bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting protein content of silage maize using remotely sensed multispectral imagery and proximal leaf sensing
Authors: Bagheri Nikrooz , Rahimi Jahangirlou Maryam , Jaberi Aghdam Mehryar
Published: November 2022

Timely estimation of silage maize protein provides an effective decision to adapt optimized strategies for nitrogen fertilizer management and also harvesting time for farmers. So, this research aimed to investigate whether using vegetative indices (VIs) derived from UAV remotely sensed multispectral (with 520–900 nm wavelengths) imagery and also Soil Plant Analysis Development (SPAD) greenness index can be used to detect the leaf protein concentration (LPC) of silage maize, as a function of various nitrogen rates (0, 50, 100, and 150% of recommended dosage). Results of principal component analysis (PCA) suggested that LPC was highly correlated with leaf greenness index in all developmental stages. In addition, LPC was highly correlated with most of the VIs investigated. A PCA clustering showed the meaningful pattern of N rates. Higher LPC values, VIs, and greenness index were more concentrated in the higher nitrogen (N100% and N150%) sectors. Nitrogen Reflectance Index (NRI) was identified as the most important VIs to monitor and predict LPC in the silage maize field, showing a strong polynomial relationship with LPC in both eight-leaf collar (V8) (R2 = 0.81, p ≤ 0.01) and tasseling (VT) (R2 = 0.98, p ≤ 0.001) stages. In addition, among VIs, the Normalized Difference Vegetation Index (NDVI) demonstrated a significant linear regression relationship with LPC (R2 = 0.80, p ≤ 0.01) in the VT. Findings suggested the high potential of VIs extracted by UAV-taken multispectral imagery and also SPAD proximal sensing to help farmers rapidly diagnose LPC in silage maize, in line with the objectives of precision farming.
Female sterilisation in India: Examining the role of women’s own decision making and information given to client
Authors: Jana Arjun , Shekhar Chander
Published: November 2022

India has a very high prevalence of female sterilisation compared to other countries in the world, with a prevailing situation of very low level of information about contraceptive options given to women. It is well established in demographic research that, there exists a strong association between knowledge of contraceptive methods and type of contraception chosen. Present study uses data from 3 consecutive rounds of National Family Health Survey (3, 4 & 5). The sample contains currently married women who started using the current method 5 years prior to each round of survey. Multilevel Logistic Regression and Fairlie Decomposition Model are used to analyse the effect of information given to respondents and decision-making power regarding contraceptive methods on choice of female sterilisation. Women, who are informed about available methods, have lower chance (45.8%, 37.5% & 40% for NFHS 3, 4 & 5 respectively) to opt for sterilisation after controlling all other factors. If woman is the sole decision maker for contraceptive choice, the chance of sterilisation reduces than cases where decision is taken only by husband or jointly. Information about other methods also contributes towards reducing the chance of female sterilisation over the time. Information about contraceptive methods is found to be a major factor in controlling choice of temporary or permanent method. Thus, major focus for the policy makers should be to make information regarding contraceptives more accessible for women.
Freestyling in war and peace: rap and transitional justice in Colombia
Authors: Quishpe Rafael , Escobar Samuel Augusto , Soto Juan Francisco
Published: November 2022

Rap, as with other musical genres, can contain narratives about Colombia's armed conflict. Members of armed groups, such as the Fuerzas Armadas Revolucionarias de Colombia – Ejército del Pueblo (‘Revolutionary Armed Forces of Colombia – People's Army’; FARC-EP), and civilians have used rap as a means of expressing war-related issues and their causes and consequences. Following the signing of the peace agreement with the FARC-EP in 2016, Colombia's new transitional justice system mainly has focused on a restorative rationale rather than a retributive one. Transitional justice, as a set of mechanisms and processes designed to overcome a violent past, demands peace-building narratives that protect the memory of past horrors while setting the stage for reconciliation. This article analyses the interplay of transitional justice and rap from the personal experiences, perspectives and lyrics of two former combatants and two groups from civil society that rap based in Bogotá, other cities and rural municipalities. These cases provide insight into how rap can relate to transitional justice, sometimes acting as a supportive tool for its goals and sometimes by providing a counter-narrative.
Existential Suffering as a Legitimization of Euthanasia
Authors: Doomen Jasper
Published: November 2022

Several countries have legalized euthanasia on the basis of medically diagnosable suffering over the last decennial; the criteria to which they adhere differ. The topic of this article is euthanasia on the basis of existential suffering. This article presents a recent proposal to legalize euthanasia for people who experience such suffering and then discusses the issue of what the value of life may be, and whether the standard that life is normally something positive should be accepted. This provides the foundation to answer the question of whether euthanasia on the basis of existential suffering should be allowed.
Internal reference genes with the potential for normalizing quantitative PCR results for oral fluid specimens
Authors: Cheng Ting-Yu , Zimmerman Jeffrey J. , Giménez-Lirola Luis G.
Published: November 2022

In basic research, testing of oral fluid specimens by real-time quantitative polymerase chain reaction (qPCR) has been used to evaluate changes in gene expression levels following experimental treatments. In diagnostic medicine, qPCR has been used to detect DNA/RNA transcripts indicative of bacterial or viral infections. Normalization of qPCR using endogenous and exogenous reference genes is a well-established strategy for ensuring result comparability by controlling sample-to-sample variation introduced during sampling, storage, and qPCR testing. In this review, the majority of recent publications in human (n= 136) and veterinary (n= 179) medicine did not describe the use of internal reference genes in qPCRs for oral fluid specimens (52.9% animal studies; 57.0% human studies). However, the use of endogenous reference genes has not been fully explored or validated for oral fluid specimens. The lack of valid internal reference genes inherent to the oral fluid matrix will continue to hamper the reliability, reproducibility, and generalizability of oral fluid qPCR assays until this issue is addressed.
Mit dem Masterstudium in Pflege zum Psychiatric Mental Health Nurse Practitioner
Authors: Fischer Susan , Wolfensberger Peter
Published: November 2022

Zusammenfassung. Advanced Practice bezeichnet die erweiterte klinische Praxis von Gesundheitsfachpersonen, die sie sich im Rahmen eines Masterstudiums an einer Fachhochschule oder an einer Universität in einem Fachgebiet spezialisieren. Das bisher generalistisch ausgerichtete Masterstudium der schweizerischen Fachhochschulen erfährt einen Wandel. Neue Vertiefungsrichtungen wie die „Psychiatric Mental Health Nurse Practitioner“ stärken die Kompetenzentwicklung und verändern das Tätigkeitsfeld in der Pflegepraxis.
In die Lehre integrierte Kommunikationstrainings
Authors: Watzek Dörte , Scura Ninetta , Robert Sibylle Matt , Bähler Gisela , Weishaupt Esther , Düvel Angela
Published: November 2022

Zusammenfassung. Gesprächsführung ist im klinischen Alltag einer der wesentlichen sogenannten weichen Faktoren, die Angehörige aller Gesundheitsberufe gut beherrschen sollten. Die Berner Fachhochschule, Departement Gesundheit baut seit Jahren auf Kommunikationstrainings mit professionellen Schauspieler_innen. Ehemalige Studierende wurden danach gefragt, wie sie im Rückblick aus dem Praxisalltag diese Lehrform bewerten.
Fortbildung – just in time
Authors: Krüger Lars , Mannebach Thomas , Luderer Christiane
Published: November 2022

Zusammenfassung. Fortbildungen für Pflegende gehören zum Berufsalltag. Die Autorenschaft geht zunächst der Frage nach, welche Formen der Fortbildung es gibt. Anschließend wird Bezug auf die Erkenntnisse einer Beobachtungsstudie zur zeitlichen Verortung von Kurzfortbildungen für Pflegende auf der Intensivstation genommen. Im Mittelpunkt stehen dabei die Bewertungen ausgewählter Veranstaltungen innerhalb der Studie.
Seismic Constraints on Crustal and Uppermost Mantle Structure Beneath the Hawaiian Swell: Implications for Plume‐Lithosphere Interactions
Authors: Le Ba Manh , Yang Ting , Morgan Jason P.
Published: November 2022

We infer the lithospheric structure beneath the Hawaiian Swell based on a joint inversion of ambient noise and teleseismic Rayleigh waves collected during the PLUME experiment. These combined datasets let us use Rayleigh waves with a period range of 8–50 s that provides imaging resolution for the shallow lithosphere and constrains interactions between the upwelling plume and migrating plate. We find an elongated low‐velocity anomaly beneath the lithosphere along the island chain that connects to the plume conduit, consistent with the melting region associated with a restite hotspot swell root that has mechanically eroded the base of its overlying lithosphere. It could also be consistent with a plume refracted by the overriding plate motion if the plume could manage to deeply erode the lithospheric base, as only a more viscous restite root is seen to do in thermomechanical experiments. There is also a low‐velocity body beneath the North Arch that coincides with the location of recent off‐chain volcanic fields discovered there. Its location relative to the Molokai Fracture Zone (MFZ) supports the concept that swell‐root material has preferentially spread beneath the younger side of the MFZ. We also find a clear low‐velocity anomaly associated with the uppermost ∼50 km of the fracture zone lithosphere. The relatively well‐resolved shallow lithospheric structure determined here allows us to estimate the volumes of underplating and the total flux of the rising plume material that is added beneath the Hawaiian lithosphere, which we constrain to be in the range of 0.5–0.6 km3/yr.
Coupling Crustal‐Scale Rift Architecture With Passive Margin Salt Tectonics: A Geodynamic Modeling Approach
Authors: Pichel Leonardo M. , Huismans Ritske S. , Gawthorpe Robert , Faleide Jan Inge , Theunissen Thomas
Published: November 2022

Continental rifted margins are often associated with widespread, thick evaporite (i.e., salt) deposits and pronounced salt tectonics. The majority of salt basins formed during the latest stages of rifting, prior to continental breakup. We use 2D thermo‐mechanical finite element modeling of lithospheric extension to investigate the interplay between rifted margin architecture, late syn‐rift salt deposition, and post‐rift salt tectonics. We focus on four different types of continental margins: (a) narrow, (b) intermediate, (c) wide, and (d) ultra‐wide margins. We evaluate the: (a) interplay between laterally variable syn‐rift extension, salt deposition and salt tectonics, (b) influence of syn‐rift basin architecture on post‐rift salt flow, (c) spatial and temporal distribution of salt‐related structural domains, and (d) contrasting styles of salt tectonics for different margin types. Narrow and intermediate margins form partially isolated salt basins associated with prominent base‐salt relief, limited translation but significant diapirism, and minibasin development. Wide and ultra‐wide margins form wide salt basins with subtle base‐salt relief that results in significant seaward salt expulsion and overburden translation. These wide margins demonstrate significant updip extension with the development of post‐rift normal faults and rollovers, mid‐margin translation associated with complex diapirism and downdip diapir shortening. All margins contain a distal salt nappe that varies in width and complexity. We also test the effect of different salt viscosities, relative post‐salt progradation rates, and pre‐salt sediment thicknesses. The results are comparable to several examples of salt‐bearing rifted margins and improve our understanding of their dynamics and on the controls on their salt tectonics variability.
Identification and interrogation of the gene regulatory network of CEBPA-double mutant acute myeloid leukemia
Authors: Adamo Assunta , Chin Paulynn , Keane Peter , Assi Salam A. , Potluri Sandeep , Kellaway Sophie G. , Coleman Daniel , Ames Luke , Ptasinska Anetta , Delwel H. Ruud , Cockerill Peter N. , Bonifer Constanze
Published: November 2022

Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy caused by mutations in genes encoding transcriptional and epigenetic regulators together with signaling genes. It is characterized by a disturbance of differentiation and abnormal proliferation of hematopoietic progenitors. We have previously shown that each AML subtype establishes its own core gene regulatory network (GRN), consisting of transcription factors binding to their target genes and imposing a specific gene expression pattern that is required for AML maintenance. In this study, we integrate gene expression, open chromatin and ChIP data with promoter-capture Hi-C data to define a refined core GRN common to all patients with CEBPA-double mutant (CEBPAN/C) AML. These mutations disrupt the structure of a major regulator of myelopoiesis. We identify the binding sites of mutated C/EBPα proteins in primary cells, we show that C/EBPα, AP-1 factors and RUNX1 colocalize and are required for AML maintenance, and we employ single cell experiments to link important network nodes to the specific differentiation trajectory from leukemic stem to blast cells. Taken together, our study provides an important resource which predicts the specific therapeutic vulnerabilities of this AML subtype in human cells.
Ablation of sphingosine kinase 2 suppresses fatty liver-associated hepatocellular carcinoma via downregulation of ceramide transfer protein
Authors: Liu Xin Tracy , Chung Long Hoa , Liu Da , Chen Jinbiao , Huang Yu , Teo Jonathan D. , Han Xingxing Daisy , Zhao Yinan , Guan Fiona H. X. , Tran Collin , Lee Jun Yup , Couttas Timothy A. , Liu Ken , McCaughan Geoffery W. , Gorrell Mark D. , Don Anthony S. , Zhang Shubiao , Qi Yanfei
Published: November 2022

Hepatocellular carcinoma (HCC) accounts for 90% of primary liver cancer, the third leading cause of cancer-associated death worldwide. With the increasing prevalence of metabolic conditions, non-alcoholic fatty liver disease (NAFLD) is emerging as the fastest-growing HCC risk factor, and it imposes an additional layer of difficulty in HCC management. Dysregulated hepatic lipids are generally believed to constitute a deleterious environment cultivating the development of NAFLD-associated HCC. However, exactly which lipids or lipid regulators drive this process remains elusive. We report herein that sphingosine kinase 2 (SphK2), a key sphingolipid metabolic enzyme, plays a critical role in NAFLD-associated HCC. Ablation of Sphk2 suppressed HCC development in NAFLD livers via inhibition of hepatocyte proliferation both in vivo and in vitro. Mechanistically, SphK2 deficiency led to downregulation of ceramide transfer protein (CERT) that, in turn, decreased the ratio of pro-cancer sphingomyelin (SM) to anti-cancer ceramide. Overexpression of CERT restored hepatocyte proliferation, colony growth and cell cycle progression. In conclusion, the current study demonstrates that SphK2 is an essential lipid regulator in NAFLD-associated HCC, providing experimental evidence to support clinical trials of SphK2 inhibitors as systemic therapies against HCC.
Sensory nerves enhance triple-negative breast cancer invasion and metastasis via the axon guidance molecule PlexinB3
Authors: Le Thanh T. , Payne Samantha L. , Buckwald Maia N. , Hayes Lily A. , Parker Savannah R. , Burge Christopher B. , Oudin Madeleine J.
Published: November 2022

In breast cancer, nerve presence has been correlated with more invasive disease and worse prognosis, yet the mechanisms by which different types of peripheral nerves drive tumor progression remain poorly understood. In this study, we identified sensory nerves as more abundant in human triple-negative breast cancer (TNBC) tumors. Co-injection of sensory neurons isolated from the dorsal root ganglia (DRG) of adult female mice with human TNBC cells in immunocompromised mice increased the number of lung metastases. Direct in vitro co-culture of human TNBC cells with the dorsal root ganglia (DRG) of adult female mice revealed that TNBC cells adhere to sensory neuron fibers leading to an increase in migration speed. Species-specific RNA sequencing revealed that co-culture of TNBC cells with sensory nerves upregulates the expression of genes associated with cell migration and adhesion in cancer cells. We demonstrated that lack of the semaphorin receptor PlexinB3 in cancer cells attenuate their adhesion to and migration on sensory nerves. Together, our results identify a mechanism by which nerves contribute to breast cancer migration and metastasis by inducing a shift in TNBC cell gene expression and support the rationale for disrupting neuron-cancer cell interactions to target metastasis.
Detection of microsatellite instability high (MSI-H) status by targeted plasma-based genotyping in metastatic breast cancer
Authors: Vidula Neelima , Lipman Andrew , Kato Shumei , Weipert Caroline , Hesler Katherine , Azzi Georges , Elkhanany Ahmed , Juric Dejan , Rodriguez Estelamari , Faulkner Colleen , Makhlouf Paul , Price Kristin , O’Shaughnessy Joyce , Bardia Aditya
Published: November 2022

We evaluate microsatellite instability-high (MSI-H) status with cell-free DNA (cfDNA) in metastatic breast cancer (MBC) and the association with clinico-genomic characteristics. Patients with MSI-H in cfDNA (Guardant360®, 74 gene next-generation sequencing (NGS) with MBC are identified. We conduct a retrospective review. The median number of alterations and a median maximum mutant allelic fraction (MAF) in MSI-H and non-MSI-H cohorts are compared with Mann–Whitney U-test. Of 6718 patients with breast cancer with ≥1 plasma NGS alteration, 42 (0.63%) have MSI-H. A median number of genomic alterations per sample is 11 in MSI-H vs. 3 in non-MSI-H (Mann–Whitney U-test p < 0.0001) and the median maximum MAF is 16.8% in MSI-H vs. 2.6% in non-MSI-H (Mann–Whitney U-test p < 0.0001). The co-existing genomic landscape is heterogeneous. The median response duration for seven patients receiving immunotherapy is 92 days (range 29–273 days). CfDNA can identify MSI-H in MBC. Research is needed to validate immunotherapy usage in cfDNA-detected MSI-H MBC.
A multicenter study of genetic testing for Parkinson’s disease in the clinical setting
Authors: Kovanda Anja , Rački Valentino , Bergant Gaber , Georgiev Dejan , Flisar Dušan , Papić Eliša , Brankovic Marija , Jankovic Milena , Svetel Marina , Teran Nataša , Maver Aleš , Kostic Vladimir S. , Novakovic Ivana , Pirtošek Zvezdan , Rakuša Martin , Vuletić Vladimira , Peterlin Borut
Published: November 2022

Parkinson’s disease (PD) guidelines lack clear criteria for genetic evaluation. We assessed the yield and rationale of genetic testing for PD in a routine clinical setting on a multicenter cohort of 149 early-onset and familial patients by exome sequencing and semi-quantitative multiplex ligation-dependent probe amplification of evidence-based PD-associated gene panel. We show that genetic testing for PD should be considered for both early-onset and familial patients alike, and a clinical yield of about 10% in the Caucasian population can be expected.
Coherent control of electron spin qubits in silicon using a global field
Authors: Vahapoglu E. , Slack-Smith J. P. , Leon R. C. C. , Lim W. H. , Hudson F. E. , Day T. , Cifuentes J. D. , Tanttu T. , Yang C. H. , Saraiva A. , Abrosimov N. V. , Pohl H.-J. , Thewalt M. L. W. , Laucht A. , Dzurak A. S. , Pla J. J.
Published: November 2022

Silicon spin qubits promise to leverage the extraordinary progress in silicon nanoelectronic device fabrication over the past half century to deliver large-scale quantum processors. Despite the scalability advantage of using silicon technology, realising a quantum computer with the millions of qubits required to run some of the most demanding quantum algorithms poses several outstanding challenges, including how to control many qubits simultaneously. Recently, compact 3D microwave dielectric resonators were proposed as a way to deliver the magnetic fields for spin qubit control across an entire quantum chip using only a single microwave source. Although spin resonance of individual electrons in the globally applied microwave field was demonstrated, the spins were controlled incoherently. Here we report coherent Rabi oscillations of single electron spin qubits in a planar SiMOS quantum dot device using a global magnetic field generated off-chip. The observation of coherent qubit control driven by a dielectric resonator establishes a credible pathway to achieving large-scale control in a spin-based quantum computer.
Optimisation of electron spin qubits in electrically driven multi-donor quantum dots
Authors: Sarkar Abhikbrata , Hochstetter Joel , Kha Allen , Hu Xuedong , Simmons Michelle Y. , Rahman Rajib , Culcer Dimitrie
Published: November 2022

Multi-donor quantum dots have been at the forefront of recent progress in Si-based quantum computation. Among them, 2P: 1P spin qubits have a built-in dipole moment, making them ideal for electron dipole spin resonance (EDSR) using the donor hyperfine interaction, and thus all-electrical spin operation. We report fast EDSR, with Tπ ~ 10 − 50 ns and a Rabi ratio (T1/Tπ) ~ 106. The fastest EDSR time Tπ occurs when the 2P: 1P axis is ∥ [111], while the best Rabi ratio occurs when it is ∥ [100]. Sensitivity to random telegraph noise due to nearby charge defects depends strongly on the location of the nearby defects. The qubit is robust against 1/f noise provided it is operated away from the charge anti-crossing. Entanglement via exchange is several orders of magnitude faster than dipole-dipole coupling. These findings pave the way towards fast, low-power, coherent and scalable donor dot-based quantum computing.
Phenotypic trait variation in a long-term multisite common garden experiment of Scots pine in Scotland
Authors: Beaton Joan , Perry Annika , Cottrell Joan , Iason Glenn , Stockan Jenni , Cavers Stephen
Published: November 2022

Multisite common garden experiments, exposing common pools of genetic diversity to a range of environments, allow quantification of plastic and genetic components of trait variation. For tree species, such studies must be long term as they typically only express mature traits after many years. As well as evaluating standing genetic diversity, these experiments provide an ongoing test of genetic variation against changing environmental conditions and form a vital resource for understanding how species respond to abiotic and biotic variation. Finally, quantitative assessments of phenotypic variation are essential to pair with rapidly accumulating genomic data to advance understanding of the genetic basis of trait variation, and its interaction with climatic change. We describe a multisite, population-progeny, common garden experiment of the economically and ecologically important tree species, Scots pine, collected from across its native range in Scotland and grown in three contrasting environments. Phenotypic traits, including height, stem diameter and budburst were measured over 14 growing seasons from nursery to field site. The datasets presented have a wide range of applications.
Whole-embryonic identification of maternal microchimeric cell types in mouse using single-cell RNA sequencing
Authors: Fujimoto Kana , Nakajima Akira , Hori Shohei , Tanaka Yumiko , Shirasaki Yoshitaka , Uemura Sotaro , Irie Naoki
Published: November 2022

Even though the mother and the fetus of placental mammals are immunologically non-self with respect to one other, mutual exchange of small numbers of cells between them is known to occur. Maternal cells entering the fetus, called maternal microchimeric cells (MMc cells), are thought to be involved in different physiological phenomena, such as establishing immune tolerance, tissue repair, and the pathogenesis or deterioration of some inflammatory diseases and congenital malformations. While specific MMc cell types have been reported as associated with these phenomena, the contribution of MMc cells to these different outcomes remains unknown. As one possibility, we hypothesized that different embryos have differing repertoires of MMc cell types, leading to or biasing embryos toward different fates. To date, no studies have succeeded in identifying the MMc cell type repertoire of a single embryo. Accordingly, here, we isolated MMc cells from whole mouse embryos, determined their types, and analyzed their MMc cell type variability. By combining our previously established, whole-embryonic MMc isolation method with single-cell RNA sequencing, we successfully estimated the cell type repertoires of MMc cells isolated from 26 mouse embryos. The majority of MMc cells were immune-related cells, such as myeloid cells and granulocytes. We also detected stem cell-like MMc cells expressing proliferation marker genes and terminally differentiated cells. As hypothesized, we noted statistically significant inter-individual variation in the proportion of immune-related cells in the different embryos. We here successfully estimated MMc cell types in individual whole mouse embryos. The proportion of immune-related cells significantly differed among the individual embryos, suggesting that the variations are one of the potential mechanisms underlying the differing MMc-related physiological phenomena in offspring. These findings provide insight into cell-level epigenetics by maternal cells.
Grafting of short elastin-like peptides using an electric field
Authors: Pramounmat Nuttanit , Asaei Sogol , Hostert Jacob D. , Young Kathleen , von Recum Horst A. , Renner Julie N.
Published: November 2022

Surface-grafted elastin has found a wide range of uses such as sensing, tissue engineering and capture/release applications because of its ability to undergo stimuli-responsive phase transition. While various methods exist to control surface grafting in general, it is still difficult to control orientation as attachment occurs. This study investigates using an electric field as a new approach to control the surface-grafting of short elastin-like polypeptide (ELP). Characterization of ELP grafting to gold via quartz crystal microbalance with dissipation, atomic force microscopy and temperature ramping experiments revealed that the charge/hydrophobicity of the peptides, rearrangement kinetics and an applied electric field impacted the grafted morphology of ELP. Specifically, an ELP with a negative charge on the opposite end of the surface-binding moiety assembled in a more upright orientation, and a sufficient electric field pushed the charge away from the surface compared to when the same peptide was assembled in no electric field. In addition, this study demonstrated that assembling charged ELP in an applied electric field impacts transition behavior. Overall, this study reveals new strategies for achieving desirable and predictable surface properties of surface-bound ELP.
The use of biological amniotic membranes in the treatment of recurrent macular holes
Authors: Qiao Gang , Xie Lijun , Zou Qiangxing , He Chunmei , Zhang Xiaojuan , Tang Ziyan , Zou Shuai , Cao Kui
Published: November 2022

To evaluate the clinical therapeutic effects of a technique in which biological amniotic membranes (bAMs) are used in the treatment of patients with recurrent macular holes. In this prospective nonrandomized case series study, 23 eyes of 23 patients with recurrent macular holes who had already undergone surgery with pars plana vitrectomy with internal limiting membrane peeling were evaluated. In the surgery, a bAM was used to cover the macular area, and C3F8 tamponade was performed on these patients. Phacoemulsification combined with intraocular lens implantation was performed simultaneously in patients who had cataracts. Patients were followed up for at least half a year. The main outcomes were whether the macular hole closed, the morphological changes in the macular graft, the best-corrected visual acuity, intraocular pressure (IOP) and other indicators. In all eyes, the recurrent macular holes were closed. Two cases (8.69%, 2/23) had bAM shifting half a month after surgery, and these patients underwent a second surgery to adjust the position of the bAM and perform C3F8 tamponade. In the 6-month follow-up, 21 patients (91.30%, 21/23) had improved visual acuity (VA), and 2 patients (8.69%, 2/23) had no change in VA. The mean VA increased from 1.73 ± 0.32 before surgery to 1.12 ± 0.42 after surgery (t = 10.63, P = 0.00 < 0.01), and the mean IOP decreased from 22.13 ± 5.56 before surgery to 17.23 ± 1.71 after surgery (t = 5.14, P = 0.00 < 0.01). No serious complications occurred in any of the cases. The technique of using a biological amniotic membrane can be an effective treatment for patients with recurrent macular holes.
Deciphering sex-specific miRNAs as heat-recorders in zebrafish
Authors: van Gelderen Tosca A. , Montfort Jérôme , Álvarez-Dios José Antonio , Thermes Violette , Piferrer Francesc , Bobe Julien , Ribas Laia
Published: November 2022

In the last decade, a plethora of microRNAs (miRNAs) has been reported in a wide variety of physiological processes, including reproduction, in many aquatic organisms. However, miRNAome alterations occurred by environmental cues due to water temperature increment have not yet been elucidated. With the aim to identify epigenetic regulations mediated by miRNAs in the gonads in a climate change scenario, the animal model zebrafish (Danio rerio) were subjected to high temperatures during sex differentiation, a treatment that results in male-skewed sex ratios in the adulthood. Once the fish reached adulthood, gonads were sequenced by high-throughput technologies and a total of 23 and 1 differentially expressed miRNAs in ovaries and testes, respectively, were identified two months after the heat treatment. Most of these heat-recorder miRNAs were involved in human sex-related cancer and about 400 predicted-target genes were obtained, some with reproduction-related functions. Their synteny in the zebrafish genome was, for more than half of the predicted target genes, in the chromosomes 7, 2, 4, 3 and 11 in the ovaries, chromosome 4 being the place where the sex-associated-region (sar) is localized in wild zebrafish. Further, spatial localization in the gonads of two selected heat-recorder miRNAs (miR-122-5p and miR-146-5p) showed exclusive expression in the ovarian germ cells. The present study expands the catalog of sex-specific miRNAs and deciphers, for the first time, thermosensitive miRNAs in the zebrafish gonads that might be used as potential epimarkers to predict environmental past events.
Implication of EEG theta/alpha and theta/beta ratio in Alzheimer’s and Lewy body disease
Authors: Baik Kyoungwon , Jung Jin Ho , Jeong Seong Ho , Chung Seok Jong , Yoo Han Soo , Lee Phil Hyu , Sohn Young H. , Kang Seung Wan , Ye Byoung Seok
Published: November 2022

We evaluated the patterns of quantitative electroencephalography (EEG) in patients with Alzheimer’s disease (AD), Lewy body disease (LBD), and mixed disease. Sixteen patients with AD, 38 with LBD, 20 with mixed disease, and 17 control participants were recruited and underwent EEG. The theta/alpha ratio and theta/beta ratio were measured. The relationship of the log-transformed theta/alpha ratio (TAR) and theta/beta ratio (TBR) with the disease group, the presence of AD and LBD, and clinical symptoms were evaluated. Participants in the LBD and mixed disease groups had higher TBR in all lobes except for occipital lobe than those in the control group. The presence of LBD was independently associated with higher TBR in all lobes and higher central and parietal TAR, while the presence of AD was not. Among cognitively impaired patients, higher TAR was associated with the language, memory, and visuospatial dysfunction, while higher TBR was associated with the memory and frontal/executive dysfunction. Increased TBR in all lobar regions and temporal TAR were associated with the hallucinations, while cognitive fluctuations and the severity of Parkinsonism were not. Increased TBR could be a biomarker for LBD, independent of AD, while the presence of mixed disease could be reflected as increased TAR.
Learning complex dependency structure of gene regulatory networks from high dimensional microarray data with Gaussian Bayesian networks
Authors: Graafland Catharina E. , Gutiérrez José M.
Published: November 2022

Reconstruction of Gene Regulatory Networks (GRNs) of gene expression data with Probabilistic Network Models (PNMs) is an open problem. Gene expression datasets consist of thousand of genes with relatively small sample sizes (i.e. are large-p-small-n). Moreover, dependencies of various orders coexist in the datasets. On the one hand transcription factor encoding genes act like hubs and regulate target genes, on the other hand target genes show local dependencies. In the field of Undirected Network Models (UNMs)—a subclass of PNMs—the Glasso algorithm has been proposed to deal with high dimensional microarray datasets forcing sparsity. To overcome the problem of the complex structure of interactions, modifications of the default Glasso algorithm have been developed that integrate the expected dependency structure in the UNMs beforehand. In this work we advocate the use of a simple score-based Hill Climbing algorithm (HC) that learns Gaussian Bayesian networks leaning on directed acyclic graphs. We compare HC with Glasso and variants in the UNM framework based on their capability to reconstruct GRNs from microarray data from the benchmarking synthetic dataset from the DREAM5 challenge and from real-world data from theEscherichia coligenome. We conclude that dependencies in complex data are learned best by the HC algorithm, presenting them most accurately and efficiently, simultaneously modelling strong local and weaker but significant global connections coexisting in the gene expression dataset. The HC algorithm adapts intrinsically to the complex dependency structure of the dataset, without forcing a specific structure in advance.
Environmental pathways affecting gene expression (E.PAGE) as an R package to predict gene–environment associations
Authors: Muralidharan Sachin , Ali Sarah , Yang Lilin , Badshah Joshua , Zahir Syeda Farah , Ali Rubbiya A. , Chandra Janin , Frazer Ian H. , Thomas Ranjeny , Mehdi Ahmed M.
Published: November 2022

The purpose of this study is to manually and semi-automatically curate a database and develop an R package that will act as a comprehensive resource to understand how biological processes are dysregulated due to interactions with environmental factors. The initial database search run on the Gene Expression Omnibus and the Molecular Signature Database retrieved a total of 90,018 articles. After title and abstract screening against pre-set criteria, a total of 237 datasets were selected and 522 gene modules were manually annotated. We then curated a database containing four environmental factors, cigarette smoking, diet, infections and toxic chemicals, along with a total of 25,789 genes that had an association with one or more of gene modules. The database and statistical analysis package was then tested with the differentially expressed genes obtained from the published literature related to type 1 diabetes, rheumatoid arthritis, small cell lung cancer, COVID-19, cobalt exposure and smoking. On testing, we uncovered statistically enriched biological processes, which revealed pathways associated with environmental factors and the genes. The curated database and enrichment tool are available as R packages at https://github.com/AhmedMehdiLab/E.PATH and https://github.com/AhmedMehdiLab/E.PAGE respectively.
Automated whole slide image analysis for a translational quantification of liver fibrosis
Authors: Serdjebi Cindy , Bertotti Karine , Huang Pinzhu , Wei Guangyan , Skelton-Badlani Disha , Leclercq Isabelle A. , Barbes Damien , Lepoivre Bastien , Popov Yury V. , Julé Yvon
Published: November 2022

Current literature highlights the need for precise histological quantitative assessment of fibrosis which cannot be achieved by conventional scoring systems, inherent to their discontinuous values and reader-dependent variability. Here we used an automated image analysis software to measure fibrosis deposition in two relevant preclinical models of liver fibrosis, and established correlation with other quantitative fibrosis descriptors. Longitudinal quantification of liver fibrosis was carried out during progression of post-necrotic (CCl4-induced) and metabolic (HF-CDAA feeding) models of chronic liver disease in mice. Whole slide images of picrosirius red-stained liver sections were analyzed using a fully automated, unsupervised software. Fibrosis was characterized by a significant increase of collagen proportionate area (CPA) at weeks 3 (CCl4) and 8 (HF-CDAA) with a progressive increase up to week 18 and 24, respectively. CPA was compared to collagen content assessed biochemically by hydroxyproline assay (HYP) and by standard histological staging systems. CPA showed a high correlation with HYP content for CCl4 (r = 0.8268) and HF-CDAA (r = 0.6799) models. High correlations were also found with Ishak score or its modified version (r = 0.9705) for CCl4 and HF-CDAA (r = 0.9062) as well as with NASH CRN for HF-CDAA (r = 0.7937). Such correlations support the use of automated digital analysis as a reliable tool to evaluate the dynamics of liver fibrosis and efficacy of antifibrotic drug candidates in preclinical models.
Developmental trajectories of eye movements in oral and silent reading for beginning readers: a longitudinal investigation
Authors: Kim Young-Suk Grace , Little Callie , Petscher Yaacov , Vorstius Christian
Published: November 2022

Eye movements provide a sensitive window into cognitive processing during reading. In the present study, we investigated beginning readers’ longitudinal changes in temporal and spatial measures of eye movements during oral versus silent reading, the extent to which variation in eye movements is attributable to individual differences and text differences, and the functional form of growth trajectories of eye-movement variables. Data were from 363 English-speaking children (52% male; 59.8% White) in the US who were followed longitudinally from Grade 1 to Grade 3. Results showed a rapid decrease in temporal eye-movement measures (e.g., first fixation) and an increase in spatial eye-movement measures (initial landing position) in both oral and silent reading. The majority of variance in eye movements was attributable to individual differences whereas some variance in initial landing position was due to text differences. Most eye-movement measures had nonlinear growth trajectories where fast development tapered off near the end of Grade 3 while initial fixation count and total gaze count in silent reading had a linear growth trajectory. The findings provide a first large-scale look into the developmental progression of eye movements during oral and silent reading during a critical period when reading skills rapidly develop.
The influence of bone marrow edema for the assessment of the boundaries of necrotic lesions in patients with osteonecrosis of the femoral head
Authors: Ikemura Satoshi , Motomura Goro , Yamaguchi Ryosuke , Utsunomiya Takeshi , Hamai Satoshi , Fujii Masanori , kawahara Shinya , Sato Taishi , Hara Daisuke , shiomoto Kyohei , Yamamoto Takuaki , Nakashima Yasuharu
Published: November 2022

This study aimed to investigate the influence of bone marrow edema (BME) for the assessment of the boundaries of necrotic lesions using unenhanced and contrast-enhanced (CE) magnetic resonance (MR) images in patients with osteonecrosis of the femoral head (ONFH). We retrospectively reviewed 72 consecutive hips in 55 patients of ONFH that were Association Research Circulation Osseous (ARCO) stage III or higher and underwent both unenhanced and contrast-enhanced MR imaging between January 2005 and February 2016. The degree of extension of BMEs, and the boundaries of the necrotic lesions were compared using unenhanced and CE MR images on both mid coronal and mid oblique-axial slices. Forty-two percent of the coronal T1 images, 40% of the coronal fat-saturated T2 images, and 48% of the oblique-axial T1 images showed differences in the boundaries of necrotic lesion, by comparison with those of CET1-weighted MR images. The boundaries of necrotic lesions were clearly detected in all hips on CE coronal slices and 97% of all hips on CE oblique-axial slices. The BME grade in the difference group was significantly higher than in the non-difference group on the coronal plane (P = 0.0058). There were significant differences between the BME grade and duration from the onset of hip pain to MR imaging examination. Multivariate analyses revealed that the duration from the onset to MR imaging examination in both coronal (P = 0.0008) and oblique-axial slices (P = 0.0143) were independently associated with differences in the boundary of necrotic lesion between T1 and CET1-weighted MR images. Our findings suggest that unenhanced MR image may be insufficient for a precise assessment of the boundaries of the necrotic lesions for ONFH cases in the early phase of subchondral collapse due to the diffuse BME.
Insights from ozone and particulate matter pollution control in New York City applied to Beijing
Authors: Zhang Jie , Wang Junfeng , Sun Yele , Li Jingyi , Ninneman Matthew , Ye Jianhuai , Li Ke , Crandall Brian , Mao Jingbo , Xu Weiqi , Schwab Margaret J. , Li Weijun , Ge Xinlei , Chen Mindong , Ying Qi , Zhang Qi , Schwab James J.
Published: November 2022

Strict emission control policies implemented in two megacities of New York City (NYC) and Beijing show impacts on the non-linear relationship of their ozone (O3) and fine particulate matter (PM2.5) during summertime. Here we show these non-linear O3-PM2.5 relationships including a positive linear part reflecting the O3/PM2.5 co-occurrence and a negative power function part reflecting the O3 formation suppression by PM2.5 based on the multiyear surface observations. The control policies targeting sulfur dioxide and PM2.5, then volatile organic compounds and nitrogen oxides, changed the PM2.5 chemical composition which resulted in an increased linear slope that indicates a weaker O3 control effect than occurred for PM2.5. These policies also enhanced the relative PM2.5 suppression effect as shown by an increase in the power function coefficient. Model simulations suggest that regional equal percentage emission reductions for Beijing and other Chinese megacities will be necessary to avoid further increase in the O3/PM2.5 linear slope and continuing occurrences of high levels of ozone.
Cloning the Dirac cones of bilayer graphene to the zone center by selenium adsorption
Authors: Lin Meng-Kai , Zhao Jun , Hlevyack Joseph A. , Chiang T.-C.
Published: November 2022

Dirac cones can foster extraordinary electronic effects, as exemplified by the case of graphene layers. Angle-resolved photoemission reveals that adsorption of selenium (Se) vapor on bilayer graphene creates a symmetric hybrid clone of the Dirac cones at the zone center. A detailed analysis aided by first-principles calculations shows that the adsorbed layer consists of an ordered array of Se8 molecules. The uncovered cloning mechanism illustrates a method to generate electronic features of scientific and technological interests by gentle surface modification via van der Waals adsorption.
Exploring two-dimensional van der Waals heavy-fermion material: Data mining theoretical approach
Authors: Jang Bo Gyu , Lee Changhoon , Zhu Jian-Xin , Shim Ji Hoon
Published: November 2022

The discovery of two-dimensional (2D) van der Waals (vdW) materials often provides interesting playgrounds to explore novel phenomena. One of the missing components in 2D vdW materials is the intrinsic heavy-fermion systems, which can provide an additional degree of freedom to study quantum critical point (QCP), unconventional superconductivity, and emergent phenomena in vdW heterostructures. Here, we investigate 2D vdW heavy-fermion candidates through the database of experimentally known compounds based on dynamical mean-field theory calculation combined with density functional theory (DFT+DMFT). We have found that the Kondo resonance state of CeSiI does not change upon exfoliation and can be easily controlled by strain and surface doping. Our result indicates that CeSiI is an ideal 2D vdW heavy-fermion material and the quantum critical point can be identified by external perturbations.
Representational ethical model calibration
Authors: Carruthers Robert , Straw Isabel , Ruffle James K. , Herron Daniel , Nelson Amy , Bzdok Danilo , Fernandez-Reyes Delmiro , Rees Geraint , Nachev Parashkev
Published: November 2022

Equity is widely held to be fundamental to the ethics of healthcare. In the context of clinical decision-making, it rests on the comparative fidelity of the intelligence – evidence-based or intuitive – guiding the management of each individual patient. Though brought to recent attention by the individuating power of contemporary machine learning, such epistemic equity arises in the context of any decision guidance, whether traditional or innovative. Yet no general framework for its quantification, let alone assurance, currently exists. Here we formulate epistemic equity in terms of model fidelity evaluated over learnt multidimensional representations of identity crafted to maximise the captured diversity of the population, introducing a comprehensive framework forRepresentational Ethical Model Calibration. We demonstrate the use of the framework on large-scale multimodal data from UK Biobank to derive diverse representations of the population, quantify model performance, and institute responsive remediation. We offer our approach as a principled solution to quantifying and assuring epistemic equity in healthcare, with applications across the research, clinical, and regulatory domains.
Disorganized functional architecture of amygdala subregional networks in obsessive-compulsive disorder
Authors: Cao Lingxiao , Li Hailong , Liu Jing , Jiang Jiaxin , Li Bin , Li Xue , Zhang Suming , Gao Yingxue , Liang Kaili , Hu Xinyue , Bao Weijie , Qiu Hui , Lu Lu , Zhang Lianqing , Hu Xinyu , Gong Qiyong , Huang Xiaoqi
Published: November 2022

A precise understanding of amygdala-centered subtle networks may help refine neurocircuitry models of obsessive-compulsive disorder (OCD). We applied connectivity-based parcellation methodology to segment the amygdala based on resting-state fMRI data of 92 medication-free OCD patients without comorbidity and 90 matched healthy controls (HC). The amygdala was parcellated into two subregions corresponding to basolateral amygdala (BLA) and centromedial amygdala (CMA). Amygdala subregional functional connectivity (FC) maps were generated and group differences were evaluated with diagnosis-by-subregion flexible factorial ANOVA. We found significant diagnosis × subregion FC interactions in insula, supplementary motor area (SMA), midcingulate cortex (MCC), superior temporal gyrus (STG) and postcentral gyrus (PCG). In HC, the BLA demonstrated stronger connectivity with above regions compared to CMA, whereas in OCD, the connectivity pattern reversed to stronger CMA connectivity comparing to BLA. Relative to HC, OCD patients exhibited hypoconnectivity between left BLA and left insula, and hyperconnectivity between right CMA and SMA, MCC, insula, STG, and PCG. Moreover, OCD patients showed reduced volume of left BLA and right CMA compared to HC. Our findings characterized disorganized functional architecture of amygdala subregional networks in accordance with structural defects, providing direct evidence regarding the specific role of amygdala subregions in the neurocircuitry models of OCD.