bluuebunny/crossref_metadata_2025_split huggingface dataset:
A transcriptome-wide association study identifies susceptibility genes for Parkinson’s disease
Authors: Yao Shi , Zhang Xi , Zou Shu-Cheng , Zhu Yong , Li Bo , Kuang Wei-Ping , Guo Yan , Li Xiao-Song , Li Liang , Wang Xiao-Ye 
Published: September 2021

AbstractGenome-wide association study (GWAS) has seen great strides in revealing initial insights into the genetic architecture of Parkinson’s disease (PD). Since GWAS signals often reside in non-coding regions, relatively few of the associations have implicated specific biological mechanisms. Here, we aimed to integrate the GWAS results with large-scale expression quantitative trait loci (eQTL) in 13 brain tissues to identify candidate causal genes for PD. We conducted a transcriptome-wide association study (TWAS) for PD using the summary statistics of over 480,000 individuals from the most recent PD GWAS. We identified 18 genes significantly associated with PD after Bonferroni corrections. The most significant gene, LRRC37A2, was associated with PD in all 13 brain tissues, such as in the hypothalamus (P = 6.12 × 10−22) and nucleus accumbens basal ganglia (P = 5.62 × 10−21). We also identified eight conditionally independent genes, including four new genes at known PD loci: CD38, LRRC37A2, RNF40, and ZSWIM7. Through conditional analyses, we demonstrated that several of the GWAS significant signals on PD could be driven by genetically regulated gene expression. The most significant TWAS gene LRRC37A2 accounts for 0.855 of the GWAS signal at its loci, and ZSWIM7 accounts for all the GWAS signals at its loci. We further identified several phenotypes previously associated with PD by querying the single nucleotide polymorphisms (SNPs) in the final model of the identified genes in phenome databases. In conclusion, we prioritized genes that are likely to affect PD by using a TWAS approach and identified phenotypes associated with PD.
3D integration and measurement of a semiconductor double quantum dot with a high-impedance TiN resonator
Authors: Holman Nathan , Rosenberg D. , Yost D. , Yoder J. L. , Das R. , Oliver William D. , McDermott R. , Eriksson M. A. 
Published: September 2021

AbstractOne major challenge to scaling quantum dot qubits is the dense wiring requirements, making it difficult to envision fabricating large 2D arrays of nearest-neighbor-coupled qubits necessary for error correction. We describe a method to ameliorate this issue by spacing out the qubits using superconducting resonators facilitated by 3D integration. To prove the viability of this approach, we use integration to couple an off-chip high-impedance TiN resonator to a double quantum dot in a Si/SiGe heterostructure. Using the resonator as a dispersive gate sensor, we tune the device down to the single electron regime with an SNR = 5.36. Characterizing the individual systems shows 3D integration can be done while maintaining low-charge noise for the quantum dots and high-quality factors for the superconducting resonator (single photon QL = 2.14 × 104 with Qi ≈ 3 × 105), necessary for readout and high-fidelity two-qubit gates.
Comparative effects of alive and pasteurized Akkermansia muciniphila on normal diet-fed mice
Authors: Ashrafian Fatemeh , Keshavarz Azizi Raftar Shahrbanoo , Shahryari Arefeh , Behrouzi Ava , Yaghoubfar Rezvan , Lari Arezou , Moradi Hamid Reza , Khatami Shohreh , Omrani Mir Davood , Vaziri Farzam , Masotti Andrea , Siadat Seyed Davar 
Published: September 2021

AbstractRecently, Akkermansia muciniphila an anaerobic member of the gut microbiota, has been proposed as a next-generation probiotic. The aim of this study was evaluation of the effect of alive and pasteurized A. muciniphila on health status, intestinal integrity, immune response, lipid metabolism, and gut microbial composition in normal-diet fed mice as well as direct effects of the bacterium on Caco-2 cell line. A total of 30 mice were distributed into three different groups, control, alive, and pasteurized A. muciniphila-treated group. After acclimation, control and treatment groups were administrated with PBS and 109 CFU/200µL of bacterial suspension for 5 weeks, respectively. Besides, Caco-2 separately exposed to alive, pasteurized A. muciniphila and PBS for 24 h. The results showed that administration of A. muciniphila leads to reduction in body, liver, and white adipose weight. Histology data revealed both treatments had no adverse effects in colon, liver, and adipose tissues as well as induced better gut structure. Moreover, biochemical parameters and inflammatory biomarkers in plasma demonstrated that pasteurized A. muciniphila had more pronounce effect. Furthermore, alive A. muciniphia had better effects on the modulation of gene expression related to fatty acid synthesis, energy homeostasis, and immune response in the liver; meanwhile, these effects in the adipose was more in the pasteurized A. muciniphila administration. More importantly, the improvement of gut health by enhancing strengthen intestinal integrity and maintaining immune homeostasis was seen in both treatments; notably, pasteurized A. muciniphila had more effective. Similarly, treatment with the pasteurized form more effectively upregulated tight junction and regulated immune response-related genes in Caco-2 cell line. Both treatments triggered the improvement of microbiota communities, particularly the alive form. Therefore, both forms of A. muciniphila could modulate lipid and immune homeostasis, improved some gut microbiota, and promoted the overall health, while all these effects were dominantly observed in pasteurized form. In conclusion, pasteurized A. muciniphila can be considered as new medical supplement to maintain health state and prevent diseases in normal mice through different mechanisms.
Hypersensitivity in teeth affected by molar-incisor hypomineralization (MIH)
Authors: Linner Thomas , Khazaei Yeganeh , Bücher Katharina , Pfisterer Jan , Hickel Reinhard , Kühnisch Jan 
Published: September 2021

AbstractTooth hypersensitivity is a common symptom in patients with molar-incisor hypomineralization (MIH). Therefore, this clinical study aimed to assess potential associations between patient- and tooth-related variables and the intensity of hypersensitivity in MIH-affected permanent teeth compared to healthy controls. Fifty-seven MIH patients and 20 healthy adolescents with a total of 350 MIH-affected and 193 healthy teeth were included in this study. The intensity of hypersensitivity was measured after cold air stimulation using the Schiff Cold Air Sensitivity Scale (SCASS) by the dentist and visual analogue scale (VAS) by the patient. Tooth hypersensitivity was low in non-MIH teeth (97.9% of the group had zero SCASS and VAS values). In contrast, MIH-affected teeth with demarcated opacities and atypical restorations had moderate SCASS and VAS values, whereas teeth with enamel breakdown were mostly linked to severe hypersensitivity. The logistic regression model confirmed a significantly lower level of hypersensitivity in MIH patients aged ≥ 8 years (OR 0.06, 95% CI 0.01–0.50, p = 0.009) and higher levels in molar teeth (OR 5.49, 95% CI 1.42–21.27, p = 0.014) and teeth with enamel disintegration (OR 4.61, 95% CI 1.68–12.63, p = 0.003). These results indicate that MIH-related tooth hypersensitivity seems to be present in disintegrated molars immediately after tooth eruption.
Endomicroscopy of the human cochlea using a micro-optical coherence tomography catheter
Authors: Iyer Janani S. , Yin Biwei , Stankovic Konstantina M. , Tearney Guillermo J. 
Published: September 2021

AbstractSensorineural hearing loss (SNHL) is one of the most profound public health concerns of the modern era, affecting 466 million people today, and projected to affect 900 million by the year 2050. Advances in both diagnostics and therapeutics for SNHL have been impeded by the human cochlea’s inaccessibility for in vivo imaging, resulting from its extremely small size, convoluted coiled configuration, fragility, and deep encasement in dense bone. Here, we develop and demonstrate the ability of a sub-millimeter-diameter, flexible endoscopic probe interfaced with a micro-optical coherence tomography (μOCT) imaging system to enable micron-scale imaging of the inner ear’s sensory epithelium in cadaveric human inner ears.
Numerical modelling and experimental verification of thermal effects in living cells exposed to high-power pulses of THz radiation
Authors: Sitnikov D. S. , Pronkin A. A. , Ilina I. V. , Revkova V. A. , Konoplyannikov M. A. , Kalsin V. A. , Baklaushev V. P. 
Published: September 2021

AbstractExposure of cells or biological tissues to high-power pulses of terahertz (THz) radiation leads to changes in a variety of intracellular processes. However, the role of heating effects due to strong absorption of THz radiation by water molecules still stays unclear. In this study, we performed numerical modelling in order to estimate the thermal impact on water of a single THz pulse as well as a series of THz pulses. A finite-element (FE) model that provides numerical solutions for the heat conduction equation is employed to compute the temperature increase. A simple expression for temperature estimation in the center of the spot of THz radiation is presented for given frequency and fluence of the THz pulse. It has been demonstrated that thermal effect is determined by either the average power of radiation or by the fluence of a single THz pulse depending on pulse repetition rate. Human dermal fibroblasts have been exposed to THz pulses (with an energy of $$15\,\upmu \hbox {J}$$

15

μ
J

and repetition rate of 100 Hz) to estimate the thermal effect. Analysis of heat shock proteins expression has demonstrated no statistically significant difference ($$p < 0.05$$

p
<
0.05

) between control and experimental groups after 3 h of irradiation.
A universal vaccine candidate against Plasmodium vivax malaria confers protective immunity against the three PvCSP alleles
Authors: Gimenez Alba Marina , Salman Ahmed M. , Marques Rodolfo F. , López-Camacho César , Harrison Kate , Kim Young Chan , Janse Chris J. , Soares Irene S. , Reyes-Sandoval Arturo 
Published: September 2021

AbstractMalaria is a highly prevalent parasitic disease in regions with tropical and subtropical climates worldwide. Among the species of Plasmodium causing human malaria, P. vivax is the second most prevalent and the most geographically widespread species. A major target of a pre-erythrocytic vaccine is the P. vivax circumsporozoite protein (PvCSP). In previous studies, we fused two recombinant proteins representing three allelic variants of PvCSP (VK210, VK247 and P. vivax-like) to the mumps virus nucleocapsid protein to enhance immune responses against PvCSP. The objective of the present study was to evaluate the protective efficacy of these recombinants in mice challenged with transgenic P. berghei parasites expressing PvCSP allelic variants. Formulations containing Poly (I:C) or Montanide ISA720 as adjuvants elicited high and long-lasting IgG antibody titers specific to each PvCSP allelic variant. Immunized mice were challenged with two existing chimeric P. berghei parasite lines expressing PvCSP-VK210 and PvCSP-VK247. We also developed a novel chimeric line expressing the third allelic variant, PvCSP-P. vivax-like, as a new murine immunization-challenge model. Our formulations conferred partial protection (significant delay in the time to reach 1% parasitemia) against challenge with the three chimeric parasites. Our results provide insights into the development of a vaccine targeting multiple strains of P. vivax.
Monitoring the response of volcanic CO2 emissions to changes in the Los Humeros hydrothermal system
Authors: Jentsch Anna , Duesing Walter , Jolie Egbert , Zimmer Martin 
Published: September 2021

AbstractCarbon dioxide is the most abundant, non-condensable gas in volcanic systems, released into the atmosphere through either diffuse or advective fluid flow. The emission of substantial amounts of CO2at Earth’s surface is not only controlled by volcanic plumes during periods of eruptive activity or fumaroles, but also by soil degassing along permeable structures in the subsurface. Monitoring of these processes is of utmost importance for volcanic hazard analyses, and is also relevant for managing geothermal resources. Fluid-bearing faults are key elements of economic value for geothermal power generation. Here, we describe for the first time how sensitively and quickly natural gas emissions react to changes within a deep hydrothermal system due to geothermal fluid reinjection. For this purpose, we deployed an automated, multi-chamber CO2flux monitoring system within the damage zone of a deep-rooted major normal fault in the Los Humeros Volcanic Complex (LHVC) in Mexico and recorded data over a period of five months. After removing the atmospheric effects on variations in CO2flux, we calculated correlation coefficients between residual CO2emissions and reinjection rates, identifying an inverse correlation of ρ = − 0.51 to − 0.66. Our results indicate that gas emissions respond to changes in reinjection rates within 24 h, proving an active hydraulic communication between the hydrothermal system and Earth’s surface. This finding is a promising indication not only for geothermal reservoir monitoring but also for advanced long-term volcanic risk analysis. Response times allow for estimation of fluid migration velocities, which is a key constraint for conceptual and numerical modelling of fluid flow in fracture-dominated systems.
Anthraquinolone and quinolizine derivatives as an alley of future treatment for COVID-19: an in silico machine learning hypothesis
Authors: Samarth Nikhil , Kabra Ritika , Singh Shailza 
Published: September 2021

AbstractCoronavirus disease 2019 (Covid-19), caused by novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), has come to the fore in Wuhan, China in December 2019 and has been spreading expeditiously all over the world due to its high transmissibility and pathogenicity. From the outbreak of COVID-19, many efforts are being made to find a way to fight this pandemic. More than 300 clinical trials are ongoing to investigate the potential therapeutic option for preventing/treating COVID-19. Considering the critical role of SARS-CoV-2 main protease (Mpro) in pathogenesis being primarily involved in polyprotein processing and virus maturation, it makes SARS-CoV-2 main protease (Mpro) as an attractive and promising antiviral target. Thus, in our study, we focused on SARS-CoV-2 main protease (Mpro), used machine learning algorithms and virtually screened small derivatives of anthraquinolone and quinolizine from PubChem that may act as potential inhibitor. Prioritisation of cavity atoms obtained through pharmacophore mapping and other physicochemical descriptors of the derivatives helped mapped important chemical features for ligand binding interaction and also for synergistic studies with molecular docking. Subsequently, these studies outcome were supported through simulation trajectories that further proved anthraquinolone and quinolizine derivatives as potential small molecules to be tested experimentally in treating COVID-19 patients.
El Niño Modoki can be mostly predicted more than 10 years ahead of time
Authors: Liang X. San , Xu Fen , Rong Yineng , Zhang Renhe , Tang Xu , Zhang Feng 
Published: September 2021

AbstractThe 2014–2015 “Monster”/“Super” El Niño failed to be predicted one year earlier due to the growing importance of a new type of El Niño, El Niño Modoki, which reportedly has much lower forecast skill with the classical models. In this study, we show that, so far as of today, this new El Niño actually can be mostly predicted at a lead time of more than 10 years. This is achieved through tracing the predictability source with an information flow-based causality analysis, which has been rigorously established from first principles during the past 16 years (e.g., Liang in Phys Rev E 94:052201, 2016). We show that the information flowing from the solar activity 45 years ago to the sea surface temperature results in a causal structure resembling the El Niño Modoki mode. Based on this, a multidimensional system is constructed out of the sunspot number series with time delays of 22–50 years. The first 25 principal components are then taken as the predictors to fulfill the prediction, which through causal AI based on the Liang–Kleeman information flow reproduces rather accurately the events thus far 12 years in advance.
Refrigeration of eggs influences the virulence of Salmonella Typhimurium
Authors: Khan Samiullah , McWhorter Andrea R. , Moyle Talia S. , Chousalkar Kapil K. 
Published: September 2021

AbstractSalmonella Typhimurium is a human pathogen associated with eggs and egg-derived products. In Australia, it is recommended that eggs should be refrigerated to prevent condensation that can enhance bacterial penetration across the eggshell. Except for the United States, the guidelines on egg refrigeration are not prescriptive. In the current study, in-vitro and in-vivo experiments were conducted to understand the role of egg storage temperatures (refrigerated vs ambient) on bacterial load and the virulence genes expression of Salmonella Typhimurium. The in-vitro egg study showed that the load of Salmonella Typhimurium significantly increased in yolk and albumen stored at 25 °C. The gene expression study showed that ompR, misL, pefA, spvA, shdA, bapA, and csgB were significantly up-regulated in the egg yolk stored at 5 °C and 25 °C for 96 h; however, an in-vivo study revealed that mice infected with egg yolk stored at 25 °C, developed salmonellosis from day 3 post-infection (p.i.). Mice fed with inoculated egg yolk, albumen, or eggshell wash stored at refrigerated temperature did not show signs of salmonellosis during the period of the experiment. Data obtained in this study highlighted the importance of egg refrigeration in terms of improving product safety.
Experimental estimation of the longitudinal component of a highly focused electromagnetic field
Authors: Maluenda David , Aviñoá Marcos , Ahmadi Kavan , Martínez-Herrero Rosario , Carnicer Artur 
Published: September 2021

AbstractThe detection of the longitudinal component of a highly focused electromagnetic beam is not a simple task. Although in recent years several methods have been reported in the literature, this measure is still not routinely performed. This paper describes a method that allows us to estimate and visualize the longitudinal component of the field in a relatively simple way. First, we measure the transverse components of the focused field in several planes normal to the optical axis. Then, we determine the complex amplitude of the two transverse field components: the phase is obtained using a phase recovery algorithm, while the phase difference between the two components is determined from the Stokes parameters. Finally, the longitudinal component is estimated using the Gauss’s theorem. Experimental results show an excellent agreement with theoretical predictions.
Prognostic prediction by hypermetabolism varies depending on the nutritional status in early amyotrophic lateral sclerosis
Authors: Nakamura Ryutaro , Kurihara Mika , Ogawa Nobuhiro , Kitamura Akihiro , Yamakawa Isamu , Bamba Shigeki , Sanada Mitsuru , Sasaki Masaya , Urushitani Makoto 
Published: September 2021

AbstractTo examine whether hypermetabolism could predict the prognosis of early amyotrophic lateral sclerosis (ALS) patients with differing nutritional profiles. This single-center, retrospective study examined the prognosis of ALS patients with hypermetabolism in relation to their nutritional status at hospitalization. The metabolic state was estimated by the ratio of measured resting energy expenditure (mREE) to lean soft tissue mass (LSTM) (mREE/LSTM), wherein patients with ratios ≥ 38 were defined as hypermetabolic. Malnutrition was defined as %ideal body weight < 0.9. Forty-eight patients were enrolled in this study. The hypermetabolic group had shorter survival in the normal-weight group but more prolonged survival in the malnutrition group. Multiplication of nutritional and metabolic factors, such as [(body mass index (BMI) − 19.8) × (mREE/LSTM − 38)], designated as BMI-muscle metabolism index (BMM index), successfully predicted the prognosis in the group with a high BMM index (≥ 1), which showed shorter survival and a faster rate of weight loss and functional decline. Multivariate analysis using the Cox model showed high BMM index was an independent poor prognostic factor (hazard ratio: 4.05; p = 0.025). Prognostic prediction by hypermetabolism varies depending on the nutritional status in ALS, and the BMM index is a consistent prognostic factor.
Continuous warming shift greening towards browning in the Southeast and Northwest High Mountain Asia
Authors: Liu Yongchang , Li Zhi , Chen Yaning 
Published: September 2021

AbstractRemote sensing and ground vegetation observation data show that climate warming promotes global vegetation greening, and the increase in air temperature in High Mountain Asia (HMA) is more than twice the global average. Under such a drastic warming in climate, how have the vegetation dynamics in HMA changed? In this study, we use the Normalized Difference Vegetation Index (NDVI) from 1982 to 2015 to evaluate the latest changes in vegetation dynamics in HMA and their climate-driving mechanisms. The results show that over the past 30 years, HMA has generally followed a “warm-wet” trend, with temperatures charting a continuous rise. During 1982–1998 precipitation increased (1.16 mm yr−1), but depicted to reverse since 1998 (− 2.73 mm yr−1). Meanwhile, the NDVI in HMA increased (0.012 per decade) prior to 1998, after which the trend reversed and declined (− 0.005 per decade). The main reason for the browning of HMA vegetation is the dual effects of warming and precipitation changes. As mentioned, the increase in air temperature in HMA exceeds the global average. The increase of water vapor pressure deficit caused by global warming accelerates the loss and consumption of surface water, and also aggravates the soil water deficit. That is to say, the abnormal increase of land evapotranspiration far exceeds the precipitation, and the regional water shortage increases. Climate change is the primary factor driving these vegetation and water dynamics, with the largest proportion reaching 41.9%.
Space-fractional quantum heat engine based on level degeneracy
Authors: Aydiner Ekrem 
Published: September 2021

AbstractIn order to examine the work and efficiency of the space-fractional quantum heat engine, we consider a model of the space-fractional quantum heat engine which has a Stirling-like cycle with a single particle under infinite potential well as an example. We numerically compute the work and efficiency for various fractional exponents. We show the work and the efficiency of the engine depending on the length of the potential well and fractional exponent of the engine. Furthermore, we show that fractional exponent plays a substantial role in the operating range of the quantum heat engine. Thus, we conclude that the fractional parameter can be used as a tuning parameter to obtain positive work and efficiency for the large size of the quantum heat engine. Additionally, the numerical results and model imply that the size of the engine can be enlarged in the nano-scale by using fractional deformations. As a result, in this study, we have not only shown that fractional deformations in space play an important role on the work and efficiency of the quantum heat engines but also introduced the concept of fractional quantum heat engines to the literature.