bluuebunny/crossref_metadata_2025_split huggingface dataset:
PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data
Authors: Cai Liming , Zhang Hongrui , Davis Charles C. 
Published: June 2022

AbstractPremiseThe application of high‐throughput sequencing, especially to herbarium specimens, is rapidly accelerating biodiversity research. Low‐coverage sequencing of total genomic DNA (genome skimming) is particularly promising and can simultaneously recover the plastid, mitochondrial, and nuclear ribosomal regions across hundreds of species. Here, we introduce PhyloHerb, a bioinformatic pipeline to efficiently assemble phylogenomic data sets derived from genome skimming.Methods and ResultsPhyloHerb uses either a built‐in database or user‐specified references to extract orthologous sequences from all three genomes using a BLAST search. It outputs FASTA files and offers a suite of utility functions to assist with alignment, partitioning, concatenation, and phylogeny inference. The program is freely available at https://github.com/lmcai/PhyloHerb/.ConclusionsWe demonstrate that PhyloHerb can accurately identify genes using a published data set from Clusiaceae. We also show via simulations that our approach is effective for highly fragmented assemblies from herbarium specimens and is scalable to thousands of species.
Analysing corporate forest disclosure: How does business value biodiversity?
Authors: Anthony Samuel Jack , Morrison‐Saunders Angus 
Published: June 2022

AbstractCorporations are failing to account for their impact on biodiversity despite accelerating extinctions. The value of biodiversity to business can be explained by an environmental philosophy spectrum, where perspectives range from anthropocentric (humans are prioritised) to ecocentric (all life is equal), made up of paradigms and values linked to biodiversity protection. We explore the biodiversity values conveyed by the 40 largest corporations responding to the CDP Forest Questionnaire using 28 specific yes/no criteria aligned with the environmental philosophy spectrum. Strong anthropocentric perspectives focused on economic contribution dominated, conveying a desire to protect company reputation, thereby legitimising operations. Corporations seemingly only protect biodiversity that hold material benefits for humans. Some biocentric/ecocentric perspectives were conveyed in terms of extinction risk and sometimes intrinsic value. This could be a response to the accelerating global biodiversity crisis, offering hope corporations can protect all forms of biodiversity and could evidence ecocentric leadership informing business strategy.
Evaluation of health behaviors and overall quality of life in younger adult African American cancer survivors
Authors: Trendowski Matthew R. , Kyko Jaclyn M. , Lusk Christine M. , Ruterbusch Julie J. , Hastert Theresa A. , Harper Felicity W. K. , Thompson Hayley , Beebe‐Dimmer Jennifer L. , Schwartz Ann G. 
Published: June 2022

AbstractBackgroundEpidemiological studies of cancer survivors have predominantly focused on non‐Hispanic White, elderly patients, despite the observation that African Americans have higher rates of mortality. Therefore, we characterized cancer survivorship in younger African American survivors using the Detroit Research on Cancer Survivors (ROCS) study to assess health behaviors and quality of life.MethodsFive hundred and seventeen patients diagnosed with any cancer between the ages of 20–49 (mean age: 42 years; SD: 6.7 years) completed a survey to identify important clinical, behavioral, and sociodemographic characteristics, measures of health literacy, and experiences of discrimination. Quality of life outcomes were evaluated in patients using FACT‐G, FACT‐Cog, and PROMIS® Anxiety and Depression scales. Stepwise linear and logistic regression were used to assess the association between quality of life measures and participant characteristics.ResultsThe mean FACT‐G score was 74.1 (SD: 21.3), while the FACT‐Cog was 55.1 (SD: 17.1) (FACT‐G range 0–108 with higher scores indicating better function; elderly cancer patient mean: 82.2; FACT‐Cog 18‐item range 0–72 points with higher scores indicating better perceived cognitive functioning; scores <54 indicating cognitive impairment). In addition, 27.1% and 21.6% of patients had a score indicative of moderate or severe anxiety and depression, respectively. Perceived discrimination and the number of discriminatory events were significantly associated with reductions in three of the four quality of life measures. Health literacy was positively associated with all four health measures, while total comorbidity count was negatively associated with three of the four measures.ConclusionYounger adult African American cancer survivors who report experiencing discrimination and suffer from multiple comorbid conditions have poorer mental and overall health. Understanding the unique clinical and socioeconomic stressors that influence this patient population is essential for reducing health disparities and improving long‐term survivorship.
Generation of cart‐pulling animation in a multiagent environment using deep learning
Authors: Wong Chien‐Chou , Cai Cheng‐En , Tsai Hao‐Ming , Liu Guan‐Ting , Wong Sai‐Keung 
Published: June 2022

AbstractIn this article, we propose a framework to generate cart‐pulling animation using deep learning in a multiagent environment. Mainly, two workers pull a cart using ropes and interact with crowd agents which exhibit following, wandering, and evasion behaviors. The main idea is to train a policy to learn an individual behavior of the workers and crowd agents. Furthermore, the challenge is that as the ropes are flexible, rewards are designed carefully so that the workers pull the ropes in a collaborative and consistent manner. Hence, the workers can pull the cart while avoiding collision with the crowd agents and surrounding static objects. In the stage of animation generation, we assign the policies deliberately to the workers and the crowd agents so that they interact with each other naturally. We conducted experiments on animal characters and the system could produce animations of characters with diverse behaviors.
Is there association of olanzapine and pulmonary embolism: A case report
Authors: Wang Lumin , Xu Yijiao , Jiang Weiwen , Liu Jiaxin , Cao Chang , Shen Yun , Xiao Xiong , Ye Yanrong 
Published: June 2022

AbstractOlanzapine is a second‐generation antipsychotic drug that is often used to treat schizophrenia and manic attacks. An increasing number of cases in recent years have shown that olanzapine is associated with vascular thromboembolic disease (VTD). Here, we reported a case of patient with history of taking aripiprazole, benzhexol, olanzapine, and sertraline for 5 years. He was admitted because of aggravated chest tightness, chest pain, and shortness of breath sustaining for 3 days. Laboratory examination and computed tomography angiography of the chest revealed new pulmonary embolus which involved the main trunk of the pulmonary artery and bilateral pulmonary arteries, with pneumonic infiltration in the left upper lobe. After thrombolytic therapy, the patient was out of danger.
Do NGS‐based techniques represent a first‐line testing in suspected Duchenne muscular dystrophy?
Authors: Hosseini Seyed Mohammad , Alizadeh Nosratollah , Amini Abolfazl , Mohammadi‐Asl Javad 
Published: June 2022

AbstractDuchenne muscular dystrophy (DMD) is caused by mutations in the dystrophin gene, which mostly affects boys. The subject was an 8‐year‐old child who had typical symptoms of muscle weakness. The NGS may be used as an efficient and cost‐effective molecular diagnostic strategy for identifying patients with DMD.
Foreign accent syndrome post tonsillectomy: A case report
Authors: Corbett Mel , O’Shea John , Van Den Berg Nadia , Lang John 
Published: June 2022

AbstractForeign Accent Syndrome (FAS) is a rare clinical entity in which affected patients experience a new pattern of speech resembling an unusual accent. Reported cases are scarce in published literature and are usually the result of a neurological insult. FAS as a complication from a general anesthetic or surgery has not been reported to date. We present the case of a healthy 27‐year‐old Australian woman who developed FAS following a tonsillectomy. Post operatively, speech patterns resembled an Irish accent. We discuss the potential mechanisms of the unusual complication as well as review the available literature surrounding FAS.
Delirium with delayed diagnosis of hereditary coproporphyria
Authors: Eroglu Seyma , Birsenogul Ilhan 
Published: June 2022

AbstractWe present a hereditary coproporphyria patient with acute psychiatric symptoms and skin lesions initially misdiagnosed with schizoaffective disorder and later developed hyperactive delirium and atrial fibrillation requiring intensive care unit admission. He recovered after administering glucose infusions and the discontinuation of porphyrinogenic medications.
Venlafaxine‐induced interstitial lung disease with COVID‐19 pandemic‐related depression
Authors: Okazaki Akihito , Kita Katsunao 
Published: June 2022

AbstractVenlafaxine‐associated pulmonary toxicity is rare, with only a few reports of pneumonitis, eosinophilic pneumonia, and asthma. We report a case of venlafaxine‐induced interstitial lung disease in a patient with coronavirus disease 2019 pandemic‐related depression. Chest imaging findings improved after discontinuation of venlafaxine and treatment with corticosteroids.
Hepatectomy guided by indocyanine green fluorescent imaging for visualizing bile leakage (with video)
Authors: Hanaki Takehiko , Tokuyasu Naruo , Sakamoto Teruhisa , Fujiwara Yoshiyuki 
Published: June 2022

AbstractUsing indocyanine green (ICG), a standard reagent used in liver function tests, bile leaks from exfoliated liver sections can be detected with higher sensitivity than naked‐eye observation. This presentation will introduce the technique of using ICG to detect bile leaks that cannot be detected by the naked eye.
Enalapril‐induced angioedema: A forgotten adverse event
Authors: Manzur‐Barbur María Carolina , Mejia‐Sanjuanelo Ana Milena , Martínez‐Ávila María Cristina , Manzur‐Jattin Fernando , García‐Dominguez Juan Camilo , Orozco‐Sebá Beatriz 
Published: June 2022

AbstractAngioedema is an edema of skin, mucosa, respiratory, and gastrointestinal tract, due to vascular permeability increase, resulting in plasma extravasation, which has been associated with multiple causes. We describe a case of a patient who was prescribed with enalapril and presented with symptoms suggestive of angioedema.
Catalytic Steam Reforming of Toluene as Model Tar Compound of Biomass Gasification over Cu/Ni/Olivine
Authors: Pan Yue , Tursun Yalkunjan , Guo Yao , Abduhani Hairat , Abulizi Abulikemu , Talifu Dilinuer , Zhong Mei 
Published: June 2022

AbstractBimetallic Cu/Ni/olivine catalysts with various Cu/Ni mass ratios were prepared for steam reforming of toluene as model tar compound. The effects of the Cu/Ni ratio, the reaction temperature, and the steam‐to‐carbon ratio (S/C) on the steam reforming of toluene were investigated in a fixed‐bed reactor. Among the catalysts, olivine coated with 3 wt % CuO and 12 wt % NiO (Cu3/Ni12/O) achieved higher catalytic performance and structural stability due to the synergistic effect of Ni and Cu. The appropriate S/C and a higher temperature were beneficial to steam reforming of toluene. The catalytic performance was not only affected by the amount but also by the types of carbon deposition. Compared with the amorphous carbon, the larger amount of graphitic carbon formed on the catalyst surface was more likely to lead to a decreased catalytic performance.
Redox‐Active Hydrocarbons: Isolation and Structural Determination of Cationic States toward Advanced Response Systems
Authors: Harimoto Takashi , Ishigaki Yusuke 
Published: June 2022

AbstractInvited for this month′s cover is the group of Prof. Yusuke Ishigaki at Hokkaido University, Japan. The cover picture shows a cyclic voltammogram drawn in the style of an ink painting, along with the structures of cationic species composed of pure hydrocarbons. The sunrise, a metaphor for X‐rays irradiated on cations, is reminiscent of the dawn of redox chemistry of hydrocarbons. Elucidation of their redox properties should provide important insights into the development of organic electronic devices. The cover was designed by YAP Co., Ltd. More information can be found in the Review by T. Harimoto and Y. Ishigaki.
Construction and Activity of an All‐Organic Heterojunction Photocatalyst Based on Melem and Pyromellitic Dianhydride
Authors: Li Yuxin , Jiang Zeyu , Dong Guohui , Ho Wingkei 
Published: June 2022

AbstractInvited for this month′s cover is the group of Wingkei Ho at The Education University of Hong Kong. The Cover shows the effect of the number of heterojunction knots in an all‐organic photocatalyst on the separation of photogenerated carriers. The heterojunction knots could improve the migration eﬃciency of carriers between Melem and the formed pyromellitic diimide. The oxygen adsorbed on the surface of the material can be reduced by electrons to the reactive oxygen species superoxide anion (⋅O2−), thereby achieving the purpose of removing pollutants. The Research Article itself is available at 10.1002/cssc.202200477.
ZPI prevents ox‐LDL‐mediated endothelial injury leading to inhibition of EndMT, inflammation, apoptosis, and oxidative stress through activating Pi3k/Akt signal pathway
Authors: Zhang Xingxu , Li Zhiqiang , Liu Xiangdong , Qin Xiaoming , Luo Jiachen , Zhang Wenming , Liu Baoxin , Wei Yidong 
Published: June 2022

AbstractOxidized low‐density lipoprotein (ox‐LDL)‐mediated endothelial dysfunction exerts an essential role in the development of atherosclerosis. Protein Z‐dependent protease inhibitor (ZPI), a member of the serine protease inhibitor superfamily, could inhibit the function of activated coagulation factor X (FXa) via interaction with protein Z (PZ). Studies have pointed out that ZPI was statistically related to atherosclerotic diseases, which may have a robust cardiovascular protective effect. However, the underlying mechanism of ZPI on ox‐LDL‐mediated endothelial injury requires further elucidation. Human umbilical vein endothelial cells (HUVECs) were treated with ox‐LDL (100 μg/ml) and ZPI (10 μg/ml). Cell viability was measured by the Cell Counting Kit‐8 (CCK‐8) assay. Cell apoptosis, oxidative stress, and endothelial‐to‐mesenchymal transition (EndMT) were analyzed by immunofluorescence (IF). Cell migration was measured using a wound‐healing assay. Quantitative real‐time polymerase chain reaction and western blot analysis were performed to determine messenger RNA and protein expression. Ox‐LDL (100 μg/ml, 48 h) significantly reduced cell viability and migration, increased EndMT, inflammation, apoptosis, and oxidative stress. The related protein expression of phosphatidylinositol 3 kinase/protein kinase B (Pi3k/Akt) signal pathway in HUVECs was also simultaneously decreased. We also discovered that ZPI treatment could prevent ox‐LDL‐mediated endothelial injury through the improvement of cell viability and alleviation of apoptosis, oxidative stress, EndMT, and inflammation. Thus, the protective effect of ZPI on HUVECs may be mediated by activation of the Pi3k/Akt signal pathway. ZPI may exert an important protective role in HUVECs dysfunction triggered by ox‐LDL via activation of the Pi3k/Akt signal pathway. Therefore, ZPI may possess potential therapeutic effects on atherosclerotic endothelial injury‐related diseases.
Phosphate moiety in FDA‐approved pharmaceutical salts and prodrugs
Authors: Fulmali Ameya , Bharate Sonali S. 
Published: June 2022

AbstractThe salification and prodrug approaches modulate the physicochemical properties and absorption, distribution, metabolism, excretion, and toxicity parameters of drugs and lead candidates. The “phosphate” is one of the key counterions/promoiety used in the salt formation and prodrug synthesis. Salification with phosphoric acid enhances the aqueous solubility and thereby facilitates the administration of a drug by the parenteral route. Phosphate moiety in prodrug synthesis mainly improves permeability by lipophilic substitution. Histamine phosphate is the first phosphate salt, and hydrocortisone phosphate was the first prodrug approved by FDA in 1939 and 1952, respectively. The orange book enlists 12 phosphate salts and 17 phosphate prodrugs. Phosphate prodrugs, namely combretastatin A‐4 diphosphate, combretastatin A‐4 phosphate, lufotrelvir, TP‐1287, pyridoxal phosphate, riboflavin phosphate, and psilocybin are clinical candidates. This review focuses on the FDA‐approved phosphate salts and prodrugs from 1939 to 2021. The biopharmaceutical advantage of phosphate salts and prodrugs over the parent molecule is also deliberated.
Generation of FLAG‐tagged Arx knock‐in mouse model
Authors: Lim Youngshin , Cho Il‐Taeg , Golden Jeffrey A. , Cho Ginam 
Published: June 2022

SummaryThe Aristaless‐related homeobox (ARX) is a paired‐like homeodomain transcription factor playing important roles in brain development. Patients with mutations in ARX have a spectrum of neurodevelopmental disorders such as epilepsy, intellectual disability, and autism spectrum disorder, with or without structural abnormalities of the brain such as lissencephaly (smooth brain), microcephaly (small brain), and/or agenesis of the corpus callosum. Mouse models have provided important clues on the pathophysiologic roles of ARX in these disorders. However, successfully isolating specific in vivo complexes of ARX, with DNA and proteins, has remained as a challenge. To facilitate in vivo detection of ARX complexes, we generated a mouse line containing one epitope of FLAG‐tag (1 × FLAG) targeted at the translational start site of the endogenous Arx gene using CRSPR/Cas9 strategy. Homozygous Flag‐Arx mice are viable and fertile without gross abnormality, suggesting that the FLAG‐tag does not perturb the normal function of ARX. Using a FLAG antibody, we successfully detected ARX with immunofluorescent staining and pulled down ARX in embryonic brain tissues. This Flag‐Arx mouse line will be a useful tool to isolate ARX complexes from mouse tissues for many applications.
Biological traits approaches in benthic marine ecology: Dead ends and new paths
Authors: de Juan Silvia , Bremner Julie , Hewitt Judi , Törnroos Anna , Mangano Maria Cristina , Thrush Simon , Hinz Hilmar 
Published: June 2022

AbstractBiological traits analysis (BTA) links community structure to both ecological functions and response to environmental drivers through species’ attributes. In consequence, it has become a popular approach in marine benthic studies. However, BTA will reach a dead end if the scientific community does not acknowledge its current shortcomings and limitations: (a) uncertainties related to data origins and a lack of standardized reporting of trait information; (b) knowledge gaps on the role of multiple interacting traits on driving the organisms’ responses to environmental variability; (c) knowledge gaps regarding the mechanistic links between traits and functions; (d) a weak focus on the spatial and temporal variability that is inherent to the trait expression of species; and, last but not least, (e) the large reliance on expert knowledge due to an enormous knowledge gap on the basic ecology of many benthic species. BTA will only reach its full potential if the scientific community is able to standardize and unify the reporting and storage of traits data and reconsider the importance of baseline observational and experimental studies to fill knowledge gaps on the mechanistic links between biological traits, functions, and environmental variability. This challenge could be assisted by embracing new technological advances in marine monitoring, such as underwater camera technology and artificial intelligence, and making use of advanced statistical approaches that consider the interactive nature and spatio‐temporal variability of biological systems. The scientific community has to abandon some dead ends and explore new paths that will improve our understanding of individual species, traits, and the functioning of benthic ecosystems.
Effects of humic acid and kaolinite on copper transport in water‐saturated porous media
Authors: Meng Qingling , Xue Honghai , Jiang Yan , Jiang Di 
Published: June 2022

AbstractMobile organic macromolecules and inorganic particles may act as carriers of strongly sorbing contaminants in subsurface materials, posing a potential facilitated transport risk. This study examined the influence of humic acid (HA) and kaolinite colloid on copper ion transport in saturated porous media. Column experiments were conducted to investigate the migration behavior and interactions of HA, kaolinite and copper under different experimental conditions in saturated porous media. The results showed that the individual presence of HA promoted the transport of Cu. However, the mixture of kaolinite and HA has less effect on Cu migration than HA alone. The presence of Cu reduced the mobility of kaolinite through the saturated porous media sand column by increasing the deposition rate of kaolinite. The transport of kaolinite increased significantly in the presence of HA, while kaolinite slightly decreased HA transport in the sand column. Compared with kaolinite, HA has a stronger ability to desorb copper from copper‐bearing sand. Considering the presence of kaolinite and HA, this study provides a reference for the fate, migration and risk assessment of heavy metal pollutants.
The Tunneling Information Management System – A tool for documenting the tunneling process in NATM projects
Authors: Huymajer Marco , Operta Dzan , Mazak‐Huemer Alexandra , Huemer Christian 
Published: June 2022

AbstractThe documentation of the tunneling process is a crucial task of every tunnel construction project. It provides evidence of the work performed and thus, serves as a basis for invoicing and for several further analyses. Therefore, continuous digitalisation of this documentation is essential. For this purpose, we provide a digital Tunneling Information Management System (TIMS), which is a prototypically implemented software tool for replacing the still common paper‐based documentation process of tunneling projects using the New Austrian Tunneling Method (NATM). The data model presented here defines the data structures managed by this tool. Based on this, the software architecture and the implementation of TIMS is shown.