bluuebunny/crossref_metadata_2025_split huggingface dataset:
Roles of two distinct alphasatellites modulating geminivirus pathogenesis
Authors: Kumar Manish , Zarreen Fauzia , Chakraborty Supriya 
Published: December 2021

Abstract
Background
Alphasatellites are small coding DNA satellites frequently associated with a begomovirus/betasatellite complex, where they are known to modulate virulence and symptom development. Two distinct alphasatellites, namely, Cotton leaf curl Multan alphasatellite (CLCuMuA), and Gossypium darwinii symptomless alphasatellite (GDarSLA) associated with Cotton leaf curl Multan virus-India (CLCuMuV-IN) and Ludwigia leaf distortion betasatellite (LuLDB) were found to be associated with yellow mosaic disease of hollyhock (Alcea rosea) plants. In this study, we show that alphasatellites CLCuMuA and GDarSLA attenuate and delay symptom development in Nicotiana benthamiana. The presence of either alphasatellites reduce the accumulation of the helper virus CLCuMuV-IN. However, the levels of the associated betasatellite, LuLDB, remains unchanged. These results suggest that the alphasatellites could contribute to the host defence and understanding their role in disease development is important for developing resistance strategies.

Methods
Tandem repeat constructs of two distinct alphasatellites, namely, CLCuMuA and GDarSLA associated with CLCuMuV-IN and LuLDB were generated. N. benthamiana plants were co-agroinoculated with CLCuMuV and its associated alphasatellites and betasatellite molecules and samples were collected at 7, 14 and 21 days post inoculation (dpi). The viral DNA molecules were quantified in N. benthamiana plants by qPCR. The sequences were analysed using the MEGA-X tool, and a phylogenetic tree was generated. Genetic diversity among the CLCuMuA and GDarSLA was analysed using the DnaSP tool.

Results
We observed a reduction in symptom severity and accumulation of helper virus in the presence of two alphasatellites isolated from naturally infected hollyhock plants. However, no reduction in the accumulation of betasatellite was observed. The phylogenetic and genetic variability study revealed the evolutionary dynamics of these distinct alphasatellites , which could explain the role of hollyhock-associated alphasatellites in plants.

Conclusions
This study provides evidence that alphasatellites have a role in symptom modulation and suppress helper virus replication without any discernible effect on the replication of the associated betasatellite.
Perillaldehyde improves cognitive function in vivo and in vitro by inhibiting neuronal damage via blocking TRPM2/NMDAR pathway
Authors: Qiu Yue , Xue Xian-jun , Liu Geng , Shen Miao-miao , Chao Chun-yan , Zhang Jie , Guo Ya-qi , Niu Qian-qian , Yu Ya-nan , Song Yu-ting , Wang Huan-huan , Wang Shuang-xi , Chen Yu-jing , Jiang Lin-hua , Li Peng , Yin Ya-ling 
Published: December 2021

Abstract
Background
Vascular cognitive dysfunction in patients with vascular dementia (VD) is a kind of severe cognitive dysfunction syndrome caused by cerebrovascular diseases. At present, effective drugs to improve the cognitive function of VD patients still need to be explored. Transient Receptor Potential Melastatin 2 (TRPM2) channel is a nonspecific cation channel that plays a key role in the toxic death of neurons. Perillaldehyde (PAE) has the protective effect of epilepsy and insomnia and other central nervous system diseases. The aim of this study is to explore whether PAE improves cognitive function in VD rats and to investigate the potential mechanisms in vivo and vitro.

Methods
VD rats were induced by bilateral common carotid arteries occlusion (2-vessel occlusion [2VO]) and treated with PAE for 4 weeks. The neuroprotective effects of PAE was subsequently assessed by the Morris water maze, hematoxylin–eosin (HE) staining, Golgi staining, electron microscopy, Neuron-specific nuclear protein (Neu N) staining, and TdT-mediated dUTP nick end labeling (TUNEL) staining. After primary hippocampal neurons were isolated, cell viability was detected by MTT assay and intracellular Ca2+ concentration was detected by calcium imaging assay. The content of Nitriteoxide (NO), Malondialdehyde (MDA) and Superoxide dismutase (SOD) activity in serum of rats were observed by Enzyme Linked Immunosorbent Assay (ELISA). Immunohistochemistry, Western blot, and Confocal laser scanning were used to detect the expression levels of N-methyl-d-asprtate receptor-2B (NR2B) and TRPM2.

Results
The results showed that PAE can improve the number and activity of neurons, increase the length and number of dendrites in hippocampus, decrease the Vv value and PE value of neuronal nucleus and mitochondrial structure significantly, increase the s value and L value in nucleus structure, decrease the s value and L value in mitochondrial structure, and improve the learning and memory ability of rats significantly. And PAE can strengthen the ability of antioxidant stress confirmed by increasing the activity of SOD and reducing the production of MDA. The results of western blot, immunohistochemistry and immunofluorescence showed that PAE could reduce the level of TRPM2 and increase the expression of NR2B.

Conclusions
Taken together, our findings provide evidence that the neuroprotective effects of PAE in VD rats maybe through TRPM2 inhibition and subsequent activation of NMDAR signaling pathway.
CIDER: an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation
Authors: Hu Zhiyuan , Ahmed Ahmed A. , Yau Christopher 
Published: December 2021

AbstractClustering of joint single-cell RNA-Seq (scRNA-Seq) data is often challenged by confounding factors, such as batch effects and biologically relevant variability. Existing batch effect removal methods typically require strong assumptions on the composition of cell populations being near identical across samples. Here, we present CIDER, a meta-clustering workflow based on inter-group similarity measures. We demonstrate that CIDER outperforms other scRNA-Seq clustering methods and integration approaches in both simulated and real datasets. Moreover, we show that CIDER can be used to assess the biological correctness of integration in real datasets, while it does not require the existence of prior cellular annotations.
Cadence discovery: study protocol for a dose-finding and mechanism of action clinical trial of sodium benzoate in people with treatment-refractory schizophrenia
Authors: Baker Andrea , Clarke Lachlan , Donovan Peter , P. J. Ungerer Jacobus , Hartel Gunter , Bruxner George , Cocchi Luca , Gordon Anne , Moudgil Vikas , Robinson Gail , Roy Digant , Sohal Ravinder , Whittle Emma , Scott James G. 
Published: December 2021

Abstract
Background
Schizophrenia is a persistent psychotic disorder often accompanied by severe disability and premature mortality. New pharmacological treatments are urgently needed. Sodium benzoate, a common food preservative holds potential to be an effective, accessible treatment for schizophrenia, though the optimal dosing and mechanism of action of the compound requires further investigation.

Methods
Individuals with persistent treatment-refractory schizophrenia (n=52) will be recruited. Patients will be randomised in a 1:1:1:1 ratio to receive treatment of one of three active doses (1000, 2000 or 4000 mg daily) of sodium benzoate or placebo for 6 weeks duration. The primary outcome measurement is change in the Positive and Negative Syndrome Scale (PANSS) total score. Secondary outcome measurements are PANSS subscales, Global Assessment of Function (GAF), Clinical Global Impression (CGI) and Patient Global Impression (PGI-I). Change in concentrations of peripheral amino acids (D-alanine, L-alanine, D-serine, L-serine, glycine and glutamate), plasma sodium benzoate, plasma catalase, 3-nitrotyrosine, malondialdehyde and high-sensitivity C-reactive protein (hs-CRP) will be determined as tertiary measures.

Discussion
This trial seeks to build upon previous research indicating potential efficacy of sodium benzoate for reduction of symptoms in individuals with treatment-refractory schizophrenia. The trial aims to improve the understanding of the mechanism of action of the compound.

Trial registration
Australian New Zealand Clinical Trials Registry (ANZCTR) ACTRN12621000327886. Registered on 23 March 2021.
Transcranial direct electrical stimulation for hand function in a stroke patient with severe upper limb paralysis due to lenticulostriate artery occlusion: a case report
Authors: Hirayama Koichiro , Fuchigami Takeshi , Morioka Shu 
Published: December 2021

Abstract
Background
Transcranial direct current stimulation, a therapeutic modality to modulate the excitability of injured and uninjured brain hemispheres in stroke patients, is expected to be effective in treating upper limb paralysis. We describe the use of transcranial direct current stimulation to improve the function and frequency of use of the paralyzed hand of a patient with lenticulostriate artery occlusion.

Case presentation
A Japanese man in his fifties developed a left internal hindfoot perforator branch infarction owing to lenticulostriate artery occlusion, and presented with severe right upper and lower limb paralysis. Multiple interventions for the paralyzed hand, primarily robot therapy, did not noticeably change his hand function or frequency of use in daily life. Therefore, transcranial direct current stimulation was used in combination with upper limb functional exercises for 20 minutes a day, five times a week, for 6 weeks. Consequently, scores for the hand items of the Fugl–Meyer Assessment of the upper extremities improved, and pain and subluxation around the shoulder joint were reduced. Furthermore, the frequency of use and the quality of movement of the paralyzed hand were improved.

Conclusions
Upper limb functional training and transcranial direct current stimulation improved the function and frequency of use of the paralyzed hand in a stroke patient with severe upper limb paralysis, suggesting that this combined intervention could effectively improve hand function in patients with severe upper limb paralysis.
Acute spinal cord compression due to spinal subdural hematoma after spinal anaesthesia in-patient under anticoagulant drug
Authors: Denou Moussa , Bankole Nourou Dine Adeniran , Hamama Mustapha , El Fatemi Nizare , El Maaqili Moulay Rachid 
Published: December 2021

Abstract
Background
Subdural spinal cord hematomas are very rare condition. They most often occur in patients with primary or secondary blood haemostasis disorders and following lumbar punctures. Early diagnosis and management preserve functional prognosis.

Case description
We report the case of a female 69-year-old patient on oral anticoagulant, Acenocoumarol 4 mg (SINTROM) for previous aortic prosthesis. The patient had undergone surgery for appendicitis under spinal anaesthesia 2 days before her admission in neurosurgery department. She was admitted in emergency for 1/5 central flaccid paraplegia with sensitive umbilical level. A spinal MRI performed showed a collection intradural in intermediate signal in T1 and hyposignal in T2 with echo gradient of 8 mm thickness extended from D8 to L2 compressing the marrow with anomalies of intramedullary signal extended from D8 to the conus medullaris. We retained indication to operate the patient early in emergency because of acute spinal cord compression. We performed T12-L2 laminectomy, durotomy and evacuated hematoma. Postoperative marked by an immediate recovery of sensitivity and an onset of motor recovery from 1/5 to 2/5 and 4/5 follow up at on year with physiotherapy.

Conclusion
Spinal cord compression due to subdural spinal hematomas not often described especially in patients with haemostasis blood disorders due to anticoagulants drugs. In addition, we should pay attention with lumbar puncture in these patients. Emergency surgery allows a good prognosis about recovery of neurological disorders.
Impact of the COVID-19 pandemic on emergency admission for patients with stroke: a time series study in Japan
Authors: Tani Takuaki , Imai Shinobu , Fushimi Kiyohide 
Published: December 2021

Abstract
Background
Appropriate treatment of stroke immediately after its onset contributes to the improved chances, while delay in hospitalisation affects stroke severity and fatality. This study aimed to determine the impact of the coronavirus disease 2019 (COVID-19) pandemic on emergency hospitalisation of patients with stroke in Japan.

Methods
This was an observational study that used nationwide administrative data of hospitalised patients diagnosed with stroke. We cross-sectionally observed patients’ background factors during April and May 2020, when the COVID-19 pandemic-related state of emergency was declared; we also observed these factors in the same period in 2019. We also modelled monthly trends in emergency stroke admissions, stroke admissions at each level of the Japan Coma Scale (JCS), fatalities within 24 h, stroke care unit use, intravenous thrombolysis administration, and mechanical thrombectomy implementation using interrupted time series (ITS) regression.

Results
There was no difference in patients’ pre-hospital baseline characteristics between the pre-pandemic and pandemic periods. However, ITS regression revealed a significant change in the number of emergency stroke admissions after the beginning of the pandemic (slope: risk ratio [RR] = 0.97, 95% confidence interval [CI]: 0.95–0.99, P = 0.027). There was a significant difference in the JCS score for impaired consciousness in emergency stroke, which was more severe during the pandemic than the pre-pandemic (JCS3 in level: RR = 1.75, 95% CI: 1.29–2.33, P < 0.001). There was no change in the total number of fatalities with COVID-19, compared with those without COVID-19, but there were significantly more fatalities within 24 h of admission (fatalities within 24 h: RR = 1.75, 95% CI: 1.29–2.33, P < 0.001).

Conclusions
The infection prevalence of COVID-19 increased the number of fatalities within 24 h as well as the severity of illness in Japan. However, there was no difference in baseline characteristics, intravenous thrombolysis administration, and mechanical thrombectomy implementation during the COVID-19 pandemic. A decrease in the number of patients and fatalities was observed from the time the state of emergency was declared until August, the period of this study.
A hybrid systems biology and systems pharmacology investigation of Zingerone’s effects on reconstructed human epidermal tissues
Authors: Amjad Elham , Sokouti Babak , Asnaashari Solmaz 
Published: December 2021

AbstractBackgroundAs individuals live longer, elderly populations can be expected to face issues. This pattern urges researchers to investigate the aging concept further to produce successful anti-aging agents. In the current study, the effects of Zingerone (a natural compound) on epidermal tissues were analyzed using a bioinformatics approach.MethodsFor this purpose, we chose the GEO dataset GSE133338 to carry out the systems biology and systems pharmacology approaches, ranging from identifying the differentially expressed genes to analyzing the gene ontology, determining similar structures of Zingerone and their features (i.e., anti-oxidant, anti-inflammatory, and skin disorders), constructing the gene–chemicals network, analyzing gene–disease relationships, and validating significant genes through the evidence presented in the literature.ResultsThe post-processing of the microarray dataset identified thirteen essential genes among control and Zingerone-treated samples. The procedure revealed various structurally similar chemical and herbal compounds with possible skin-related effects. Additionally, we studied the relationships of differentially expressed genes with skin-related diseases and validated their direct connections with skin disorders the evidence available in the literature. Also, the analysis of the microarray profiling dataset revealed the critical role of interleukins as a part of the cytokines family on skin aging progress.ConclusionsZingerone, and potentially any constituents of Zingerone (e.g., their similar compound scan functionality), can be used as therapeutic agents in managing skin disorders such as skin aging. However, the beneficial effects of Zingerone should be assessed in other models (i.e., human or animal) in future studies.
Exact solvability and two-frequency Rabi oscillation in cavity-QED setup with moving emitter
Authors: Weng Mingzhu , Wang Zhihai 
Published: December 2021

Abstract
In this paper, we investigate the energy spectrum and coherent dynamical process in a cavity-QED setup with a moving emitter, which is subject to a harmonic potential. We find that the vibration of the emitter will induce the effective Kerr and optomechanical interactions. We generalize the Bogliubov operators approach which dealt with quantum Rabi model, to our cavity-emitter-vibration system and obtain the energy spectrum exactly. Furthermore, we show that the dynamics of the system exhibit a two-frequency Rabi oscillation behavior. We explain such behavior by optomechanical-interaction–induced quantum transition between emitter-cavity dressed states. We hope that the interaction between cavity mode and moving emitter will provide a versatile platform to explore more exotic effects and potential applications in cavity-QED scenario.
Extraordinary optical transmission from a thin microcavity by macroscopic quantum effect
Authors: Zhang Lin , Hui Wu Jiu 
Published: December 2021

Abstract
The macroscopic quantum effect is revealed to elaborate the extraordinary optical transmission (EOT) from a subwavelength thin microcavity based on the uncertainty property of the transmitted electromagnetic fields after the aperture. A critical radius is found in the thin microcavity under a certain incident electromagnetic wavelength. With the aperture radius varying, the transmitted field can be divided into three regimes: I) the macroscopic quantum regime when the aperture radius is less than the critical radius, in which the field edge effect occurs and the EOT phenomenon is perfectly manifested; II) the wave-particle duality regime in the vicinity of the critical radius, in which the edge effect and diffraction phenomenon exist simultaneously; III) the wave regime when the aperture radius is greater than the critical radius, in which the near-field diffraction emerges. In addition, the influences of incident wavelength and microcavity thickness on EOT are also investigated. Our research has potential applications in advanced optical devices, such as light switch and optical manipulations.
Concordant Androgen-Regulated Expression of DivergentRhox5Promoters in Sertoli Cells
Authors: Bhardwaj Anjana , Sohni Abhishek , Lou Chih-Hong , De Gendt Karel , Zhang Fanmao , Kim Eunah , Subbarayalu Panneerdoss , Chan Waikin , Kerkhofs Stefanie , Claessens Frank , Kimmins Sarah , Rao Manjeet K , Meistrich Marvin , Wilkinson Miles F 
Published: December 2021

AbstractConcordant transcriptional regulation can generate multiple gene products that collaborate to achieve a common goal. Here we report a case of concordant transcriptional regulation that instead drives a single protein to be produced in the same cell type from divergent promoters. This gene product—the RHOX5 homeobox transcription factor—is translated from 2 different mRNAs with different 5′ untranslated regions (UTRs) transcribed from alternative promoters. Despite the fact that these 2 promoters—the proximal promoter (Pp) and the distal promoter (Pd)—exhibit different patterns of tissue-specific activity, share no obvious sequence identity, and depend on distinct transcription factors for expression, they exhibit a remarkably similar expression pattern in the testes. In particular, both depend on androgen signaling for expression in the testes, where they are specifically expressed in Sertoli cells and have a similar stage-specific expression pattern during the seminiferous epithelial cycle. We report evidence for 3 mechanisms that collaborate to drive concordant Pp/Pd expression. First, both promoters have an intrinsic ability to respond to androgen receptor and androgen. Second, the Pp acts as an enhancer to promote androgen-dependent transcription from the Pd. Third, Pd transcription is positively autoregulated by the RHOX5 protein, which is first produced developmentally from the Pp. Together, our data support a model in which the Rhox5 homeobox gene evolved multiple mechanisms to activate both of its promoters in Sertoli cells to produce Rhox5 in an androgen-dependent manner during different phases of spermatogenesis.
Regulation of Hook1-mediated endosomal sorting of clathrin-independent cargo by γ-taxilin
Authors: Higashi Satoru , Makiyama Tomohiko , Sakane Hiroshi , Nogami Satoru , Shirataki Hiromichi 
Published: December 2021

ABSTRACT
In clathrin-independent endocytosis, Hook1, a microtubule- and cargo-tethering protein, participates in sorting of cargo proteins such as CD98 (encoded by SLC3A2) and CD147 (encoded by BSG) into recycling endosomes. However, the molecular mechanism that regulates Hook1-mediated endosomal sorting is not fully understood. In the present study, we found that γ-taxilin is a novel regulator of Hook1-mediated endosomal sorting. γ-Taxilin depletion promoted both CD98-positive tubular formation and CD98 recycling. Conversely, overexpression of γ-taxilin inhibited the CD98-positive tubular formation. Depletion of Hook1, or Rab10 or Rab22a (which are both involved in Hook1-mediated endosomal sorting), attenuated the effect of γ-taxilin depletion on the CD98-positive tubular formation. γ-Taxilin depletion promoted CD147-mediated spreading of HeLa cells, suggesting that γ-taxilin might be a pivotal player in various cellular functions in which Hook1-mediated cargo proteins are involved. γ-Taxilin bound to the C-terminal region of Hook1 and inhibited its interaction with CD98; the latter interaction is necessary for sorting CD98. We suggest that γ-taxilin negatively regulates the sorting of Hook1-mediated cargo proteins into recycling endosomes by interfering with the interactions between Hook1 and the cargo proteins.
Diversity of lateral line patterns and neuromast numbers in the genus Oryzias
Authors: Seleit Ali , Ansai Satoshi , Yamahira Kazunori , Masengi Kawilarang W. A. , Naruse Kiyoshi , Centanin Lázaro 
Published: December 2021

ABSTRACT
A remarkable diversity of lateral line patterns exists in adult teleost fishes, the basis of which is largely unknown. By analysing the lateral line patterns and organ numbers in 29 Oryzias species and strains we report a rapid diversification of the lateral line system within this genus. We show a strong dependence of lateral line elaboration (number of neuromasts per cluster, number of parallel lateral lines) on adult species body size irrespective of phylogenetic relationships. In addition, we report that the degree of elaboration of the anterior lateral line, posterior lateral line and caudal neuromast clusters is tightly linked within species, arguing for a globally coordinated mechanism controlling lateral line organ numbers and patterns. We provide evidence for a polygenic control over neuromast numbers and positioning in the genus Oryzias. Our data also indicate that the diversity in lateral lines can arise as a result of differences in patterning both during embryonic development and post-embryonically, where simpler embryonic patterns generate less complex adult patterns and organ numbers, arguing for a linkage between the two processes.