bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSII-2 Effects of Natural Sources of Brackish/Saline Water on Water and Feed Intake, Digestion, Physiological Conditions, and Performance of Yearling Meat Goats
Authors: Yirga Hirut Y , Goetsch Arthur L , Puchala Ryszard , Gulich Dereje Tadesse , Encinas Fabiola L , Gipson Terry A , Dawson Lionel J 
Published: November 2023

Abstract
This experiment was aimed to determine how variables such as water intake, feed intake, ruminal conditions, digestion, blood constituent levels, energy metabolism, and performance of yearling meat goats are influenced by different natural sources of brackish/saline water. Two animal types (AT), 18 Boer (BOE) and 18 Spanish (SPA) doelings, with the age of 8.9 ± 0.306, and 9.7 ± 0.212 months, respectively were used for the experiment which lasted 17 weeks (16 weeks for the experiment and 1 week of adaptation). Drinking water treatments were fresh water (FRW), West pasture Brackish water (BRW), water classified by USGS as group 1 (GR-1), 2 (GR-2), 3 (GR-3), and the last one did not fit well with any USGS group (G-UC). Animals were fed a medium-quality grass hay primarily consisting of lespedeza and with some Johnson grass (12.2% CP, and 48% NDF on a DM basis) and a supplement was provided at 0.2% BW (DM basis) to supply trace minerals, vitamins, and protein. Average daily gain was similar (P &gt; 0.05) among treatments (16.3, 20.1, 21.1, 20.7, 23.3, and 26.5 g/day SEM = 6.378 for FRW, BRW, GR-1, GR-2, GR-3 and G-UC, respectively), and between AT (19.9 and 22.7 g/day SEM = 3.90 for BOE and SPA, respectively). Treatment did not affect water (P = 0.752; 830, 767, 821, 796, 855, and 857 g/day; SEM = 47.86) or hay intake (P = 0.862; 682, 654, 641, 674, 650, and 689 g/day SEM = 31.72), and also there were no differences between AT in intakes of water (P = 0.157; 850 and 793 g/day; SEM = 27.63) and hay (P = 0.165; 684 and 647 g/day SEM = 18.31) for BOE and SPA, respectively. Treatment had no effect on blood packed cell volume (PCV; P = 0.224; 28, 27.4, 29.7, 25.7, 26.2, 27.5%), hemoglobin concentration (tHb; P = 0.489; 11.2, 10.6, 11.2, 10.4, 10.3, 10.6 g/dL) or osmolality (310, 310, 309, 310, 309, and 309 mOsm/L) for FRW, BRW, GR-1, GR-2, GR-3 and G-UC, respectively. But there were differences between AT in PCV (P &lt; 0.001; 24.8 and 30%) and tHb (P &lt; 0.001; 9.71 and 11.7 g/dL) for BOE and SPA, respectively. Animal types differed in their heat (P = 0.046; 3.94 and 3.70 MJ/day; SEM = 0.081) and methane production (P &lt; 0.001; 0.50 and 0.42 MJ/day; SEM = 0.014) for BOE and SPA, respectively; but treatment did not affect heat energy (P = 0.861; 3.84, 3.77, 3.67, 3.88, 3.88, 3.86 MJ/day SEM = 0.1409) or methane energy (P = 0.634; 0.46, 0.43, 0.45, 0.47, 0.48, 0.48; SEM = 0.0241) for FRW, BRW, GR-1, GR-2, GR-3 and G-UC, respectively. Though differences existed between animal types, considering lack of effect of drinking water used in the studied parameters, the animals seemed resilient to the brackish water from West pasture, USGS group 1, 2, 3 and the unclassified water.
Cohabitation vs. Marriage: Mating Strategies by Education in The USA
Authors: Blasutto Fabio 
Published: November 2023

Abstract
In this paper, I analyze the determinants of cohabitation, marriage, and divorce in the USA. I first document that college graduates are more likely to marry, and less likely to cohabit and divorce, than non-college educated individuals. To account for these facts within a unified framework, I build and estimate a life-cycle model of partnership formation and dissolution where income processes differ by gender and education. I find that the main driver of education-based differences in mating strategies is that the gender wage gap is larger among college graduates. Since divorce is more costly than ending a cohabitation, marriages tend to be more stable and therefore offer women more protection from human capital depreciation during non-employment. Consequently, marriage is a more effective means of enforcing household specialization. Since college graduates have more room for household specialization, they are more likely to choose marriage. The variance of income shocks, which affects the demand for consumption insurance, is larger among college graduates. Even if the variance of income shocks could potentially explain partnership choices, simulations suggest a small role of income volatility.
Higher Education and Mortality: Legacies of an Authoritarian College Contraction
Authors: González Felipe , Martínez Luis R , Muñoz Pablo , Prem Mounu 
Published: November 2023

Abstract
We provide new evidence on the causal effect of higher education on mortality. Our empirical strategy exploits the reduction in college openings introduced by the Pinochet regime after the 1973 coup in Chile, which led to a sharp downward kink in college enrollment among those cohorts reaching college age in the following years. Using administrative data from the vital statistics, we document an upward kink in the age-specific yearly mortality rate of individuals in the affected cohorts. We estimate a negative effect of college on mortality between ages 34–74, which is larger for men, but also sizable for women. Individuals in the affected cohorts experience worse labor market outcomes, are more likely to be enrolled in the public health system, and report lower consumption of health services. This suggests that economic disadvantage and limited access to care play an important mediating role in the link between higher education and mortality.
From rules to methods: application of international intellectual property treaties in domestic courts of China
Authors: Xi Chen , Peiru Yang 
Published: November 2023

Abstract
This article reviews the methods taken by domestic courts in China in the judicial application of international intellectual property (IP) treaties. The proposition of the ‘Belt and Road’ initiative reinforced the significance of IP protection in China, and the emergence of IP courts allows for significant flexibility in the judicial application of international IP treaties. However, the domestic rules regarding treaty application provide rather limited guidance to domestic courts. Thus, the methods of treaty application in judicial practice have been inconsistent and unpredictable. This article finds that, in the vast majority of the cases, domestic law has been applied as the only legal authority. In a small number of cases, both treaty and domestic law were applied. In addition, an innovative approach should be noted in which international treaties are cited to interpret domestic law. Finally, the article puts forward some suggestions for improvement.
Poliovirus receptor–based chimeric antigen receptor T cells combined with NK-92 cells exert potent activity against glioblastoma
Authors: Pan Changqing , Zhai You , Wang Chen , Liao Zhiyi , Wang Di , Yu Mingchen , Wu Fan , Yin Yiyun , Shi Zhongfang , Li Guanzhang , Jiang Tao , Zhang Wei 
Published: November 2023

Abstract

Background
Poliovirus receptor interacts with 3 receptors: T-cell immunoglobulin immunoreceptor tyrosine-based inhibitory motif, CD96, and DNAX accessory molecule 1, which are predominantly expressed on T cells and natural killer (NK) cells. Many solid tumors, including IDH wild-type glioblastoma, have been reported to overexpress poliovirus receptor, and this overexpression is associated with poor prognosis. However, there are no preclinical or clinical trials investigating the use of cell-based immunotherapies targeting poliovirus receptor in IDH wild-type glioblastoma.

Methods
We analyzed poliovirus receptor expression in transcriptome sequencing databases and specimens from IDH wild-type glioblastoma patients. We developed poliovirus receptor targeting chimeric antigen receptor T cells using lentivirus. The antitumor activity of chimeric antigen receptor T cells was demonstrated in patient-derived glioma stem cells, intracranial and subcutaneous mouse xenograft models.

Results
We verified poliovirus receptor expression in primary glioma stem cells, surgical specimens from IDH wild-type glioblastoma patients, and organoids. Accordingly, we developed poliovirus receptor–based second-generation chimeric antigen receptor T cells. The antitumor activity of chimeric antigen receptor T cells was demonstrated in glioma stem cells and xenograft models. Tumor recurrence occurred in intracranial xenograft models because of antigen loss. The combinational therapy of tyrosine-based inhibitory motif extracellular domain–based chimeric antigen receptor T cells and NK-92 cells markedly suppressed tumor recurrence and prolonged survival.

Conclusions
Poliovirus receptor–based chimeric antigen receptor T cells were capable of killing glioma stem cells and suppressing tumor recurrence when combined with NK-92 cells.
Gaia search for (sub)stellar companions of exoplanet hosts
Authors: Michel Kai-Uwe , Mugrauer Markus 
Published: November 2023

ABSTRACT
We conduct a survey, which explores the data releases of the European Space Agency (ESA)–Gaia mission, in order to investigate the multiplicity of exoplanet hosts at distances of less than 625 pc around the Sun. With the accurate Gaia astrometry we are able to detect stellar and substellar companions of exoplanet hosts by proving the equidistance and common proper motion of these objects. Furthermore, by using the astro- and photometric data provided by the ESA–Gaia mission, we characterize the nature of the identified companions (substellar, stellar, main-sequence, or evolved), determine their properties (mass, effective temperature, and projected separation to the associated exoplanet host), and verify their orbital stability. In addition to main-sequence stars, the companions detected in this study include several brown and white dwarfs. So far in the course of our survey, the multiplicity of more than 2200 exoplanet hosts could be investigated, yielding a multiplicity rate of about 16 per cent (increased to about 19 per cent including published detections from other surveys). Finally, the derived physical properties of the companions were used to investigate the impact of the stellar multiplicity on the properties of the exoplanets and their hosts. In general, there are significant differences in the properties of these objects, dependent on the multiplicity status of their host system, e.g. higher masses of both planets and exoplanet hosts in multiple star systems. Furthermore, the masses and orbital eccentricities of multiple star planets significantly depend on the gravitational impact, induced by the companion star of the exoplanet host.
Chemodynamical study of two CEMP-no stars from the Hamburg/ESO Survey
Authors: Shejeelammal J , Goswami Aruna 
Published: November 2023

ABSTRACT
The Carbon-Enhanced Metal-Poor (CEMP) stars with no enhancement of neutron-capture elements, the so-called CEMP-no stars are believed to be the direct descendants of first-generation stars and provide a unique opportunity to probe the early Galactic nucleosynthesis. We present a detailed chemical and kinematic analysis for two extremely metal-poor stars HE 1243 − 2408 and HE 0038 − 0345 using high-resolution (R∼86 000) HERMES spectra. For the object HE 1243 − 2408, we could make a detailed comparison with the available literature values; however, only limited information is available for the other object HE 0038 − 0345. Our estimated metallicity for these two objects are −3.05 and −2.92, respectively. With estimated [C/Fe] (1.03 and 1.05) and [Ba/Fe] (−0.18 and −0.11), respectively, the objects are found to be bonafide CEMP-no stars. From the observed abundances of C, Na, Mg, and Ba (i.e. A(C), A(Na), A(Mg), A(Ba)), the objects are found to belong to Group II CEMP-no stars. A detailed abundance profile analysis indicates that the objects are accreted from dSph satellite galaxies that support hierarchical galaxy assembly. Further, our analysis shows that the progenitors of the stars are likely Pop II Core-Collapse Supernovae. The object HE 0038 − 0345 is found to be a high-energy, prograde, outer-halo object, and HE 1243 − 2408 is found to be a high-energy, retrograde, inner-halo object. Our detailed chemodynamical analysis shows that HE 1243 − 2408 is related to I’itoi structure, where as HE 0038 − 0345 is likely related to Sgr or GSE events. The mass of the progenitor galaxies of the programme stars inferred from their dynamics is at par with their likely origin in massive dSph galaxies.
Extremely strong C iv λ1550 nebular emission in the extremely low-metallicity star-forming galaxy J2229+2725
Authors: Izotov Y I , Schaerer D , Guseva N G , Thuan T X , Worseck G 
Published: November 2023

ABSTRACT
Using Hubble Space Telescope/Cosmic Origins Spectrograph observations of one of the most metal-poor dwarf star-forming galaxies (SFGs) in the local Universe, J2229+2725, we have discovered an extremely strong nebular C iv λλ1549, 1551 emission-line doublet, with an equivalent width of 43 Å, several times higher than the value observed so far in low-redshift SFGs. Together with other extreme characteristics obtained from optical spectroscopy (oxygen abundance 12 + log(O/H) = 7.085 ± 0.031, ratio O32 = I([O iii]λ5007)/I([O ii]λ3727) ∼ 53, and equivalent width of the H β emission-line EW(H β) = 577 Å), this galaxy greatly increases the range of physical properties for dwarf SFGs at low redshift and is a likely analogue of the high-redshift dwarf SFGs responsible for the reionization of the Universe. We find the ionizing radiation in J2229+2725 to be stellar in origin and the high EW(C iv λλ1549, 1551) to be due to both extreme ionization conditions and a high carbon abundance, with a corresponding log(C/O) = −0.38, that is ∼0.4 dex higher than the average value for nearby low-metallicity SFGs.
Binding of microRNA-122 to the hepatitis C virus 5′ untranslated region modifies interactions with poly(C) binding protein 2 and the NS5B viral polymerase
Authors: Scott Seth , Li You , Bermek Oya , Griffith Jack D , Lemon Stanley M , Choi Kyung H 
Published: November 2023

Abstract
Hepatitis C virus (HCV) requires two cellular factors, microRNA-122 (miR-122) and poly(C) binding protein 2 (PCBP2), for optimal replication. These host factors compete for binding to the 5′ end of the single-stranded RNA genome to regulate the viral replication cycle. To understand how they interact with the RNA, we measured binding affinities of both factors for an RNA probe representing the 5′ 45 nucleotides of the HCV genome (HCV45). Isothermal titration calorimetry revealed two, unequal miR-122 binding sites in HCV45, high-affinity (S1) and low-affinity (S2), differing roughly 100-fold in binding affinity. PCBP2 binds a site overlapping S2 with affinity similar to miR-122 binding to S2. PCBP2 circularizes the genome by also binding to the 3′ UTR, bridging the 5′ and 3′ ends of the genome. By competing with PCBP2 for binding at S2, miR-122 disrupts PCBP2-mediated genome circularization. We show that the viral RNA-dependent RNA polymerase, NS5B, also binds to HCV45, and that the binding affinity of NS5B is increased in the presence of miR-122, suggesting miR-122 promotes recruitment of the polymerase. We propose that competition between miR-122 and PCBP2 for HCV45 functions as a translation-to-replication switch, determining whether the RNA genome templates protein synthesis or RNA replication.
High-fidelity large-diversity monoclonal mammalian cell libraries by cell cycle arrested recombinase-mediated cassette exchange
Authors: Chen Chuan , Wang Zening , Kang Minhyo , Lee Ki Baek , Ge Xin 
Published: November 2023

Abstract
Mammalian cells carrying defined genetic variations have shown great potentials in both fundamental research and therapeutic development. However, their full use was limited by lack of a robust method to construct large monoclonal high-quality combinatorial libraries. This study developed cell cycle arrested recombinase-mediated cassette exchange (aRMCE), able to provide monoclonality, precise genomic integration and uniform transgene expression. Via optimized nocodazole-mediated mitotic arrest, 20% target gene replacement efficiency was achieved without antibiotic selection, and the improved aRMCE efficiency was applicable to a variety of tested cell clones, transgene targets and transfection methods. As a demonstration of this versatile method, we performed directed evolution of fragment crystallizable (Fc), for which error-prone libraries of over 107 variants were constructed and displayed as IgG on surface of CHO cells. Diversities of constructed libraries were validated by deep sequencing, and panels of novel Fc mutants were identified showing improved binding towards specific Fc gamma receptors and enhanced effector functions. Due to its large cargo capacity and compatibility with different mutagenesis approaches, we expect this mammalian cell platform technology has broad applications for directed evolution, multiplex genetic assays, cell line development and stem cell engineering.
MESPEUS: a database of metal coordination groups in proteins
Authors: Lin Geng-Yu , Su Yu-Cheng , Huang Yen Lin , Hsin Kun-Yi 
Published: November 2023

Abstract
MESPEUS is a freely accessible database which uses carefully selected metal coordination groups found in metalloprotein structures taken from the Protein Data Bank. The database contains geometrical information of metal sites within proteins, including 40 metal types. In order to completely determine the metal coordination, the symmetry-related units of a given protein structure are taken into account and are generated using the appropriate space group symmetry operations. This permits a more complete description of the metal coordination geometry by including all coordinating atoms. The user-friendly web interface allows users to directly search for a metal site of interest using several useful options, including searching for metal elements, metal-donor distances, coordination number, donor residue group, and structural resolution. These searches can be carried out singly or in combination. The details of a metal site and the metal site(s) in the whole structure can be graphically displayed using the interactive web interface. MESPEUS is automatically updated monthly by synchronizing with the PDB database. An investigation for the Mg-ATP interaction is given to demonstrate how MESPEUS can be used to extract information about metal sites by selecting structure and coordination features. MESPEUS is available at http://mespeus.nchu.edu.tw/.
BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies
Authors: Höjer Pontus , Frick Tobias , Siga Humam , Pourbozorgi Parham , Aghelpasand Hooman , Martin Marcel , Ahmadian Afshin 
Published: November 2023

Abstract
Linked-read sequencing promises a one-method approach for genome-wide insights including single nucleotide variants (SNVs), structural variants, and haplotyping. We introduce Barcode Linked Reads (BLR), an open-source haplotyping pipeline capable of handling millions of barcodes and data from multiple linked-read technologies including DBS, 10× Genomics, TELL-seq and stLFR. Running BLR on DBS linked-reads yielded megabase-scale phasing with low (&lt;0.2%) switch error rates. Of 13616 protein-coding genes phased in the GIAB benchmark set (v4.2.1), 98.6% matched the BLR phasing. In addition, large structural variants showed concordance with HPRC-HG002 reference assembly calls. Compared to diploid assembly with PacBio HiFi reads, BLR phasing was more continuous when considering switch errors. We further show that integrating long reads at low coverage (∼10×) can improve phasing contiguity and reduce switch errors in tandem repeats. When compared to Long Ranger on 10× Genomics data, BLR showed an increase in phase block N50 with low switch-error rates. For TELL-Seq and stLFR linked reads, BLR generated longer or similar phase block lengths and low switch error rates compared to results presented in the original publications. In conclusion, BLR provides a flexible workflow for comprehensive haplotype analysis of linked reads from multiple platforms.
Probabilistic cell/domain-type assignment of spatial transcriptomics data with SpatialAnno
Authors: Shi Xingjie , Yang Yi , Ma Xiaohui , Zhou Yong , Guo Zhenxing , Wang Chaolong , Liu Jin 
Published: November 2023

Abstract
In the analysis of both single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) data, classifying cells/spots into cell/domain types is an essential analytic step for many secondary analyses. Most of the existing annotation methods have been developed for scRNA-seq datasets without any consideration of spatial information. Here, we present SpatialAnno, an efficient and accurate annotation method for spatial transcriptomics datasets, with the capability to effectively leverage a large number of non-marker genes as well as ‘qualitative’ information about marker genes without using a reference dataset. Uniquely, SpatialAnno estimates low-dimensional embeddings for a large number of non-marker genes via a factor model while promoting spatial smoothness among neighboring spots via a Potts model. Using both simulated and four real spatial transcriptomics datasets from the 10x Visium, ST, Slide-seqV1/2, and seqFISH platforms, we showcase the method’s improved spatial annotation accuracy, including its robustness to the inclusion of marker genes for irrelevant cell/domain types and to various degrees of marker gene misspecification. SpatialAnno is computationally scalable and applicable to SRT datasets from different platforms. Furthermore, the estimated embeddings for cellular biological effects facilitate many downstream analyses.
Multiple sequence alignment-based RNA language model and its application to structural inference
Authors: Zhang Yikun , Lang Mei , Jiang Jiuhong , Gao Zhiqiang , Xu Fan , Litfin Thomas , Chen Ke , Singh Jaswinder , Huang Xiansong , Song Guoli , Tian Yonghong , Zhan Jian , Chen Jie , Zhou Yaoqi 
Published: November 2023

AbstractCompared with proteins, DNA and RNA are more difficult languages to interpret because four-letter coded DNA/RNA sequences have less information content than 20-letter coded protein sequences. While BERT (Bidirectional Encoder Representations from Transformers)-like language models have been developed for RNA, they are ineffective at capturing the evolutionary information from homologous sequences because unlike proteins, RNA sequences are less conserved. Here, we have developed an unsupervised multiple sequence alignment-based RNA language model (RNA-MSM) by utilizing homologous sequences from an automatic pipeline, RNAcmap, as it can provide significantly more homologous sequences than manually annotated Rfam. We demonstrate that the resulting unsupervised, two-dimensional attention maps and one-dimensional embeddings from RNA-MSM contain structural information. In fact, they can be directly mapped with high accuracy to 2D base pairing probabilities and 1D solvent accessibilities, respectively. Further fine-tuning led to significantly improved performance on these two downstream tasks compared with existing state-of-the-art techniques including SPOT-RNA2 and RNAsnap2. By comparison, RNA-FM, a BERT-based RNA language model, performs worse than one-hot encoding with its embedding in base pair and solvent-accessible surface area prediction. We anticipate that the pre-trained RNA-MSM model can be fine-tuned on many other tasks related to RNA structure and function.