circulation. We find that in the control simulation with an overturning circulation, the U.S. east of the Rockies is a region characterized by intense north-south heat exchange in the atmosphere during winter. Without the northward heat transport by the overturning circulation in the hosing experiment, this channel of atmospheric heat exchange becomes even more active through the Bjerknes compensation mechanism. Over the U.S., extreme cold weather intensifies disproportionately compared with the mean climate response after the shutdown of the overturning circulation. Our results suggest that an active overturning circulation in the present-day climate likely makes the U.S. winter less harsh and extreme.
Lossen rearrangement by Rh(iii)-catalyzed C–H activation/annulation of aryl hydroxamates with alkynes: access to quinolone-containing amino acid derivatives
Authors: Petropavlovskikh Dmitry A. , Vorobyeva Daria V. , Godovikov Ivan A. , Nefedov Sergey E. , Filippov Oleg A. , Osipov Sergey N. 
Published: October 2021

An efficient access to new CF3-containing 2-quinolones has been developed via Rh(iii)-catalyzed C–H activation/Lossen rearrangement/annulation cascade of N-pivaloyloxy-arylamides with internal alkynes bearing α-CF3-α-amino acid moiety on triple bond.
The Okabayashi Radical Hysterectomy: Basic Principle and Step-by-Step Procedure
Authors: Konishi Ikuo 
Published: October 2021

AbstractAbdominal radical hysterectomy is the standard operation for stage IB–IIB cervical cancer in the world, which was established by Professor Hidekazu Okabayashi in 1921. In this article, the basic principle and step-by-step procedure of Okabayashi radical hysterectomy are presented, especially for young doctors to understand clearly the important points of this surgery and to realize its radicality and safety for better survival and quality of life of patients with cervical cancer.
The rise of the new Polish far-right
Authors: Kosman Marcin 
Published: October 2021

Abstract
While much research has been done regarding right-wing discourse in modern Europe, the literature of Polish far-right discourse is still insufficient. The present paper discusses the discursive strategies of Grzegorz Braun, one of the leaders of Confederation Liberty and Independence, which were implemented by the politician during the 2019 Gdańsk mayoral campaign. In order to provide a comprehensive analysis of Braun’s discourse, audiovisual materials were included in the study. The findings show that Braun employs positive presentation of the Catholic Church and himself, and negative presentation of his opponents (LGBT activists, immigrants, the European Union, the elites), whom Braun considers to be in an alliance against Poland and its core values under the name of the “Gdańsk Pact”.
Let it rip: the mechanics of self-bisection in asexual planarians determines their population reproductive strategies
Authors: Goel Tapan , Ireland Danielle , Shetty Vir , Rabeler Christina , Diamond Patrick H , Collins Eva-Maria S 
Published: October 2021

Abstract
Asexual freshwater planarians reproduce by transverse bisection (binary fission) into two pieces. This process produces a head and a tail, which fully regenerate within 1–2 weeks. How planarians split into two offspring—using only their musculature and substrate traction—is a challenging biomechanics problem. We found that three different species, Dugesia japonica, Girardia tigrina and Schmidtea mediterranea, have evolved three different mechanical solutions to self-bisect. Using time lapse imaging of the fission process, we quantitatively characterize the main steps of division in the three species and extract the distinct and shared key features. Across the three species, planarians actively alter their body shape, regulate substrate traction, and use their muscles to generate tensile stresses large enough to overcome the ultimate tensile strength of the tissue. Moreover, we show that how each planarian species divides dictates how resources are split among its offspring. This ultimately determines offspring survival and reproductive success. Thus, heterospecific differences in the mechanics of self-bisection of individual worms explain the observed differences in the population reproductive strategies of different planarian species.
Coulomb and nuclear interactions in the dynamics of weakly-bound neutron-halo breakup on heavy target *
Authors: Mukeru B. , Tomio Lauro 
Published: October 2021

Abstract
Within our aim to clarify some aspects of the breakup dynamics of loosely-bound neutron-halo projectiles on a heavy target, we apply the continuum discretized coupled-channel formalism to investigate the beryllium 11Be breakup on a lead 208Pb target at

= 140 MeV incident energy. By evidencing that the continuum–continuum couplings are much stronger in the nuclear breakup than in the Coulomb breakup, we conclude that the strength of these couplings in the total breakup is dominated by the nuclear contribution, with the diagonal monopole nuclear potential in the projectile–target center-of-mass having negligible effect on the total and nuclear breakup cross-sections. For this kind of reaction, we show that the condition for the total breakup to approach its dominant component in the absorption region is strongly dependent on the continuum–continuum couplings and the diagonal monopole nuclear potential.
Strain induced electronic transition in 1T′ MoTe2: high pressure Raman, x-ray diffraction, resistivity measurements and first principles theoretical studies
Authors: Ghosh Bishnupada , Saha Pinku , Mukherjee Bidisha , Samanta Debabrata , Shukla Gaurav , Mukherjee Goutam Dev 
Published: October 2021

Abstract
A detailed high pressure study is carried out on 1T′  MoTe2 using x-ray diffraction (XRD) and Raman spectroscopy measurements up to about 30.5 GPa along with a room temperature resistivity measurement up to 14.3(4) GPa and density functional theory calculations. Though high-pressure XRD measurements show no structural transition, all the lattice parameters exhibit anomalous changes in the pressure region 8.4 to 12.7 GPa. The compressibility of the sample is found to be reduced by almost four times above 12.7 GPa with respect to that below 8.4 GPa. The anomalies in the Raman mode corresponding to the out of plane vibrations of Mo atoms sitting in the unit cell surface indicate a strong electron–phonon coupling possibly mediated by differential strain inside the unit cell. A rapid decrease in resistivity value up to about 7.0(2) GPa of pressure agrees well with the increase in the density of states (DOS) at the Fermi energy with pressure. Pressure evolution of band structure, as well as DOS at the Fermi level, shows an enhancement of the metallic character of the sample. First principle calculations show increased stress in the x and y directions compared to the z-direction with the application of pressure.
A plan-based causal decision theory
Authors: Rothfus Gerard J 
Published: October 2021

Abstract
In ‘An argument against causal decision theory’, Jack Spencer shows that standard formulations of causal decision theory run afoul of his Guaranteed Principle. In the sequential choice problem he employs to make this case, the transgression stems from an awkward discrepancy between how causalists typically value present vs future acts. This note suggests a version of causal decision theory that avoids this incongruity and so respects the Guaranteed Principle in Spencer’s problem. However, this formulation, and hence symmetric appraisal of present and future acts, is also shown to be insufficient to secure causalist satisfaction of the Guaranteed Principle in general.
SCANCell reveals diverse inter-cluster interaction patterns in systemic lupus erythematosus across the disease spectrum
Authors: Zhang Lulu , Liu Xiao , Chen Xiaoxiang , Warden Antony R , Yu Youyi , Huang Baozhen , Ding Xianting 
Published: October 2021

Abstract

Motivation
High-dimensional mass cytometry (CyTOF), which provides both cellular signatures and inter-cluster interactions like the antagonism between immune activation and suppression, and the pro-inflammatory synergy, sheds light on the cellular and molecular basis of disease pathogenesis. However, revealing the aberrance of inter-cluster communication networks in CyTOF datasets remains a significant challenge.

Results
Here, we developed Sample Classification and direct Association Network among Cell clusters (SCANCell) that quantifies the direct association (DA) network of cell clusters. SCANCell was applied to profile inter-cluster interaction patterns of a well-recruited systemic lupus erythematosus (SLE) cohort, including 8 healthy controls, 10 active SLE patients (APs) and 8 remission SLE patients (RPs). SCANCell identified decreased inter-cluster interactions of CD8+ T cells in APs compared with RPs, and enhanced DA of CD8+ T cells after stimulation with immunostimulatory cytokine interleukin-2 in vitro. These discoveries prove that SCANCell can uncover pathology- and drug stimulation-associated inter-cluster interactions, which potentially benefits understanding of pathogenesis and novel therapeutic strategies.

Availability and implementation
The main processing scripts of SCNACell are available at https://github.com/Lxc417/SCANCell. Other codes for the following data statistics are available from the corresponding author upon request.

Supplementary information
Supplementary data are available at Bioinformatics online.