bluuebunny/crossref_metadata_2025_split huggingface dataset:
Attitudes of Turkish veterinarians towards animal welfare
Authors: Sabuncuoglu N , Coban O 
Published: January 2023

AbstractA survey was carried out to examine the attitudes of Turkish veterinarians towards animal welfare issues. The email questionnaire consisted of three sections of statements with a five-point Likert scale for choices of answer. The first section included statements examining the attitudes of Turkish veterinarians to animal welfare issues relating to European Union (EU) Legislation (93/119/EC, 95/29/EC, 2002/4EC and Council Regulation 1/2005). In the second, statements were designed to ascertain veterinarian attitudes towards the recently-passed Animal Protection Law, TR-5199. The statements in the last section were designed to assess the respondents' personal beliefs on a variety of welfare topics. The survey was sent to 615 veterinarians and the response rate was 40.2%. Turkish veterinarians expressed considerable support for the implications of animal welfare with the exception of statements regarding ‘stunning of ruminants pre-slaughter’, ‘phasing out of battery cages for poultry’ and ‘not operating on animals for aesthetic purposes’. In addition, they did not agree with the statements related to ‘ethological needs of farm animals’ and ‘effectiveness of EU laws and legislation in Turkey’. Females had higher mean values than males. The results of the survey indicated that significant concern for animal welfare issues is seen in the Turkish veterinarian population. Although the process of becoming a fully-integrated member of the EU will not occur rapidly, the influence of veterinarians could potentially enhance animal welfare in Turkey.
A pilot study to assess whether high expansion CO2-enriched foam is acceptable for on-farm emergency killing of poultry
Authors: Gerritzen MA , Sparrey J 
Published: January 2023

AbstractThis pilot experiment was conducted to ascertain whether CO2-enriched high expansion foam could be an acceptable and efficient alternative in emergency killing of poultry. This method could have wide-ranging applications but with particular emphasis on small (backyard) flocks, free-range sheds or open (naturally-ventilated) housings. The objectives of the study were as follows: 1) to determine whether the injection of foam and being covered with foam leads to fear or panic reactions in birds; 2) to determine the time taken to render birds unconscious and dead and 3) to determine whether any pathological abnormalities are observed post mortem. Six laying hens were individually exposed to increasing levels of CO2 foam with an expansion rate of 300:1. The test box containing individual birds filled with foam within 30 s. During foaming, two out of six birds tried to escape from the test box (1–2 attempts per bird). Apart from displaying greater alertness, birds showed no aversive reactions to the CO2 foam. Twenty-to-thirty seconds after being covered with foam, five of the six birds demonstrated one or two forcable or convulsive movements. Movement patterns and muscle jerks immediately following this convulsive movement led us to believe that birds lost consciousness at this moment and, within approximately three minutes, all birds had ceased to have a heartbeat. Macroscopic post mortem examination of the birds revealed no abnormalities and microscopic examination showed moderate bronchiolar bleeding and a small amount of alveolar bleeding. After assessing behavioural parameters, measurements of heart rate and pathological data, it is our conclusion that CO2 foam has the potential to be an acceptable method of killing poultry. It is advisable for this method to be examined on a larger scale in order to assess the implications of physiological (EEG and ECG) measurements on welfare.
The Effects of Intrusion on the Behaviour of Caged Laboratory Rats (Rattus Norvegicus): Consequences for Welfare
Authors: Barclay R 
Published: January 2023

AbstractThis experiment examines the consequences and welfare implications of the introduction of new rats to established (resident) caged laboratory rat groups. The effects on investigatory and aggressive behaviours of the established and the newly introduced rats were measured. The aggressive status within each established resident group was known prior to the introduction; the status of each intruder rat was also known. Single-sex groups of both male and female residents and intruders were studied. Two important conclusions arise from the results of the experiment. First, contrary to reports in a number of publications, there were no effects of male resident social status on their investigatory or aggressive behaviour towards male intruder rats. There was, however, a significant effect of social status among female residents on their investigatory behaviour towards intruders; unexpectedly, it was the subordinates followed by the dominant animals that showed the highest investigatory response. Second, aggression by intruders of both sexes depended upon their social status in their resident group. In the case of male intruders, aggressive behaviour towards residents was a reflection of their previous social status irrespective of how much aggression they received from residents. Among females, a similar pattern emerged, with the dominant females initiating the most aggression; however, this behaviour was dependent upon how much aggression was received from residents and on the resident’s social status, with resident subordinates and dominants responding with the most aggressive behaviour. The results are interpreted in terms of putative competitive strategies adopted by rats in a confined (cage) environment, and their welfare implications are discussed.
Immodest flirt or competent governor: translating gender in colonial and post-colonial South Asian historiography
Authors: Khoja Neelam 
Published: January 2023

AbstractThis article examines how an eighteenth-century woman, Mughlani Begum, is depicted in the most informative contemporary Persian auto/biography and how the descriptions, anecdotes, and analysis of her life contained therein, including the brief period she was Punjab's governor, changed as the primary source was translated into or summarised in English. The original Persian and colonial English translations and histories are read alongside an Urdu history of the Punjab, which begs the question: why was the life of a female governor reduced to that of an ‘immodest flirt’ in English sources, while her identity is incredibly nuanced in Persian and Urdu sources? Indeed, post-colonial historians writing in English rarely reference Persian originals: hence, they reproduce what colonial-period English writers before them said, and they completely ignore Urdu histories. While it is nearly impossible to understand the reasons why historians writing in English choose to depict Mughlani Begum in such a flattened way, we can be more critical of our readings of histories written in English, especially when original accounts are available. This article argues for consideration of how transmission of knowledge, language politics, and gender biases inflect historiography and misrepresent historical events and people of the Punjab—especially women.
Observations of Gravity Wave Refraction and Its Causes and Consequences
Authors: Geldenhuys M. , Kaifler B. , Preusse P. , Ungermann J. , Alexander P. , Krasauskas L. , Rhode S. , Woiwode W. , Ern M. , Rapp M. , Riese M. 
Published: January 2023

AbstractHorizontal gravity wave (GW) refraction was observed around the Andes and Drake Passage during the SouthTRAC campaign. GWs interact with the background wind through refraction and dissipation. This interaction helps to drive midatmospheric circulations and slows down the polar vortex by taking GW momentum flux (GWMF) from one location to another. The SouthTRAC campaign was composed to gain improved understanding of the propagation and dissipation of GWs. This study uses observational data from this campaign collected by the German High Altitude Long Range research aircraft on 12 September 2019. During the campaign a minor sudden stratospheric warming in the southern hemisphere occurred, which heavily influenced GW propagation and refraction and thus also the location and amount of GWMF deposition. Observations include measurements from below the aircraft by Gimballed Limb Observer for Radiance Imaging of the Atmosphere and above the aircraft by Airborne Lidar for the Middle Atmosphere. Refraction is identified in two different GW packets as low as ≈4 km and as high as 58 km. One GW packet of orographic origin and one of nonorographic origin is used to investigate refraction. Observations are supplemented by the Gravity‐wave Regional Or Global Ray Tracer, a simplified mountain wave model, ERA5 data and high‐resolution (3 km) WRF data. Contrary to some previous studies we find that refraction makes a noteworthy contribution in the amount and the location of GWMF deposition. This case study highlights the importance of refraction and provides compelling arguments that models should account for this.
Oxidative stress-triggered Wnt signaling perturbation characterizes the tipping point of lung adeno-to-squamous transdifferentiation
Authors: Fang Zhaoyuan , Han Xiangkun , Chen Yueqing , Tong Xinyuan , Xue Yun , Yao Shun , Tang Shijie , Pan Yunjian , Sun Yihua , Wang Xue , Jin Yujuan , Chen Haiquan , Hu Liang , Hui Lijian , Li Lin , Chen Luonan , Ji Hongbin 
Published: January 2023

AbstractLkb1 deficiency confers the Kras-mutant lung cancer with strong plasticity and the potential for adeno-to-squamous transdifferentiation (AST). However, it remains largely unknown how Lkb1 deficiency dynamically regulates AST. Using the classical AST mouse model (KrasLSL-G12D/+;Lkb1flox/flox, KL), we here comprehensively analyze the temporal transcriptomic dynamics of lung tumors at different stages by dynamic network biomarker (DNB) and identify the tipping point at which the Wnt signaling is abruptly suppressed by the excessive accumulation of reactive oxygen species (ROS) through its downstream effector FOXO3A. Bidirectional genetic perturbation of the Wnt pathway using two different Ctnnb1 conditional knockout mouse strains confirms its essential role in the negative regulation of AST. Importantly, pharmacological activation of the Wnt pathway before but not after the tipping point inhibits squamous transdifferentiation, highlighting the irreversibility of AST after crossing the tipping point. Through comparative transcriptomic analyses of mouse and human tumors, we find that the lineage-specific transcription factors (TFs) of adenocarcinoma and squamous cell carcinoma form a “Yin-Yang” counteracting network. Interestingly, inactivation of the Wnt pathway preferentially suppresses the adenomatous lineage TF network and thus disrupts the “Yin-Yang” homeostasis to lean towards the squamous lineage, whereas ectopic expression of NKX2-1, an adenomatous lineage TF, significantly dampens such phenotypic transition accelerated by the Wnt pathway inactivation. The negative correlation between the Wnt pathway and AST is further observed in a large cohort of human lung adenosquamous carcinoma. Collectively, our study identifies the tipping point of AST and highlights an essential role of the ROS-Wnt axis in dynamically orchestrating the homeostasis between adeno- and squamous-specific TF networks at the AST tipping point.
The HAPSTR2 retrogene buffers stress signaling and resilience in mammals
Authors: Amici David R. , Cingoz Harun , Alasady Milad J. , Alhayek Sammy , Phoumyvong Claire M. , Sahni Nidhi , Yi S. Stephen , Mendillo Marc L. 
Published: January 2023

AbstractWe recently identified HAPSTR1 (C16orf72) as a key component in a novel pathway which regulates the cellular response to molecular stressors, such as DNA damage, nutrient scarcity, and protein misfolding. Here, we identify a functional paralog to HAPSTR1: HAPSTR2. HAPSTR2 formed early in mammalian evolution, via genomic integration of a reverse transcribed HAPSTR1 transcript, and has since been preserved under purifying selection. HAPSTR2, expressed primarily in neural and germline tissues and a subset of cancers, retains established biochemical features of HAPSTR1 to achieve two functions. In normal physiology, HAPSTR2 directly interacts with HAPSTR1, markedly augmenting HAPSTR1 protein stability in a manner independent from HAPSTR1’s canonical E3 ligase, HUWE1. Alternatively, in the context of HAPSTR1 loss, HAPSTR2 expression is sufficient to buffer stress signaling and resilience. Thus, we discover a mammalian retrogene which safeguards fitness.
Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials
Authors: Herreros D. , Lederman R. R. , Krieger J. M. , Jiménez-Moreno A. , Martínez M. , Myška D. , Strelak D. , Filipovic J. , Sorzano C. O. S. , Carazo J. M. 
Published: January 2023

AbstractThe new developments in Cryo-EM Single Particle Analysis are helping us to understand how the macromolecular structure and function meet to drive biological processes. By capturing many states at the particle level, it is possible to address how macromolecules explore different conformations, information that is classically extracted through 3D classification. However, the limitations of classical approaches prevent us from fully understanding the complete conformational landscape due to the reduced number of discrete states accurately reconstructed. To characterize the whole structural spectrum of a macromolecule, we propose an extension of our Zernike3D approach, able to extract per-image continuous flexibility information directly from a particle dataset. Also, our method can be seamlessly applied to images, maps or atomic models, opening integrative possibilities. Furthermore, we introduce the ZART reconstruction algorithm, which considers the Zernike3D deformation fields to revert particle conformational changes during the reconstruction process, thus minimizing the blurring induced by molecular motions.
TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction
Authors: Sakaniwa Kentaro , Fujimura Akiko , Shibata Takuma , Shigematsu Hideki , Ekimoto Toru , Yamamoto Masaki , Ikeguchi Mitsunori , Miyake Kensuke , Ohto Umeharu , Shimizu Toshiyuki 
Published: January 2023

AbstractToll-like receptor 3 (TLR3) is a member of the TLR family, which plays an important role in the innate immune system and is responsible for recognizing viral double-stranded RNA (dsRNA). Previous biochemical and structural studies have revealed that a minimum length of approximately 40–50 base pairs of dsRNA is necessary for TLR3 binding and dimerization. However, efficient TLR3 activation requires longer dsRNA and the molecular mechanism underlying its dsRNA length-dependent activation remains unknown. Here, we report cryo-electron microscopy analyses of TLR3 complexed with longer dsRNA. TLR3 dimers laterally form a higher multimeric complex along dsRNA, providing the basis for cooperative binding and efficient signal transduction.
The power of microscopic nonclassical states to amplify the precision of macroscopic optical metrology
Authors: Ge Wenchao , Jacobs Kurt , Zubairy M. Suhail 
Published: January 2023

AbstractIt is well-known that the precision of a phase measurement with a Mach-Zehnder interferometer employing strong classic light can be greatly enhanced with the addition of weak nonclassical light. In the context of quantifying nonclassicality, the amount by which a nonclassical state can enhance precision in this way has been termed its ’metrological power’. To-date, the enhancement provided by weak nonclassical states has been calculated only for specific measurement configurations. Here we are able to optimize over all measurement configurations to obtain the maximum enhancement that can be achieved by any single or multi-mode nonclassical state together with strong classical states, for local and distributed quantum metrology employing any linear or nonlinear single-mode unitary transformation. Our analysis reveals that the quantum Fisher information for quadrature-displacement sensing is the sole property that determines the maximum achievable enhancement in all of these different scenarios, providing a unified quantification of the metrological power.
A 30-year dataset of CO2 in flowing freshwaters in the United States
Authors: Toavs Timothy R. , Hasler Caleb T. , Suski Cory D. , Midway Stephen R. 
Published: January 2023

AbstractIncreasing atmospheric carbon dioxide (CO2) concentrations have been linked to effects in a wide range of ecosystems and organisms, with negative effects of elevated CO2 documented for marine organisms. Less is known about the dynamics of CO2 in freshwaters, but the potential exists for freshwater organisms to be challenged by elevated CO2. In flowing freshwaters CO2 exhibits more variability than in lakes or the ocean, yet spatiotemporally extensive direct measures of CO2 in freshwater are rare. However, CO2 can be estimated from pH, temperature, and alkalinity—commonly collected water quality metrics. We used data from the National Water Quality Monitoring Council along with the program PHREEQC to estimate CO2 in flowing freshwaters across 35,000 sites spanning the lower 48 US states from 1990 through 2020. Site data for water chemistry measurements were spatially joined with the National Hydrology Dataset. Our resulting dataset, CDFLOW, presents an opportunity for researchers to add CO2 to their datasets for further investigation.
Chromosome-level haplotype-resolved genome assembly for Takifugu ocellatus using PacBio and Hi-C technologies
Authors: Zeng Qingmin , Zhou Zhixiong , He Qian , Li Leibin , Pu Fei , Yan Mengzhen , Xu Peng 
Published: January 2023

AbstractTakifugu species serve as a model system for evolutionary studies due to their compact genomes and diverse phenotypes. The ocellated puffer (Takifugu ocellatus), characterized by special colouration, is a scarce anadromous species in the genus Takifugu. As an ornamental and tasty fish species, T. ocellatus has moderate economic value. However, the available genomic resources for this pufferfish are still limited. Here, a chromosome-level reference genome, as well as two haploid genomes, was constructed by PacBio HiFi long sequencing and Hi-C technologies. The total length of the reference genome was 375.62 Mb with a contig N50 of 11.55 Mb. The assembled sequences were anchored to 22 chromosomes with an integration efficiency of 93.78%. Furthermore, 28,808 protein-coding genes were predicted. The haplotype-resolved reference genome of T. ocellatus provides a crucial resource for investigating the explosive speciation of the Takifugu genus, such as elucidating evolutionary histories, determining the genetic basis of trait evolution, and supporting future conservation efforts.
Genotype-specific reference interval of haptoglobin tests in a Chinese population on the BN II System
Authors: Lei Daxin , Hu Saicong , Guo Miao , Wang Jia , Ma Xiaowei , Wang Fukun , He Zhengxin 
Published: January 2023

AbstractThe distribution of Haptoglobin (HP) subtypes differs according to race and geography. It was also confirmed that the serum HP concentration was substantially affected by the HP subtypes. This study aimed to investigate the HP subtypes in northern Chinese and to establish reference intervals for the major HP subtypes using the BN II system. 1195 individuals were included in the study, grouped by haptoglobin subtype, and tested for concentrations by BN II System. Analysis of reference range was performed according to the EP28-A3c guideline. The need to establish reference ranges for subtype, gender, and age groupings was confirmed by the Z-test. The 2.5th and 97.5th percentiles were used as the upper and lower limits of the reference interval, respectively. In the population we investigated, the HP2-2 subtype had the highest proportion, accounting for 49.3%, followed by HP2-1 (38.0%), HP1-1 (7.2%). In addition, about 5.5% of individuals had HPdel-related subtypes. The concentrations of the major subtypes (HP1-1, HP2-1, HP2-2) were significantly different, and it was necessary to establish reference ranges by grouping according to the results of the Z-test. The reference intervals were as follows: HP1-1, 0.37–2.19 g/L; HP2-1, 0.38–2.12 g/L; HP2-2, 0.12–1.51 g/L. Significant differences in HP concentrations between genders and ages were found, however, it was not necessary to establish separate reference interval since the results of the Z-test was negative. We have established reference ranges of serum haptoglobin concentrations based on subtypes, which are necessary for the clinical application of haptoglobin.
Enhanced regional connectivity between western North American national parks will increase persistence of mammal species diversity
Authors: Newmark William D. , Halley John M. , Beier Paul , Cushman Samuel A. , McNeally Phoebe B. , Soulé Michael E. 
Published: January 2023

AbstractMany protected areas worldwide increasingly resemble habitat isolates embedded in human-modified landscapes. However, establishing linkages among protected areas could significantly reduce species-loss rates. Here we present a novel method having broad applicability for assessing enhanced regional connectivity on persistence of mammal diversity. We combine theoretically-derived species relaxation rates for mammal communities with empirically-derived pathways. We assess the value of enhanced regional connectivity for two hypothetical networks of national parks in western North America: the Yellowstone-Glacier network and the Mount Rainier-North Cascades network. Linking the Yellowstone and Glacier park assemblages by eliminating barriers to movement in identified mammal dispersal pathways and by incorporating adjacent wilderness areas and known ungulate migratory routes into a protected area network would greatly enlarge available habitat. This would enhance medium to large mammal species persistence time by factor of 4.3, on average, or ~ 682 generations relative to individual parks. Similarly, linking Mount Rainier and North Cascades park assemblages would enhance mammal species persistence time by a factor of 4.3, on average, or ~305 generations relative to individual parks. Enhancing regional connectivity among western North America parks could serve as an important template for landscape-scale conservation in the 21st century.
SO3H-functionalized carbon fibers for the catalytic transformation of glycerol to glycerol tert-butyl ethers
Authors: Ptaszyńska Karolina , Malaika Anna , Kapska Magdalena , Kozłowski Mieczysław 
Published: January 2023

AbstractCarbon fibers (CFs) of high quality were produced from hydrocarbons such as isobutane or ethylene using the catalytic chemical vapor deposition method (CCVD) and Ni catalyst. The as-prepared samples were functionalized with acidic groups using concentrated sulfuric acid or 4-benzenediazonium sulfonate (BDS) generated in situ from sulfanilic acid and sodium nitrite. The morphological features of the materials were confirmed by transmission electron microscopy, whereas their physicochemical properties were characterized by means of elemental and textural analyses, thermogravimetric (TG) method, Raman spectroscopy, potentiometric back titration, and X-ray diffraction analysis. The obtained CFs were used as catalysts in glycerol etherification with tert-butyl alcohol at 110 °C under autogenous pressure. The BDS-modified CFs were particularly effective in the reaction, showing high glycerol conversions (of about 45–55% after 6 h) and substantial yields of mono- and di-glycerol ethers. It was found that the chemistry of the sample surface was crucial for the process. The high concentration of -SO3H groups decorating CFs boosted the formation of di- and tri-tert-butyl glycerol ethers. Surface oxygen functionalities also had a positive effect on the reaction, however, their impact on the catalytic performances of CFs was significantly weaker compared to that shown by -SO3H groups and it was probably due to the adsorption of reagents on the catalyst surface.