bluuebunny/crossref_metadata_2025_split huggingface dataset:
Production tests of front-end electronics for Straw Tube Trackers in HADES and PANDA experiments at FAIR
Authors: Firlej Mirosław , Fiutowski Tomasz , Idzik Marek , Korcyl Grzegorz , Lalik Rafał , Malige Akshay , Molenda Aleksandra , Moroń Jakub , Salabura Piotr , Smyrski Jerzy , Świentek Krzysztof 
Published: May 2023

Abstract
PASTTREC is an 8-channel readout Application-Specific Integrated Circuit (ASIC) designed
for the Straw Tracking System (STS) in the HADES experiment and for the Straw Tube Tracker (STT)
and the Forward Tracker (FT) detectors in the PANDA experiment, both at the FAIR facility. Since
more than 5000 ASICs were produced for both experiments, efficient qualification tests are
required. For this purpose, the multi-chip test setup and dedicated verification procedures were
developed. In this paper, the measurement results for the first batch of 140 Front-End Boards
(FEBs), each hosting two ASICs, are presented. Since a significant number (280) of PASTTREC chips
were tested, obtained statistical distributions of key parameters are also reported. The estimated
yield (97%) and the process-related spread of the chip parameters are discussed.
Climate seasonality and extremes influence net primary productivity across California’s grasslands, shrublands, and woodlands
Authors: Alexander Jackson D , McCafferty Mary K , Fricker Geoffrey A , James Jeremy J 
Published: May 2023

Abstract
Terrestrial vegetation is a substantial carbon sink and plays a foundational role in regional and global climate change mitigation strategies. The state of California, USA, commits to achieving carbon neutrality by 2045 in part by managing terrestrial ecosystems to sequester more than 80 MMT of CO2. We used a 35-year net primary productivity (NPP) remote sensing product with gridded climate, soil, topography, and vegetation data to evaluate spatiotemporal drivers of NPP variation and identify drivers of NPP response to extremes in water availability in California’s major grasslands, shrublands, and woodlands. We used generalized boosted models (GBMs) and linear mixed effects models (LMMs) to identify influential predictors of NPP and characterize their relationships with NPP across seven major vegetation cover types: annual grasslands, blue oak, chamise-redshank chaparral, coastal scrub, coastal oak woodland, mixed chaparral, and montane hardwood. Climate seasonality, specifically greater precipitation and warmer minimum temperatures in early spring and winter, was associated with greater NPP across space, particularly in chaparral, blue oak, and grassland systems. Maximum annual temperature and climatic water deficit (CWD) showed a negative relationship with NPP in most vegetation cover types, particularly chaparral and coastal scrub. We found a significant decrease in NPP over time in most vegetation types, appearing to coincide with the 2012–2016 California mega-drought. However, response to water availability extremes differed by vegetation type. In most vegetation types, especially grasslands, increases in NPP in extreme wet years were greater than declines in NPP in dry years. Our analysis characterizes several climate risks and conservation opportunities in using California’s natural lands to store carbon. Namely, shifts in climate seasonality and water availability extremes threaten these systems’ ability to fix carbon, yet hotspots of NPP resilience may exist and could be enhanced through conservation and restoration. Additional mechanistic work can help illuminate these opportunities and prioritize conservation decision making.
Local support of climate change policies in Germany over time
Authors: Levi Sebastian , Wolf Ingo , Sommer Stephan , Howe Peter D 
Published: May 2023

Abstract
Political conflicts about energy and climate change policies often have local implications, yet little is known about local public opinion towards these policies. Here, we estimate support towards 26 climate change mitigation policies for 402 German counties and for up to four points of time using multilevel regression and poststratification. We find that local support for climate policies varies by up to 60 percentage points across German counties with large disparities between the rural and urban population. While support for the expansion of wind power plants and solar power plants have converged over the last years, attitudes on the phase-out of coal power have polarized across regions. Using a spatial panel analysis, we find that support for the expansion of wind and solar plants correlate with the actual development of solar and wind capacities in these regions. Moreover, the spread of climate policy opinion is strongly determined by spatial diffusion as change in one region positively influences the trajectory of policy opinion among its neighbors.
Thermal inkjet bioprinting drastically alters cell phenotype
Authors: Ablanedo Morales Patricia , Rodriguez Brittany , Furth Michael E , Molina Kayla B , Boland Andrew J , Mohl Jonaton E , Boland Thomas 
Published: May 2023

Abstract
Since the first description of inkjet bioprinting of cells in 2003, quantifying the input and measuring the output of the printers has been the hallmark of the field of bioprinting, as it is virtually impossible to characterize cells that are inside the printing orifices or extrusion needles. We will describe here some recent discoveries of cell behavior due to inkjet bioprinting. Primary and immortalized adult dermal fibroblasts were expanded for 2–3 passages upon receiving. The cells were harvested, resuspended in PBS, and bioprinted into a 96-well plate with pluriSTEM media. Cells were then transferred either into precoated 96-well plates or 20 µl drops were pipetted for hanging drop culture. IPC differentiation protocols were applied and the induction was begun approximately 45 min after printing. When differentiating aggregates, the initiation happened 45 min after the aggregates were transferred into the 96 wells. Standard immunostaining and RNA sequencing (RNA-Seq) were used to analyze the cell phenotypes. Preliminary results indicate that all cells expressed the three pluripotency markers oct-4, nanog, and sox-2. After applying a cardiomyocyte differentiation protocol, the cells stained positively for troponin-3. The cells also elongated and became more cardiomyocyte-like in their morphology. We analyzed bulk RNA seq data and our preliminary results show upregulation of some genes that have been implicated as stem cell markers: EPCAM, LEFTY1, ZFP42, and TEX19. In addition, differential expression of genes associated with pluripotency-relevant pathways shows some pathways are off like the MAPK/p38, MAPK/JNK1-3 which is expected for a pluripotent state. We also have data supporting the activation of the hippo pathway with transcriptional co-activator with PDZ binding motif (TAZ) highly upregulated and yes-associated protein staining the cell body. In addition, GSK3B is off and TGFB1, LIF/PIK3, and AKT1 are on as expected for pluripotency. Examining the gene network of upregulated genes, one can clearly distinguish the pivotal role of FOS, FOXO1, and PIK3 all related to pluripotency. Bioprinted fibroblasts will at least temporarily adopt a more primitive or dedifferentiated state, reminiscent of pluripotency. While immunochemistry shows the classic transcription factors required for pluripotency, gene expression shows a more nuanced picture of the transformations that occur upon printing. Understanding these transformations, even if temporary will be crucial when trying to build tissues using bioprinting technologies.
Evolution of microstructure in nickel-based C-HRA-2 alloy during welding thermal simulation
Authors: Kou Dongxu , Chen Zhongyi , Chen Zhengzong , Li Yongqing , Ma Yonglin , Li Yiming 
Published: May 2023

Abstract
The welding heat-affected zone (HAZ) of C-HRA-2 nickel-based alloy at different welding peak temperatures (Tp) (850 to 1450 °C) was obtained through welding thermal simulation. The microstructure of the different simulated HAZs was characterized by an optical microscope (OM), a scanning electron microscope (SEM), and a transmission electron microscope (TEM). The microhardness of simulated HAZs was examined using a microhardness tester. The results indicated that fine and dispersed M23C6 carbides were identified along the grain boundaries in the simulated HAZs at 1050 and 1150 °C. In the simulated HAZs above 1250 °C, eutectic microstructure of γ matrix bonded with M23C6 carbides was identified close to the grain boundaries due to constitutional liquation. The liquefaction of γ matrix and M23C6 carbides primarily accounted for the simulated HAZ liquation of C-HRA-2 alloy during continuous welding heating. The content of the liquefied phase was increased as Tp was increased. The liquefied phase was converted into the eutectic microstructure of γ matrix and M23C6 carbides in the cooling process. Besides 1050, 1150, and 1450 °C, the microstructures under other Tp were similar to the microstructure of the Base Metal (BM). The microhardness distribution of simulated HAZs tended to be higher in the middle and lower at both ends with the increase of Tp. Furthermore, the result indicated that the microhardness of the simulated HAZ was the closest to BM at 1050 °C.
Regulating electron transfer pathway in Au/W18O49 heterostructures by structural design for revealing the photocatalytic mechanism of metal/semiconductor heterostructures
Authors: Zhang Yuheng , Wang Yanan , Yang Shuai , He Fangyu , Yan Jun , Yang Zhengwen , Zhou Dacheng , Wang Qi , Qiu Jianbei 
Published: May 2023

Abstract
The construction of metal/semiconductor heterostructures is a useful technique for improving the electron-hole separation of Semiconductor Photocatalysts. However, there only are a few studies on the mechanism of electron transfer between metal/semiconductor heterostructures. Therefore, through the intelligent design of the material structure, two metal/semiconductor heterostructures (Au/W18O49 heterostructure) were fabricated with identical composition but different structures by different preparation methods: (1) The heterostructure of Au nanoparticles at the tip of sea urchin W18O49 was achieved through photoreduction method; (2) the heterostructure of Au nanoparticles at the root of sea urchin W18O49 was achieved via chemical reduction method, and their electron transfer paths were studied. The results demonstrated that the two materials went through completely different electron transfer paths, and these different electron transfer path also leads to an opposite set of photocatalytic properties. The heterostructure achieved through photoreduction has the best photocatalytic performance. Nevertheless, the photocatalytic performance of the heterostructure prepared by chemical reduction is far inferior to that of the heterostructure prepared by photoreduction, and even inferior to the original W18O49 sample. Therefore, we believe that the structural characteristics of metal/semiconductor heterostructure have a great influence on the electron transfer path. Our work renders useful information that may facilitate the design of heterostructure photocatalyst based on metal/semiconductors.
Biophysical modeling of the electric field magnitude and distribution induced by electrical stimulation with intracerebral electrodes
Authors: Alonso Fabiola , Mercadal Borja , Salvador Ricardo , Ruffini Giulio , Bartolomei Fabrice , Wendling Fabrice , Modolo Julien 
Published: May 2023

Abstract
Intracranial electrodes are used clinically for diagnostic or therapeutic purposes, notably in drug-refractory epilepsy (DRE) among others. Visualization and quantification of the energy delivered through such electrodes is key to understanding how the resulting electric fields modulate neuronal excitability, i.e. the ratio between excitation and inhibition. Quantifying the electric field induced by electrical stimulation in a patient-specific manner is challenging, because these electric fields depend on a number of factors: electrode trajectory with respect to folded brain anatomy, biophysical (electrical conductivity / permittivity) properties of brain tissue and stimulation parameters such as electrode contacts position and intensity. Here, we aimed to evaluate various biophysical models for characterizing the electric fields induced by electrical stimulation in DRE patients undergoing stereoelectroencephalography (SEEG) recordings in the context of pre-surgical evaluation. This stimulation was performed with multiple-contact intracranial electrodes used in routine clinical practice. We introduced realistic 3D models of electrode geometry and trajectory in the neocortex. For the electrodes, we compared point (0D) and line (1D) sources approximations. For brain tissue, we considered three configurations of increasing complexity: a 6-layer spherical model, a toy model with a sulcus representation, replicating results from previous approaches; and went beyond the state-of-the-art by using a realistic head model geometry. Electrode geometry influenced the electric field distribution at close distances (∼3 mm) from the electrode axis. For larger distances, the volume conductor geometry and electrical conductivity dominated electric field distribution. These results are the first step towards accurate and computationally tractable patient-specific models of electric fields induced by neuromodulation and neurostimulation procedures.
Real-time frequency estimation of a qubit without single-shot-readout
Authors: Zohar I , Haylock B , Romach Y , Arshad M J , Halay N , Drucker N , Stöhr R , Denisenko A , Cohen Y , Bonato C , Finkler A 
Published: May 2023

Abstract
Quantum sensors can potentially achieve the Heisenberg limit of sensitivity over a large dynamic range using quantum algorithms. The adaptive phase estimation algorithm (PEA) is one example that was proven to achieve such high sensitivities with single-shot readout (SSR) sensors. However, using the adaptive PEA on a non-SSR sensor is not trivial due to the low contrast nature of the measurement. The standard approach to account for the averaged nature of the measurement in this PEA algorithm is to use a method based on ‘majority voting’. Although it is easy to implement, this method is more prone to mistakes due to noise in the measurement. To reduce these mistakes, a binomial distribution technique from a batch selection was recently shown theoretically to be superior, as all ranges of outcomes from an averaged measurement are considered. Here we apply, for the first time, real-time non-adaptive PEA on a non-SSR sensor with the binomial distribution approach. We compare the mean square error of the binomial distribution method to the majority-voting approach using the nitrogen-vacancy center in diamond at ambient conditions as a non-SSR sensor. Our results suggest that the binomial distribution approach achieves better accuracy with the same sensing times. To further shorten the sensing time, we propose an adaptive algorithm that controls the readout phase and, therefore, the measurement basis set. We show by numerical simulation that adding the adaptive protocol can further improve the accuracy in a future real-time experiment.
Regulatory T-cell dysfunction and its implication for cell therapy
Authors: Valentini Nicolas , Requejo Cier Christopher J , Lamarche Caroline 
Published: May 2023

Summary
Regulatory T cells (Tregs) are a subtype of CD4+ T cells that can mediate immune tolerance by a multitude of immunomodulatory mechanisms. Treg-based adoptive immunotherapy is currently being tested in multiple phases I and II clinical trials in transplantation and autoimmune diseases. We have learned from the work done on conventional T cells that distinct mechanistic states can define their dysfunctions, such as exhaustion, senescence, and anergy. All three can negatively impact the therapeutic effectiveness of T-cell-based therapies. However, whether Tregs are susceptible to such dysfunctional states is not well studied, and results are sometimes found to be controversial. In addition, Treg instability and loss of FOXP3 expression is another Treg-specific dysfunction that can decreasein their suppressive potential. A better understanding of Treg biology and pathological states will be needed to compare and interpret the results of the different clinical and preclinical trials. We will review herein Tregs' mechanisms of action, describe different T-cell dysfunction subtypes and how and if they apply to Tregs (exhaustion, senescence, anergy, and instability), and finally how this knowledge should be taken into consideration when designing and interpreting Treg adoptive immunotherapy trials.
Real-World Effectiveness of Nirmatrelvir/Ritonavir on Coronavirus Disease 2019–Associated Hospitalization Prevention: A Population-based Cohort Study in the Province of Quebec, Canada
Authors: Kaboré Jean-Luc , Laffont Benoît , Diop Mamadou , Tardif Melanie R , Turgeon Alexis F , Dumaresq Jeannot , Luong Me-Linh , Cauchon Michel , Chapdelaine Hugo , Claveau David , Brosseau Marc , Haddad Elie , Benigeri Mike 
Published: May 2023

Abstract

Background
Nirmatrelvir/ritonavir has shown to reduce COVID-19 hospitalization and death before Omicron, but updated real-world evidence studies are needed. This study aimed to assess whether nirmatrelvir/ritonavir reduces the risk of COVID-19–associated hospitalization among high-risk outpatients.

Methods
A retrospective cohort study of outpatients with SARS-CoV-2 between March 15 and 15 October 2022, using data from the Quebec clinico-administrative databases. Outpatients treated with nirmatrelvir/ritonavir were compared with infected ones not receiving nirmatrelvir/ritonavir using propensity-score matching. Relative risk (RR) of COVID-19–associated hospitalization within 30 days was assessed using a Poisson regression.

Results
A total of 8402 treated outpatients were matched to controls. Regardless of vaccination status, nirmatrelvir/ritonavir treatment was associated with a 69% reduced RR of hospitalization (RR: .31; 95% CI: .28; .36; number needed to treat [NNT] = 13). The effect was more pronounced in outpatients with incomplete primary vaccination (RR: .04; 95% CI: .03; .06; NNT = 8), while no benefit was found in those with a complete primary vaccination (RR: .93; 95% CI: .78; 1.08). Subgroups analysis among high-risk outpatients with a complete primary vaccination showed that nirmatrelvir/ritonavir treatment was associated with a significant decrease in the RR of hospitalization in severely immunocompromised outpatients (RR: .66; 95% CI: .50; .89; NNT = 16) and in high-risk outpatients aged ≥70 years (RR: .50; 95% CI: .34; .74; NNT = 10) when the last dose of the vaccine was received at least 6 months ago.

Conclusions
Nirmatrelvir/ritonavir reduces the risk of COVID-19–associated hospitalization among incompletely vaccinated high-risk outpatients and among some subgroups of completely vaccinated high-risk outpatients.
First Whole-Genome Sequence and Flow Cytometry Genome Size Data for the Lichen-Forming FungusRamalina farinacea(Ascomycota)
Authors: Llewellyn Theo , Mian Sahr , Hill Rowena , Leitch Ilia J , Gaya Ester 
Published: May 2023

AbstractLichen-forming fungi are a diverse and ecologically important group of obligate mutualistic symbionts. Due to difficulties with maintaining them in culture and their extremely slow growth, lichenologists are increasingly opting for metagenomic sequencing followed by symbiont genome separation using bioinformatic pipelines. However, without knowing the true genome size of the lichen-forming fungus, we cannot quantify the completeness of the genome assembly and the efficacy of the bioinformatic filtering. To address this issue, we report here the first whole-genome assembly for the lichen-forming fungus Ramalina farinacea (L.) Ach. sequenced with Oxford Nanopore long-read technology alongside direct measurements of its genome size using flow cytometry. The assembly showed high contiguity (N50 = 1.55 Mb) and gene set completeness (BUSCO = 95.8%). The highly robust genome size of 33.61 Mb/1C (coefficients of variation = 2.98) that was obtained showed our assembly covered 97% of the entire genome. Our results demonstrate that accurate genome size measurements can be obtained directly from lichen thalli and used to provide a benchmark for assessing true cytometric completeness of metagenome-derived assemblies.
Mycobacterium tuberculosis Elevates SLIT2 Expression Within the Host and Contributes to Oxidative Stress Responses During Infection
Authors: Borbora Salik Miskat , Satish Bijewar Ashish , Sundar Smriti , B Mahima , Bhatt Sneha , Balaji Kithiganahalli Narayanaswamy 
Published: May 2023

Abstract
During infection, Mycobacterium tuberculosis (Mtb) rewires distinct host signaling pathways, resulting in pathogen-favorable outcomes. Oxidative stress build-up is a key cellular manifestation that occurs due to the cumulative effect of elevated reactive oxygen species (ROS) generation and the inept ability of the cell to mitigate ROS levels. Here, we report the Mtb-induced expression of the neuronal ligand SLIT2 to be instrumental in ROS accumulation during infection. Loss-of-function analysis revealed the heightened expression of SLIT2 to be dependent on the Mtb-mediated phosphorylation of the P38/JNK pathways. Activation of these kinases resulted in the loss of the repressive H3K27me3 signature on the Slit2 promoter. Furthermore, SLIT2 promoted the expression of Vanin1 (VNN1), which contributed to copious levels of ROS within the host. Thus, we dissect the pathway leading to the robust expression of SLIT2 during Mtb infection while outlining the potential consequences of SLIT2 upregulation in infected macrophages.
Crucial role of iron in epigenetic rewriting during adipocyte differentiation mediated by JMJD1A and TET2 activity
Authors: Suzuki Tomohiro , Komatsu Tetsuro , Shibata Hiroshi , Tanioka Akiko , Vargas Diana , Kawabata-Iwakawa Reika , Miura Fumihito , Masuda Shinnosuke , Hayashi Mayuko , Tanimura-Inagaki Kyoko , Morita Sumiyo , Kohmaru Junki , Adachi Koji , Tobo Masayuki , Obinata Hideru , Hirayama Tasuku , Kimura Hiroshi , Sakai Juro , Nagasawa Hideko , Itabashi Hideyuki , Hatada Izuho , Ito Takashi , Inagaki Takeshi 
Published: May 2023

Abstract
Iron metabolism is closely associated with the pathogenesis of obesity. However, the mechanism of the iron-dependent regulation of adipocyte differentiation remains unclear. Here, we show that iron is essential for rewriting of epigenetic marks during adipocyte differentiation. Iron supply through lysosome-mediated ferritinophagy was found to be crucial during the early stage of adipocyte differentiation, and iron deficiency during this period suppressed subsequent terminal differentiation. This was associated with demethylation of both repressive histone marks and DNA in the genomic regions of adipocyte differentiation-associated genes, 　including Pparg, which encodes PPARγ, the master regulator of adipocyte differentiation. In addition, we identified several epigenetic demethylases to be responsible for iron-dependent adipocyte differentiation, with the histone demethylase jumonji domain-containing 1A and the DNA demethylase ten-eleven translocation 2 as the major enzymes. The interrelationship between repressive histone marks and DNA methylation was indicated by an integrated genome-wide association analysis, and was also supported by the findings that both histone and DNA demethylation were suppressed by either the inhibition of lysosomal ferritin flux or the knockdown of iron chaperone poly(rC)-binding protein 2. In summary, epigenetic regulations through iron-dependent control of epigenetic enzyme activities play an important role in the organized gene expression mechanisms of adipogenesis.