bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting the side effects of drugs using matrix factorization on spontaneous reporting database
Authors: Fukuto Kohei , Takagi Tatsuya , Tian Yu-Shi 
Published: December 2021

AbstractThe severe side effects of some drugs can threaten the lives of patients and financially jeopardize pharmaceutical companies. Computational methods utilizing chemical, biological, and phenotypic features have been used to address this problem by predicting the side effects. Among these methods, the matrix factorization method, which utilizes the side-effect history of different drugs, has yielded promising results. However, approaches that encapsulate all the characteristics of side-effect prediction have not been investigated to date. To address this gap, we applied the logistic matrix factorization algorithm to a database of spontaneous reports to construct a prediction with higher accuracy. We expressed the distinction in the importance of drug-side effect pairs by a weighting strategy and addressed the cold-start problem via an attribute-to-feature mapping method. Consequently, our proposed model improved the prediction accuracy by 2.5% and efficiently handled the cold-start problem. The proposed methodology is expected to benefit applications such as warning systems in clinical settings.
Surveillance of avian influenza viruses from 2009 to 2013 in South Korea
Authors: Nam Jeong-Hyun , Españo Erica , Song Eun-Jung , Shim Sang-Mu , Na Woonsung , Jeong Seo-Hee , Kim Jiyeon , Jang Jaebong , Song Daesub , Kim Jeong-Ki 
Published: December 2021

AbstractAvian influenza viruses (AIVs) are carried by wild migratory waterfowl across migratory flyways. To determine the strains of circulating AIVs that may pose a risk to poultry and humans, regular surveillance studies must be performed. Here, we report the surveillance of circulating AIVs in South Korea during the winter seasons of 2009–2013. A total of 126 AIVs were isolated from 7942 fecal samples from wild migratory birds, with a total isolation rate of 1.59%. H1‒H7 and H9‒H11 hemagglutinin (HA) subtypes, and N1‒N3, N5, and N7‒N9 neuraminidase (NA) subtypes were successfully isolated, with H6 and N2 as the most predominant HA and NA subtypes, respectively. Sequence identity search showed that the HA and NA genes of the isolates were highly similar to those of low-pathogenicity influenza strains from the East Asian-Australasian flyway. No match was found for the HA genes of high-pathogenicity influenza strains. Thus, the AIV strains circulating in wild migratory birds from 2009 to 2013 in South Korea likely had low pathogenicity. Continuous surveillance studies such as this one must be performed to identify potential precursors of influenza viruses that may threaten animal and human health.
Safe electrophysiologic profile of dexmedetomidine in different experimental arrhythmia models
Authors: Ellermann Christian , Brandt Jonas , Wolfes Julian , Willy Kevin , Wegner Felix K. , Leitz Patrick , Lange Philipp S. , Reinke Florian , Eckardt Lars , Frommeyer Gerrit 
Published: December 2021

AbstractPrevious studies suggest an impact of dexmedetomidine on cardiac electrophysiology. However, experimental data is sparse. Therefore, purpose of this study was to investigate the influence of dexmedetomidine on different experimental models of proarrhythmia. 50 rabbit hearts were explanted and retrogradely perfused. The first group (n = 12) was treated with dexmedetomidine in ascending concentrations (3, 5 and 10 µM). Dexmedetomidine did not substantially alter action potential duration (APD) but reduced spatial dispersion of repolarization (SDR) and rendered the action potentials rectangular, resulting in no proarrhythmia. In further 12 hearts, erythromycin (300 µM) was administered to simulate long-QT-syndrome-2 (LQT2). Additional treatment with dexmedetomidine reduced SDR, thereby suppressing torsade de pointes. In the third group (n = 14), 0.5 µM veratridine was added to reduce the repolarization reserve. Further administration of dexmedetomidine did not influence APD, SDR or the occurrence of arrhythmias. In the last group (n = 12), a combination of acetylcholine (1 µM) and isoproterenol (1 µM) was used to facilitate atrial fibrillation. Additional treatment with dexmedetomidine prolonged the atrial APD but did not reduce AF episodes. In this study, dexmedetomidine did not significantly alter cardiac repolarization duration and was not proarrhythmic in different models of ventricular and atrial arrhythmias. Of note, dexmedetomidine might be antiarrhythmic in acquired LQT2 by reducing SDR.
Gas origin linked to paleo BSR
Authors: de la Cruz Vargas-Cordero Iván , Villar-Muñoz Lucia , Tinivella Umberta , Giustiniani Michela , Bangs Nathan , Bento Joaquim P. , Contreras-Reyes Eduardo 
Published: December 2021

AbstractThe Central-South Chile margin is an excellent site to address the changes in the gas hydrate system since the last deglaciation associated with tectonic uplift and great earthquakes. However, the dynamic of the gas hydrate/free gas system along south central Chile is currently not well understood. From geophysical data and modeling analyses, we evaluate gas hydrate/free gas concentrations along a seismic line, derive geothermal gradients, and model past positions of the Bottom Simulating Reflector (BSR; until 13,000 years BP). The results reveal high hydrate/free gas concentrations and local geothermal gradient anomalies related to fluid migration through faults linked to seafloor mud volcanoes. The BSR-derived geothermal gradient, the base of free gas layers, BSR distribution and models of the paleo-BSR form a basis to evaluate the origin of the gas. If paleo-BSR coincides with the base of the free gas, the gas presence can be related to the gas hydrate dissociation due to climate change and geological evolution. Only if the base of free gas reflector is deeper than the paleo-BSR, a deeper gas supply can be invoked.
Cognitive profiling and proteomic analysis of the modafinil analogue S-CE-123 in experienced aged rats
Authors: Gyertyán István , Lubec Jana , Ernyey Alíz Judit , Gerner Christopher , Kassai Ferenc , Kalaba Predrag , Kozma Kata , Cobankovic Iva , Brenner Gábor , Wackerlig Judith , Franschitz Eva , Urban Ernst , Langer Thierry , Malikovic Jovana , Lubec Gert 
Published: December 2021

AbstractThe lack of novel cognitive enhancer drugs in the clinic highlights the prediction problems of animal assays. The objective of the current study was to test a putative cognitive enhancer in a rodent cognitive test system with improved translational validity and clinical predictivity. Cognitive profiling was complemented with post mortem proteomic analysis. Twenty-seven male Lister Hooded rats (26 months old) having learned several cognitive tasks were subchronically treated with S-CE-123 (CE-123) in a randomized blind experiment. Rats were sacrificed after the last behavioural procedure and plasma and brains were collected. A label-free quantification approach was used to characterize proteomic changes in the synaptosomal fraction of the prefrontal cortex. CE-123 markedly enhanced motivation which resulted in superior performance in a new-to-learn operant discrimination task and in a cooperation assay of social cognition, and mildly increased impulsivity. The compound did not affect attention, spatial and motor learning. Proteomic quantification revealed 182 protein groups significantly different between treatment groups containing several proteins associated with aging and neurodegeneration. Bioinformatic analysis showed the most relevant clusters delineating synaptic vesicle recycling, synapse organisation and antioxidant activity. The cognitive profile of CE-123 mapped by the test system resembles that of modafinil in the clinic showing the translational validity of the test system. The findings of modulated synaptic systems are paralleling behavioral results and are in line with previous evidence for the role of altered synaptosomal protein groups in mechanisms of cognitive function.
Self-observation of a virtual body-double engaged in social interaction reduces persecutory thoughts
Authors: Gorisse Geoffrey , Senel Gizem , Banakou Domna , Beacco Alejandro , Oliva Ramon , Freeman Daniel , Slater Mel 
Published: December 2021

AbstractThe proportion of the population who experience persecutory thoughts is 10–15%. People then engage in safety-seeking behaviours, typically avoiding social interactions, which prevents disconfirmatory experiences and hence paranoia persists. Here we show that persecutory thoughts can be reduced if prior to engaging in social interaction in VR participants first see their virtual body-double doing so. Thirty non-clinical participants were recruited to take part in a study, where they were embodied in a virtual body that closely resembled themselves, and asked to interact with members of a crowd. In the Random condition (n = 15) they observed their body-double wandering around but not engaging with the crowd. In the Targeted condition the body-double correctly interacted with members of the crowd. The Green Paranoid Thoughts Scale was measured 1 week before and 1 week after the exposure and decreased only for those in the Targeted condition. The results suggest that the observation of the body-double correctly carrying out a social interaction task in VR may lead to anxiety-reducing mental rehearsal for interaction thus overcoming safety behaviours. The results also extend knowledge of the effects of vicarious agency, suggesting that identification with the actions of body-double can influence subsequent psychological state.
Using a climate attribution statistic to inform judgments about changing fisheries sustainability
Authors: Litzow Michael A. , Malick Michael J. , Abookire Alisa A. , Duffy-Anderson Janet , Laurel Benjamin J. , Ressler Patrick H. , Rogers Lauren A. 
Published: December 2021

AbstractSustainability—maintaining catches within the historical range of socially and ecologically acceptable values—is key to fisheries success. Climate change may rapidly threaten sustainability, and recognizing these instances is important for effective climate adaptation. Here, we present one approach for evaluating changing sustainability under a changing climate. We use Bayesian regression models to compare fish population processes under historical climate norms and emerging anthropogenic extremes. To define anthropogenic extremes we use the Fraction of Attributable Risk (FAR), which estimates the proportion of risk for extreme ocean temperatures that can be attributed to human influence. We illustrate our approach with estimates of recruitment (production of young fish, a key determinant of sustainability) for two exploited fishes (Pacific cod Gadus macrocephalus and walleye pollock G. chalcogrammus) in a rapidly warming ecosystem, the Gulf of Alaska. We show that recruitment distributions for both species have shifted towards zero during anthropogenic climate extremes. Predictions based on the projected incidence of anthropogenic temperature extremes indicate that expected recruitment, and therefore fisheries sustainability, is markedly lower in the current climate than during recent decades. Using FAR to analyze changing population processes may help fisheries managers and stakeholders to recognize situations when historical sustainability expectations should be reevaluated.
Species ethnobotanical values rather than regional species pool determine plant diversity in agroforestry systems
Authors: N’Woueni Daniel K. , Gaoue Orou G. 
Published: December 2021

AbstractThe conversion of natural systems into farms and agroecosystems is the main cause of biodiversity loss. In human-dominated landscapes, understanding the interactions between agroforestry systems and adjacent natural vegetation is fundamental to developing sustainable agricultural systems. Species can move between these two systems with natural systems providing the regional pool of species that shape the agricultural values and conservation value of the agroforestry systems. We investigated the influence of neighboring natural habitats on traditional agroforestry systems in the buffer zone of Pendjari Biosphere Reserve in Benin to understand the contribution of regional processes on the quality of agroforestry systems. We expected that agroforestry parklands adjacent to natural vegetation with high species diversity will also have higher plant species diversity. We found no similarity in plant species composition between agroforestry systems and adjacent natural habitats. A small proportion of species in adjacent natural habitats were found in agroforestry systems. The proportion of shared species was not significantly influenced by plant diversity in adjacent natural habitats or the distance from the agroforestry systems to the natural adjacent habitat. However, plant diversity in agroforestry systems was strongly associated with site ethnobotanical values indicating that farmers act as a supplemental but severe environmental filter of the regional species pool. Our study suggests that promoting the plantation of plants with high ethnobotanical use-value is a potentially viable strategy for sustainable agriculture and ecological restoration in Biosphere reserves.
A case control study of occupation and cardiovascular disease risk in Japanese men and women
Authors: Fukai Kota , Furuya Yuko , Nakazawa Shoko , Kojimahara Noriko , Hoshi Keika , Toyota Akihiro , Tatemichi Masayuki 
Published: December 2021

AbstractWe aimed to investigate the risks of cardiovascular diseases associated with specific occupations, using a nation-wide, multicentre, hospital-based registry data from the Inpatient Clinico-Occupational Survey. The analysis included 539,110 controls (non-circulatory disease) and 23,792 cases (cerebral infarction, intracerebral/subarachnoid hemorrhage, acute myocardial infarction) aged ≥ 20 years who were initially hospitalized during 2005–2015. The participants’ occupational and clinical histories were collected by interviewers and medical doctors. Occupations were coded into 81 categories according to the Japanese standard occupation classification. Multivariable logistic regression analysis adjusted for age, admission year and hospital, smoking, alcohol consumption, hypertension, and shift-work was conducted by sex using general clerical workers as the reference. Increased risks of cerebral infarction, intracerebral hemorrhage, subarachnoid hemorrhage, and acute myocardial infarction, were observed in 15, 20, 25, and 1 occupation(s) in men, and 9, 2, 2, and 10 occupations in women. Motor vehicle drivers, food and drink preparatory workers, fishery workers, cargo workers, civil engineer workers, and other manual workers in men and other manual workers in women faced increased risks of all three stroke subtypes. Our findings demonstrate associations between specific occupations and the risk of cardiovascular disease incidence and suggest that the risk may vary by occupation.
Podocalyxin promotes an impermeable epithelium and inhibits pro-implantation factors to negatively regulate endometrial receptivity
Authors: Heng Sophea , Samarajeewa Nirukshi , Wang Yao , Paule Sarah G. , Breen James , Nie Guiying 
Published: December 2021

AbstractEmbryo implantation is a key step in establishing pregnancy and a major limiting factor in IVF. Implantation requires a receptive endometrium but the mechanisms governing receptivity are not well understood. We have recently discovered that podocalyxin (PCX or PODXL) is a key negative regulator of human endometrial receptivity. PCX is expressed in all endometrial epithelial cells in the non-receptive endometrium but selectively down-regulated in the luminal epithelium at receptivity. We have further demonstrated that this down-regulation is essential for implantation because PCX inhibits embryo attachment and penetration. However, how PCX confers this role is unknown. In this study, through RNAseq analysis of Ishikawa cell line stably overexpressing PCX, we discovered that PCX suppresses expression of genes controlling cell adhesion and communication, but increases those governing epithelial barrier functions, especially the adherens and tight junctions. Moreover, PCX suppresses multiple factors such as LIF and signaling pathways including Wnt and calcium signaling that support receptivity but stimulates anti-implantation genes such as LEFTY2. Functional studies confirmed that PCX promotes epithelial barrier functions by increasing key epithelial junction proteins such as E-cadherin and claudin 4. PCX thus promotes an anti-adhesive and impermeable epithelium while impedes pro-implantation factors to negatively control endometrial receptivity for implantation.
Analysis of cytokines in the aqueous humor during intravitreal Ranibizumab treatment of diabetic macular edema
Authors: de Freitas Luiz Guilherme Azevedo , Isaac David Leonardo Cruvinel , Abud Murilo Batista , Segundo Alexandre Dantas Soares Quintas , Barros Mariana Larissa Alvino , de Albuquerque Gabriela Caroline Monteiro , Guimarães Bruna Dantas Aires , de Morais Clarice Neuenschwander Lins , de Ávila Marcos Pereira 
Published: December 2021

AbstractThis study aimed to analyze the concentrations of VEGF, b-FGF, TNF, interleukin (IL)-1, IL-6, IL-8, IL-10, and IL-12 in the aqueous humor of patients with diabetic macular edema with and without peripheral retinal ischemia and to ascertain the changes in the levels of these molecules during treatment with ranibizumab. A therapeutic, prospective, randomized interventional study was carried out. Twenty-four eyes from 24 patients were studied and divided into 3 groups. Group 1 (9 eyes) included patients with diabetic macular edema without peripheral ischemia. Group 2 (10 eyes) included patients with diabetic macular edema with peripheral ischemia. Group 3 (5 eyes), the control group, included patients without systemic and/or eye diseases. Patients in Groups 1 and 2 received 3 intravitreal injections of 2 mg/0.05 ml ranibizumab at an interval of approximately 30 days. Before administering the injections, the aqueous humor was collected. In the control group, aqueous humor was collected before facetectomy. During treatment, the median IL-6 concentration significantly increased in Group 1 but showed a slight but not significant decrease in Group 2. Interleukin 8 levels were significantly different at the end of treatment compared to the beginning in Groups 1 and 2. TNF, IL-1, IL-10, and IL-12 levels were practically unchanged in both groups. VEGF was significantly reduced at the end of the study in Groups 1 and 2. B-FGF was not detected in most of the studied patients, and in those with detectable levels, there was no significant variation. There was a significant increase in the median level of interleukin 6 in the group without ischemia and a significant decrease in VEGF in both groups. The cytokines TNF, IL-1, IL-10, and IL-12 did not show significant variation.
Er:YAG laser irradiation enhances bacterial and lipopolysaccharide clearance and human gingival fibroblast adhesion on titanium discs
Authors: Wang Chen-Ying , Lee Bor-Shiunn , Jhang Ya-Ting , Ma Kevin Sheng-Kai , Huang Chen-Pang , Fu Kuan-Lun , Lai Chern-Hsiung , Tseng Wan-Yu , Kuo Mark Yen-Ping , Chen Yi-Wen 
Published: December 2021

AbstractTo investigate the effect of Er:YAG laser treatment on lipopolysaccharide (LPS) clearance and fibroblast adhesion on titanium disks. Grade IV titanium discs (n = 216) were used and allocated to 6 groups. Group 1 was the negative control without Porphyromonas gingivalis inoculation. Discs in Groups 2–6 were incubated with P. gingivalis to form a biofilm. Group 3 received 0.12% chlorhexidine irrigation and Group 4 received titanium curettage to remove the biofilm. Group 5 was treated with Er:YAG laser irradiation and Group 6 was treated with titanium curettage plus Er:YAG laser irradiation. The contact angle and surface roughness were measured after the various treatments. The surface microstructure and residual bacteria were examined using scanning electron microscopy and confocal laser scanning microscopy, respectively. Residual LPS was examined using a limulus amoebocyte lysate assay and human gingival fibroblast adhesion was quantified using fluorescent microscopy. Curettage plus Er:YAG laser irradiation was the most effective method for removing bacteria and LPS. No significant difference in the amount of fibroblast adhesion was found between the control and Group 6. Combined use of Er:YAG laser irradiation and curettage optimizes LPS clearance and fibroblast adhesion on titanium discs.
Optimised techniques for high-throughput screening of differentiated SH-SY5Y cells and application for neurite outgrowth assays
Authors: Dravid Anusha , Raos Brad , Svirskis Darren , O’Carroll Simon J. 
Published: December 2021

AbstractNeuronal models are a crucial tool in neuroscientific research, helping to elucidate the molecular and cellular processes involved in disorders of the nervous system. Adapting these models to a high-throughput format enables simultaneous screening of multiple agents within a single assay. SH-SY5Y cells have been widely used as a neuronal model, yet commonly in an undifferentiated state that is not representative of mature neurons. Differentiation of the SH-SY5Y cells is a necessary step to obtain cells that express mature neuronal markers. Despite this understanding, the absence of a standardised protocol has limited the use of differentiated SH-SY5Y cells in high-throughput assay formats. Here, we describe techniques to differentiate and re-plate SH-SY5Y cells within a 96-well plate for high-throughput screening. SH-SY5Y cells seeded at an initial density of 2,500 cells/well in a 96-well plate provide sufficient space for neurites to extend, without impacting cell viability. Room temperature pre-incubation for 1 h improved the plating homogeneity within the well and the ability to analyse neurites. We then demonstrated the efficacy of our techniques by optimising it further for neurite outgrowth analysis. The presented methods achieve homogenously distributed differentiated SH-SY5Y cells, useful for researchers using these cells in high-throughput screening assays.