bluuebunny/crossref_metadata_2025_split huggingface dataset:
A global reptile assessment highlights shared conservation needs of tetrapods
Authors: Cox Neil , Young Bruce E. , Bowles Philip , Fernandez Miguel , Marin Julie , Rapacciuolo Giovanni , Böhm Monika , Brooks Thomas M. , Hedges S. Blair , Hilton-Taylor Craig , Hoffmann Michael , Jenkins Richard K. B. , Tognelli Marcelo F. , Alexander Graham J. , Allison Allen , Ananjeva Natalia B. , Auliya Mark , Avila Luciano Javier , Chapple David G. , Cisneros-Heredia Diego F. , Cogger Harold G. , Colli Guarino R. , de Silva Anslem , Eisemberg Carla C. , Els Johannes , Fong G. Ansel , Grant Tandora D. , Hitchmough Rodney A. , Iskandar Djoko T. , Kidera Noriko , Martins Marcio , Meiri Shai , Mitchell Nicola J. , Molur Sanjay , Nogueira Cristiano de C. , Ortiz Juan Carlos , Penner Johannes , Rhodin Anders G. J. , Rivas Gilson A. , Rödel Mark-Oliver , Roll Uri , Sanders Kate L. , Santos-Barrera Georgina , Shea Glenn M. , Spawls Stephen , Stuart Bryan L. , Tolley Krystal A. , Trape Jean-François , Vidal Marcela A. , Wagner Philipp , Wallace Bryan P. , Xie Yan 
Published: April 2022

AbstractComprehensive assessments of species’ extinction risks have documented the extinction crisis1 and underpinned strategies for reducing those risks2. Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction3. Because global assessments have been lacking, reptiles have been omitted from conservation-prioritization analyses that encompass other tetrapods4–7. Reptiles are unusually diverse in arid regions, suggesting that they may have different conservation needs6. Here we provide a comprehensive extinction-risk assessment of reptiles and show that at least 1,829 out of 10,196 species (21.1%) are threatened—confirming a previous extrapolation8 and representing 15.6 billion years of phylogenetic diversity. Reptiles are threatened by the same major factors that threaten other tetrapods—agriculture, logging, urban development and invasive species—although the threat posed by climate change remains uncertain. Reptiles inhabiting forests, where these threats are strongest, are more threatened than those in arid habitats, contrary to our prediction. Birds, mammals and amphibians are unexpectedly good surrogates for the conservation of reptiles, although threatened reptiles with the smallest ranges tend to be isolated from other threatened tetrapods. Although some reptiles—including most species of crocodiles and turtles—require urgent, targeted action to prevent extinctions, efforts to protect other tetrapods, such as habitat preservation and control of trade and invasive species, will probably also benefit many reptiles.
Phases of stability during major hydroclimate change ending the Last Glacial in the Levant
Authors: Müller Daniela , Neugebauer Ina , Ben Dor Yoav , Enzel Yehouda , Schwab Markus J. , Tjallingii Rik , Brauer Achim 
Published: April 2022

AbstractIn-depth understanding of the reorganization of the hydrological cycle in response to global climate change is crucial in highly sensitive regions like the eastern Mediterranean, where water availability is a major factor for socioeconomic and political development. The sediments of Lake Lisan provide a unique record of hydroclimatic change during the last glacial to Holocene transition (ca. 24–11 ka) with its tremendous water level drop of ~ 240 m that finally led to its transition into the present hypersaline water body—the Dead Sea. Here we utilize high-resolution sedimentological analyses from the marginal terraces and deep lake to reconstruct an unprecedented seasonal record of the last millennia of Lake Lisan. Aragonite varve formation in intercalated intervals of our record demonstrates that a stepwise long-term lake level decline was interrupted by almost one millennium of rising or stable water level. Even periods of pronounced water level drops indicated by gypsum deposition were interrupted by decades of positive water budgets. Our results thus highlight that even during major climate change at the end of the last glacial, decadal to millennial periods of relatively stable or positive moisture supply occurred which could have been an important premise for human sedentism.
Antibody response to double SARS-CoV-2 mRNA vaccination in Japanese kidney transplant recipients
Authors: Fujieda Kumiko , Tanaka Akihito , Kikuchi Ryosuke , Takai Nami , Saito Shoji , Yasuda Yoshinari , Fujita Takashi , Kato Masashi , Furuhashi Kazuhiro , Maruyama Shoichi 
Published: April 2022

AbstractImmunocompromised patients, especially those who undergo kidney transplantation, have lower antibody levels following SARS-CoV-2 mRNA vaccination. The situation of transplant treatment, such as transplant source and immunosuppressive drugs, is different in Japan than that in other countries. Therefore, it is necessary to clarify whether antibody acquisition rates differ between Japan and other countries. This retrospective study included patients with post-kidney transplant who were attending at the Nagoya University Hospital. The anti-SARS-CoV-2 IgG antibody titers were measured between 3 weeks and 3 months after vaccination. Seventy-three patients (45 men and 28 women) were included. Of these, 23 (31.5%) showed antibody presence, and the rates of antibody acquisition were very low than those in the control group (100.0% vs. 31.5%, P < 0.05). Antibody acquisition rates were associated with body mass index (odds ratio [OR]: 1.21, 95% confidence interval [CI]: 1.04–1.39, P < 0.05) and the duration between transplantation and vaccination (OR: 1.01, 95% CI: 1.00–1.02, P < 0.05). The immunosuppressive drugs used were: prednisolone in all cases, tacrolimus in 89.0%, cyclosporine in 9.6%, and mofetil mycophenolate in 97.3%. None of the patients were excluded from receiving two doses of the vaccine due to adverse effects. The study indicated that vaccination-induced antibody acquisition rates against SARS-CoV-2 were extremely low in Japanese patients who underwent post-kidney transplantation. Thus, despite two doses of vaccination, it is necessary to closely monitor infection control in such patients.
Distribution of bacteriologically positive and bacteriologically negative pulmonary tuberculosis in Northwest China: spatiotemporal analysis
Authors: Jiang Hualin , Sun Xiaolu , Hua Zhongqiu , Liu Haini , Cao Yi , Ren Dan , Qi Xin , Zhang Tianhua , Zhang Shaoru 
Published: April 2022

AbstractPulmonary tuberculosis (PTB) is a major health issue in Northwest China. Most previous studies on the spatiotemporal patterns of PTB considered all PTB cases as a whole; they did not distinguish notified bacteriologically positive PTB (BP-PTB) and notified bacteriologically negative PTB (BN-PTB). Thus, the spatiotemporal characteristics of notified BP-PTB and BN-PTB are still unclear. A retrospective county-level spatial epidemiological study (2011–2018) was conducted in Shaanxi, Northwest China. In total, 44,894 BP-PTB cases were notified, with an average annual incidence rate of 14.80 per 100,000 persons between 2011 and 2018. Global Moran’s I values for notified BP-PTB ranged from 0.19 to 0.49 (P < 0.001). Anselin’s local Moran’s I analysis showed that the high–high (HH) cluster for notified BP-PTB incidence was mainly located in the southernmost region. The primary spatiotemporal cluster for notified BP-PTB (LLR = 612.52, RR = 1.77, P < 0.001) occurred in the central region of the Guanzhong Plain in 2011. In total, 116,447 BN-PTB cases were notified, with an average annual incidence rate of 38.38 per 100,000 persons between 2011 and 2018. Global Moran’s I values for notified BN-PTB ranged from 0.39 to 0.69 (P < 0.001). The HH clusters of notified BN-PTB were mainly located in the north between 2011 and 2014 and in the south after 2015. The primary spatiotemporal cluster for notified BN-PTB (LLR = 1084.59, RR = 1.85, P < 0.001) occurred in the mountainous areas of the southernmost region from 2014 to 2017. Spatiotemporal clustering of BP-PTB and BN-PTB was detected in the poverty-stricken mountainous areas of Shaanxi, Northwest China. Our study provides evidence for intensifying PTB control activities in these geographical clusters.
Obstetric outcomes during delivery hospitalizations among obese pregnant women in the United States
Authors: Rubens Muni , Ramamoorthy Venkataraghavan , Saxena Anshul , McGranaghan Peter , Veledar Emir , Hernandez Agueda 
Published: April 2022

AbstractThe rates of both maternal and fetal adverse outcomes increase significantly with higher body mass index. The aim of this study was to calculate national estimates of adverse maternal and fetal outcomes and associated hospitalization cost among obese pregnant women using a national database. This study was a retrospective analysis of data retrieved from Nationwide Inpatient Sample database, collected during 2010–2014. The primary outcomes of this study were adverse maternal and fetal outcomes, hospital length of stay, and hospitalization cost. There was a total of 18,687,217 delivery-related hospitalizations, of which 1,048,323 were among obese women. Obese women were more likely to have cesarean deliveries (aOR 1.70, 95% CI 1.62–1.79) and labor inductions (aOR 1.51, 95% CI 1.42–1.60), greater length of stay after cesarean deliveries (aOR 1.14, 95% CI 1.08–1.36) and vaginal deliveries (aOR 1.48, 95% CI 1.23–1.77). They were also more likely to have pregnancy-related hypertension, preeclampsia, gestational diabetes, premature rupture of membranes, chorioamnionitis, venous thromboembolism, excessive fetal growth, and fetal distress. Obese pregnant women had significantly greater risk for adverse obstetrical outcomes, which substantially increased the hospital and economic burden. Risk stratification of pregnant patients based on obesity could also help obstetricians to make better clinical decisions and improve patient outcomes.
Characterization of Klebsiella pneumoniae isolated from patients suspected of pulmonary or bubonic plague during the Madagascar epidemic in 2017
Authors: Rakotondrasoa Andriniaina , Andrianonimiadana Lova Maminirina , Rahajandraibe Soloandry , Razafimahatratra Solohery , Andrianaivoarimanana Voahangy , Rahelinirina Soanandrasana , Crucitti Tania , Brisse Sylvain , Jeannoda Victor , Rajerison Minoarisoa , Collard Jean-Marc 
Published: April 2022

AbstractKlebsiella pneumoniae can lead to a wide range of diseases including pneumonia, bloodstream and urinary tract infections. During a short period of a pulmonary plague epidemic in October 2017 in Madagascar, 12 K. pneumoniae isolates were identified in ten sputum and two buboes aspirate samples. These isolates were from 12 patients suspected of plague, without epidemiological relationships, but were negative for Yersinia pestis in culture. Data were collected from the plague national surveillance system. The isolates were characterized by antimicrobial susceptibility testing and whole-genome sequencing. Real-time PCR was performed to confirm the presence of K. pneumoniae DNA in buboes. All isolates were identified as K. pneumoniae sensu stricto. Five isolates were extended-spectrum β-lactamases producers; eleven different sequence types were identified. Five isolates belonged to known hypervirulent sequence types. Our results demonstrate community-acquired pneumonia caused by K. pneumoniae isolates in patients suspected of plague stressing the importance of bed-side differential diagnosis.
Significance of the broad non-bony attachments of the anterior cruciate ligament on the tibial side
Authors: Muro Satoru , Kim Jiyoon , Tsukada Sachiyuki , Akita Keiichi 
Published: April 2022

AbstractKnowledge of the anatomy of the anterior cruciate ligament (ACL) is important to understand the function and pathology of the knee joint. However, on the tibial side of ACL, its structural relationships with the articular cartilage and lateral meniscus remain unclear. Furthermore, conventional research methods are limited to analyzing the bone attachments. We provide a comprehensive, three-dimensional anatomical description of the tibial side of the ACL that questions the principle that “a ligament is necessarily a structure connecting a bone to another bone.” In our study, 11 knees from 6 cadavers were used for macroscopic anatomical examinations, serial-section histological analyses, and three-dimensional reconstructions. The attachments of the tibial side of ACL consisted of attachments to the bone (102.6 ± 27.5 mm2), articular cartilage (40.9 ± 13.6 mm2), and lateral meniscus (6.5 ± 4.6 mm2), suggesting that the ACL has close structural relationships with the articular cartilage and lateral meniscus. Our study demonstrates that the tibial side of the ACL is not attached to the bone surface only and provides new perspectives on ligamentous attachments. Considering its attachment to the articular cartilage would enable more accurate functional evaluations of the mechanical tensioning of the ACL.
Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia
Authors: Dranenko Natalia O. , Tutukina Maria N. , Gelfand Mikhail S. , Kondrashov Fyodor A. , Bochkareva Olga O. 
Published: April 2022

AbstractUntil recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans. We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny and composition of effectors indicate horizontal gene transfer between E. coli adapted to different hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals.
High altitude is associated with pTau deposition, neuroinflammation, and myelin loss
Authors: Iacono Diego , Murphy Erin K. , Sherman Paul M. , Chapapas Holly , Cerqueira Bianca , Christensen Christine , Perl Daniel P. , Sladky John 
Published: April 2022

AbstractMammals are able to adapt to high altitude (HA) if appropriate acclimation occurs. However, specific occupations (professional climbers, pilots, astronauts and other) can be exposed to HA without acclimation and be at a higher risk of brain consequences. In particular, US Air Force U2-pilots have been shown to develop white matter hyperintensities (WMH) on MRI. Whether WMH are due to hypoxia or hypobaria effects is not understood. We compared swine brains exposed to 5000 feet (1524 m) above sea level (SL) with 21% fraction inspired O2 (FiO2) (Control group [C]; n = 5) vs. 30,000 feet (9144 m) above SL with 100% FiO2 group (hypobaric group [HYPOBAR]; n = 6). We performed neuropathologic assessments, molecular analyses, immunohistochemistry (IHC), Western Blotting (WB), and stereology analyses to detect differences between HYPOBAR vs. Controls. Increased neuronal insoluble hyperphosphorylated-Tau (pTau) accumulation was observed across different brain regions, at histological level, in the HYPOBAR vs. Controls. Stereology-based cell counting demonstrated a significant difference (p < 0.01) in pTau positive neurons between HYPOBAR and C in the Hippocampus. Higher levels of soluble pTau in the Hippocampus of HYPOBAR vs. Controls were also detected by WB analyses. Additionally, WB demonstrated an increase of IBA-1 in the Cerebellum and a decrease of myelin basic protein (MBP) in the Hippocampus and Cerebellum of HYPOBAR vs. Controls. These findings illustrate, for the first time, changes occurring in large mammalian brains after exposure to nonhypoxic-hypobaria and open new pathophysiological views on the interaction among hypobaria, pTau accumulation, neuroinflammation, and myelination in large mammals exposed to HA.
Point cloud registration method for maize plants based on conical surface fitting—ICP
Authors: Zhang Kai’xing , Chen He , Wu Hao , Zhao Xiu’yan , Zhou Chang’an 
Published: April 2022

AbstractReconstructing three-dimensional (3D) point cloud model of maize plants can provide reliable data for its growth observation and agricultural machinery research. The existing data collection systems and registration methods have low collection efficiency and poor registration accuracy. A point cloud registration method for maize plants based on conical surface fitting—iterative closest point (ICP) with automatic point cloud collection platform was proposed in this paper. Firstly, a Kinect V2 was selected to cooperate with an automatic point cloud collection platform to collect multi-angle point clouds. Then, the conical surface fitting algorithm was employed to fit the point clouds of the flowerpot wall to acquire the fitted rotation axis for coarse registration. Finally, the interval ICP registration algorithm was used for precise registration, and the Delaunay triangle meshing algorithm was chosen to triangulate the point clouds of maize plants. The maize plant at the flowering and kernel stage was selected for reconstruction experiments, the results show that: the full-angle registration takes 57.32 s, and the registration mean distance error is 1.98 mm. The measured value’s relative errors between the reconstructed model and the material object of maize plant are controlled within 5%, the reconstructed model can replace maize plants for research.
Nephrotoxicity evaluation and proteomic analysis in kidneys of rats exposed to thioacetamide
Authors: Lim Ji-youn , Jung Woon-Won , Kim Woojin , Moon Kyoung-Sik , Sul Donggeun 
Published: April 2022

AbstractThioacetamide (TAA) was administered orally at 0, 10, and 30 mg/kg body weight (BW) daily to Sprague–Dawley rats aged 6–7 weeks for 28 consecutive days. Nephrotoxicity and proteomics were evaluated in the kidneys of rats exposed to TAA. The BW decreased, however, the relative kidneys weight increased. No significant histopathologic abnormalities were found in the kidneys. The numbers of monocytes and platelets were significantly increased. However, the mean corpuscular volume and hematocrit values were decreased significantly in rats exposed to 30 mg/kg BW TAA. The expression levels of Kim-1 and NGAL were increased 4 to 5-fold in the kidneys, resulting in significant nephrotoxicity. Proteomic analysis was conducted and a total of 5221 proteins spots were resolved. Of these, 3 and 21 protein spots were up- and downregulated, respectively. The validation of seven proteins was performed by Western blot analysis. The expression level of ASAP2 was significantly upregulated, whereas RGS14, MAP7Dl, IL-3Rα, Tmod1, NQO2, and MUP were reduced. Sixteen isoforms of MUP were found by the 2DE immunoblot assay and were significantly downregulated with increasing exposure to TAA. MUP isoforms were compared in the liver, kidneys, and urine of untreated rats and a total of 43 isoforms were found.
Detection of environmental pollutant cadmium in water using a visual bacterial biosensor
Authors: Hui Chang-ye , Guo Yan , Li Han , Gao Chao-xian , Yi Juan 
Published: April 2022

AbstractCadmium (Cd) contamination in water and soil is considered an environmental pollutant. Food crops can absorb and accumulate bioavailable Cd. Continuous monitoring of Cd levels in the environment can minimize exposure and harm to humans. Visual pigments have been demonstrated to have great potential in the development of minimal-equipment biosensors. In the present study, a metabolically engineered bacterium was employed to produce blue-purple pigment violacein responsive to toxic Cd(II). The high stability of the bisindole pigment contributed to determining the violacein at wavelengths of 578 nm. Visual and quantifiable signals could be captured after a 1.5-h Cd(II) exposure. This novel biosensor showed significantly stronger responses to Cd(II) than to other heavy metals including Pb(II), Zn(II), and Hg(II). A significant increase in pigment signal was found to respond to as low as 0.049 μM Cd(II). The naked eye can detect the color change when violacein-based biosensor is exposed to 25 μM Cd(II). A high-throughput method for rapid determination of soluble Cd(II) in environmental water was developed using a colorimetric microplate.
A VSV-based assay quantifies coronavirus Mpro/3CLpro/Nsp5 main protease activity and chemical inhibition
Authors: Heilmann Emmanuel , Costacurta Francesco , Geley Stephan , Mogadashi Seyad Arad , Volland Andre , Rupp Bernhard , Harris Reuben Stewart , von Laer Dorothee 
Published: April 2022

AbstractProtease inhibitors are among the most powerful antiviral drugs. However, for SARS-CoV-2 only a small number of protease inhibitors have been identified thus far and there is still a great need for assays that efficiently report protease activity and inhibition in living cells. Here, we engineer a safe VSV-based system to report both gain- and loss-of-function of coronavirus main protease (Mpro/3CLpro/Nsp5) activity in living cells. We use SARS-CoV-2 3CLpro in this system to confirm susceptibility to known inhibitors (boceprevir, GC376, PF-00835231, and PF-07321332/nirmatrelvir) and reevaluate other reported inhibitors (baicalein, ebselen, carmofur, ethacridine, ivermectin, masitinib, darunavir, and atazanavir). Moreover, we show that the system can be adapted to report both the function and the chemical inhibition of proteases from different coronavirus species as well as from distantly related viruses. Together with the fact that live cell assays also reflect compound permeability and toxicity, we anticipate that this system will be useful for both identification and optimization of additional coronavirus protease inhibitors.