bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatic mapping of a more precise Aspergillus niger degradome
Authors: Dong Zixing , Yang Shuangshuang , Lee Byong H. 
Published: January 2021

AbstractAspergillus niger has the ability to produce a large variety of proteases, which are of particular importance for protein digestion, intracellular protein turnover, cell signaling, flavour development, extracellular matrix remodeling and microbial defense. However, the A. niger degradome (the full repertoire of peptidases encoded by the A. niger genome) available is not accurate and comprehensive. Herein, we have utilized annotations of A. niger proteases in AspGD, JGI, and version 12.2 MEROPS database to compile an index of at least 232 putative proteases that are distributed into the 71 families/subfamilies and 26 clans of the 6 known catalytic classes, which represents ~ 1.64% of the 14,165 putative A. niger protein content. The composition of the A. niger degradome comprises ~ 7.3% aspartic, ~ 2.2% glutamic, ~ 6.0% threonine, ~ 17.7% cysteine, ~ 31.0% serine, and ~ 35.8% metallopeptidases. One hundred and two proteases have been reassigned into the above six classes, while the active sites and/or metal-binding residues of 110 proteases were recharacterized. The probable physiological functions and active site architectures of these peptidases were also investigated. This work provides a more precise overview of the complete degradome of A. niger, which will no doubt constitute a valuable resource and starting point for further experimental studies on the biochemical characterization and physiological roles of these proteases.
Topoisomerase IV tracks behind the replication fork and the SeqA complex during DNA replication in Escherichia coli
Authors: Helgesen Emily , Sætre Frank , Skarstad Kirsten 
Published: January 2021

AbstractTopoisomerase IV (TopoIV) is a vital bacterial enzyme which disentangles newly replicated DNA and enables segregation of daughter chromosomes. In bacteria, DNA replication and segregation are concurrent processes. This means that TopoIV must continually remove inter-DNA linkages during replication. There exists a short time lag of about 10–20 min between replication and segregation in which the daughter chromosomes are intertwined. Exactly where TopoIV binds during the cell cycle has been the subject of much debate. We show here that TopoIV localizes to the origin proximal side of the fork trailing protein SeqA and follows the movement pattern of the replication machinery in the cell.
Ammonium and organic carbon co-removal under feammox-coupled-with-heterotrophy condition as an efficient approach for nitrogen treatment
Authors: Le Chung Phuong , Nguyen Hai Thi , Nguyen Toi Duy , Nguyen Quyen Huynh Minh , Pham Hai The , Dinh Hang Thuy 
Published: January 2021

AbstractNitrification is the rate limiting step in the nitrogen removal processes since nitrifiers have high oxygen demand, but poorly compete with aerobic heterotrophs. In a laboratory-scaled system, we investigated a process of ammonium oxidation under ferric-iron reducing condition (feammox) in the presence of organic carbon using influents with high NH4+ and COD contents, and ferrihydrite as the only electron acceptor. Batch incubations testing influents with different NH4+ and COD concentrations revealed that the [COD]/[NH4+] ratio of 1.4 and the influent redox potential ranging from − 20 to + 20 mV led to the highest removal efficiencies, i.e. 98.3% for NH4+ and 58.8% for COD. N2 was detected as the only product of NH4+ conversion, whereas NO2− and NO3− were not detected. While operating continuously with influent having a [COD]/[NH4+] ratio of 1.4, the system efficiently removed NH4+ (> 91%) and COD (> 54%) within 6 day retention time. Fluorescence in situ hybridization analyses using Cy3-labeled 16S rRNA oligonucleotide probes revealed that gamma-proteobacteria dominated in the microbial community attaching to the matrix bed of the system. The iron-reduction dependent NH4+ and COD co-removal with a thorough conversion of NH4+ to N2 demonstrated in this study would be a novel approach for nitrogen treatment.
Transcriptomics analysis for the identification of potential age-related genes and cells associated with three major urogenital cancers
Authors: Cao Jinlong , Li Jianpeng , Yang Xin , Li Pan , Yao Zhiqiang , Han Dali , Ying Lijun , Wang Lijie , Tian Junqiang 
Published: January 2021

AbstractAge is one of the most important risk factors of the occurrence for tumor patients. The majority of patients with urogenital cancers are the elderly, whose clinical characteristics are greatly affected by age and ageing. Our study aimed to explore age-related genes, cells, and biological changes in three common urogenital cancers via integrative bioinformatics analysis. First, mRNA (count format) and clinical data for bladder cancer, prostate cancer and renal cell carcinoma were downloaded from the Cancer Genome Atlas (TCGA). Through the comparison of clinicopathological characteristics, genes expression and cells infiltration between the old group and the young group, it was found that the clinical characteristics, genes and cells in the tumor microenvironment of different ages were quite different. And 4 key cells, 14 hub genes and some potential pathways were identified and considered as important factors. More importantly, we analyzed the differential landscape of the genes and cells from different perspectives, and confirmed its importance. In conclusion, we identified genes and cell types associated with age-related changes in the tumour microenvironment in urogenital cancer patients. These genes and cell types may play a critical role in the age-associated differences in clinicopathological characteristics among urogenital cancers, thus providing a link between ageing and cancer occurrence. The findings of this study may pave the way for the development of age-tailored approaches to treat cancer and other age-related diseases.
Neural representations of own-voice in the human auditory cortex
Authors: Hosaka Taishi , Kimura Marino , Yotsumoto Yuko 
Published: January 2021

AbstractWe have a keen sensitivity when it comes to the perception of our own voices. We can detect not only the differences between ourselves and others, but also slight modifications of our own voices. Here, we examined the neural correlates underlying such sensitive perception of one’s own voice. In the experiments, we modified the subjects’ own voices by using five types of filters. The subjects rated the similarity of the presented voices to their own. We compared BOLD (Blood Oxygen Level Dependent) signals between the voices that subjects rated as least similar to their own voice and those they rated as most similar. The contrast revealed that the bilateral superior temporal gyrus exhibited greater activities while listening to the voice least similar to their own voice and lesser activation while listening to the voice most similar to their own. Our results suggest that the superior temporal gyrus is involved in neural sharpening for the own-voice. The lesser degree of activations observed by the voices that were similar to the own-voice indicates that these areas not only respond to the differences between self and others, but also respond to the finer details of own-voices.
Prediction of pharmacological activities from chemical structures with graph convolutional neural networks
Authors: Sakai Miyuki , Nagayasu Kazuki , Shibui Norihiro , Andoh Chihiro , Takayama Kaito , Shirakawa Hisashi , Kaneko Shuji 
Published: January 2021

AbstractMany therapeutic drugs are compounds that can be represented by simple chemical structures, which contain important determinants of affinity at the site of action. Recently, graph convolutional neural network (GCN) models have exhibited excellent results in classifying the activity of such compounds. For models that make quantitative predictions of activity, more complex information has been utilized, such as the three-dimensional structures of compounds and the amino acid sequences of their respective target proteins. As another approach, we hypothesized that if sufficient experimental data were available and there were enough nodes in hidden layers, a simple compound representation would quantitatively predict activity with satisfactory accuracy. In this study, we report that GCN models constructed solely from the two-dimensional structural information of compounds demonstrated a high degree of activity predictability against 127 diverse targets from the ChEMBL database. Using the information entropy as a metric, we also show that the structural diversity had less effect on the prediction performance. Finally, we report that virtual screening using the constructed model identified a new serotonin transporter inhibitor with activity comparable to that of a marketed drug in vitro and exhibited antidepressant effects in behavioural studies.
Quantification of narrow band UVB radiation doses in phototherapy using diacetylene based film dosimeters
Authors: Mittal Apoorva , Kumar Manoj , Gopishankar N. , Kumar Pratik , Verma Akhilesh K. 
Published: January 2021

AbstractNarrow band ultraviolet B (NB UVB) radiation doses are administered during phototherapy for various dermatological ailments. Precise quantification of these doses is vital because the absorbed irradiation can cause adverse photochemical reactions which can lead to potential phototherapeutic side effects. The paper presents development of diacetylene based dosimeter for the determination of therapeutic NB UVB doses during phototherapy. The amide terminated diacetylene analogues have been synthesized by tailoring them with different functional groups. The synthesized diacetylene monomers have been introduced in a polyvinyl alcohol binder solution to obtain a film dosimeter. The influence of different headgroups on the colorimetric response to UV radiation has been studied. Among all the synthesized diacetylene analogues, the naphthylamine substituted diacetylene exhibited excellent color transition from white to blue color at 100 mJ cm−2 NB UVB radiation dose. The developed amide films can be easily pasted on multiple sites of the patient’s skin to monitor doses during phototherapy simultaneously at different anatomical regions. The digital image processing of the scanned images of the irradiated films facilitates rapid dose measurement which enables facile implementation of the developed film dosimeters and promising application in routine clinical dosimetry.
Increased red cell distribution width predicts severity of drug-induced liver injury: a retrospective study
Authors: Li Xu , Xu Hongqin , Gao Pujun 
Published: January 2021

AbstractWe used a retrospective study design to evaluated the predictive value of red cell distribution width (RDW) for drug-induced liver injury (DILI) severity in Chinese patients with liver biopsy to assist with early DILI management. We included 164 DILI patients with complete laboratory information and medical history. We compared outcomes of 36 patients with severe DILI with outcomes of a control group of 128 patients with mild-to-moderate DILI. Multivariate analyses of risk factors for severe liver injury in Chinese patients with DILI revealed an estimated adjusted odds ratio (AOR) (95% CI) of 4.938 (1.088–22.412) in patients with drinking. Risk for serious liver injury was also increased significantly in patients with dyslipidemia [AOR (95% CI) 3.926 (1.282–12.026)], higher serum total bile acid (TBA) levels [AOR (95% CI) 1.014 (1.009–1.020)] and higher RDW [AOR (95% CI) 1.582 (1.261–1.986)]. The result for area under the curve of 0.905 for TBA levels indicated this variable had high diagnostic performance for predicting DILI severity. Based on an area under the curve value of 0.855, RDW also had superior diagnostic performance in prediction of DILI severity. This performance was not significantly different compared with TBA and was superior compared with other variables, which had area under values ranging from poor to failure (0.527–0.714).The risk for severe DILI was associated with drinking, dyslipidemia, higher TBA levels and RDW values. This study found that RDW and TBA levels were predictors of DILI severity in Chinese patients.
Perceptual decisions are biased toward relevant prior choices
Authors: Feigin Helen , Baror Shira , Bar Moshe , Zaidel Adam 
Published: January 2021

AbstractPerceptual decisions are biased by recent perceptual history—a phenomenon termed 'serial dependence.' Here, we investigated what aspects of perceptual decisions lead to serial dependence, and disambiguated the influences of low-level sensory information, prior choices and motor actions. Participants discriminated whether a brief visual stimulus lay to left/right of the screen center. Following a series of biased ‘prior’ location discriminations, subsequent ‘test’ location discriminations were biased toward the prior choices, even when these were reported via different motor actions (using different keys), and when the prior and test stimuli differed in color. By contrast, prior discriminations about an irrelevant stimulus feature (color) did not substantially influence subsequent location discriminations, even though these were reported via the same motor actions. Additionally, when color (not location) was discriminated, a bias in prior stimulus locations no longer influenced subsequent location discriminations. Although low-level stimuli and motor actions did not trigger serial-dependence on their own, similarity of these features across discriminations boosted the effect. These findings suggest that relevance across perceptual decisions is a key factor for serial dependence. Accordingly, serial dependence likely reflects a high-level mechanism by which the brain predicts and interprets new incoming sensory information in accordance with relevant prior choices.
Highly expressed SLCO1B3 inhibits the occurrence and development of breast cancer and can be used as a clinical indicator of prognosis
Authors: Tang Tiantian , Wang Guiying , Liu Sihua , Zhang Zhaoxue , Liu Chen , Li Fang , Liu Xudi , Meng Lingjiao , Yang Huichai , Li Chunxiao , Sang Meixiang , Zhao Lianmei 
Published: January 2021

AbstractThe role of organic anion transporting polypeptide 1B3 (SLCO1B3) in breast cancer is still controversial. The clinical immunohistochemical results showed that a greater proportion of patients with negative lymph nodes, AJCC stage I, and histological grade 1 (P < 0.05) was positively correlated with stronger expression of SLCO1B3, and DFS and OS were also increased significantly in these patients (P = 0.041, P = 0.001). Further subgroup analysis showed that DFS and OS were significantly enhanced with the increased expression of SLCO1B3 in the ER positive subgroup. The cellular function assay showed that the ability of cell proliferation, migration and invasion was significantly enhanced after knockdown of SLCO1B3 expression in breast cancer cell lines. In contrast, the ability of cell proliferation, migration and invasion was significantly reduced after overexpress the SLCO1B3 in breast cancer cell lines (P < 0.05). Overexpression or knockdown of SLCO1B3 had no effect on the apoptotic ability of breast cancer cells. High level of SLCO1B3 expression can inhibit the proliferation, invasion and migration of breast cancer cells, leading to better prognosis of patients. The role of SLCO1B3 in breast cancer may be related to estrogen. SLCO1B3 will become a potential biomarker for breast cancer diagnosis and prognosis assessment.
Nonlinear vibration of a buckled/damaged BNC nanobeam transversally impacted by a high-speed C60
Authors: Shi Jiao , Yang Likui , Shen Jianhu , Cai Kun 
Published: January 2021

AbstractNanotube can be used as a mass sensor. To design a mass sensor for evaluating a high-speed nanoparticle, in this study, we investigated the impact vibration of a cantilever nanobeam being transversally collided by a high-speed C60 at the beam's free end with an incident velocity of vIn. The capped beam contains alternately two boron nitride zones and two carbon zones on its cross section. Hence, the relaxed beam has elliptic cross section. The vibration properties were demonstrated by molecular dynamics simulation results. Beat vibration of a slim beam can be found easily. The 1st and the 2nd order natural frequencies (f1 and f2) of the beam illustrate the vibration of beam along the short and the long axes of its elliptic cross section, respectively. f2 decreases with increasing temperature. A minimal value of vIn leads to the local buckling of the beam, and a different minimal vIn leading to damage of the beam. For the same system at a specified temperature, f2 varies with vIn. When the beam bends almost uniformly, f2 decreases linearly with vIn. If vIn becomes higher, the beam has a cross section which buckles locally, and the buckling position varies during vibration. If vIn approaches the damage velocity, a fixed contraflexture point may appear on the beam due to its strong buckling. Above the damage velocity, f2 decreases sharply. These results have a potential application in design of a mass sensor.
Impact of changes in waist-to-hip ratio after kidney transplantation on cardiovascular outcomes
Authors: Gwon Jun Gyo , Choi Jimi , Jung Cheol Woong , Lee Chang Hun , Oh Se Won , Jo Sang-Kyung , Cho Won Yong , Park Jae Berm , Huh Kyu Ha , Ro Han , Han Seungyeup , Cho Jang-Hee , Lee Sik , Yang Jaeseok , Kim Myung-Gyu 
Published: January 2021

AbstractRecently, waist to hip ratio (WHR) has been reported to be a better indicator of predicting cardiovascular outcomes than body mass index (BMI). We evaluated the effects of pre or post-transplant changes of WHR or BMI on the new onset cardiovascular diseases (CVD) in recipients of kidney transplantation (KT). A total of 572 patients were enrolled from a multicenter observational cohort (KNOW-KT). Measurement of WHR and BMI was done at pre-KT, first and last visit year after KT, and the changes of these parameters and their effect on the incident CVD were analyzed. During the median follow up period of 32.73 ± 15.26 months, the new onset CVD developed in 31 out of 572 patients. The older age, diabetes mellitus and increase of WHR from pre KT or previous follow up year were found to be independent factors predicting the new onset CVD in these patients. However, baseline BMI, WHR prior to KT did not predict the incident CVD. The new metabolic burden, presented as increase of WHR in KT patients has a critical impact on the development of new onset CVD. Strategies to prevent the metabolic burden after KT might improve cardiovascular outcomes and patient’s survival.
Pharmacokinetics and pharmacodynamics integration of danofloxacin against Eschrichia coli in piglet ileum ultrafiltration probe model
Authors: Yang Yuqi , Cheng Ping , Xiao Tianshi , Ulziikhutag Jargalsaikhan , Yu Hongxiao , Li Jiarui , Liu Ruimeng , Muhammad Ishfaq , Zhang Xiuying 
Published: January 2021

AbstractImproper use of antibiotics results in poor treatment and severe bacterial resistance. In this study, ultrafiltration probes were successfully placed in the ileum of piglets with the aid of anesthetic. After the fluoroquinolone antimicrobial drug danofloxacin (DAN) was intramuscularly administered, blood and ileum ultrafiltrate were collected at different time points and then determined by High Performance Liquid Chromatography (HPLC). Pharmacokinetics (PK) parameters for plasma and ileum ultrafiltrate were calculated by WinNonlin software. The DAN concentration in ileum ultrafiltrate was much higher than that in plasma during the period 1.2–48 h. The DAN concentration in plasma reached its maximum at 1.10 ± 0.03 h, but reached at 6.00 ± 0.00 h in the ileum ultrafiltrate. The mean Cmaxof the ileum is 13.59 times that of plasma. The elimination half-life (T1/2β) in the ileum ultrafiltrate (6.84 ± 1.49 h) was shorter than those in plasma (7.58 ± 3.20 h). The MIC, MBC and MPC of DAN in MH broth againstEscherichia coli(O158) were 0.5 µg/mL, 0.5 µg/mL and 4 µg/mL, respectively. Both in vitro and ex vivo kill curves indicated that the killing mechanism of DAN againstE. coliis concentration-dependent. The AUC/MPC ratio is 21.33 ± 2.14. Mean PK/PD index (AUC24h/MIC) for ileum ultrafiltrate that achieved bacteriostatic, bactericidal, and eradication were 99.85, 155.57, and 218.02 h, respectively. Three different dosages (1.49 mg/kg, 2.42 mg/kg, and 3.24 mg/kg) were calculated respectively based on AUC24h/MIC ratio above, which might provide a novel approach to the rational design of dosage schedules.
Intramedullary injury combined with osteoporosis therapeutics regulates targeted local osteogenesis
Authors: Miyazaki-Asato Yoko , Koi Kiyono , Fujimoto Hiroki , Kakura Kae , Kido Hirofumi , Yanagi Tsukasa , Yamashita Junro 
Published: January 2021

AbstractBone marrow ablation prompts transient bone formation in nearly the entire medullary cavity before marrow regeneration occurs. Here, we establish a procedure to direct bone formation in a desired particular site within the medullary cavity for support of biomedical devices. Local intramedullary injury was performed in the tibiae of rats and parathyroid hormone (PTH), alendronate, or saline was administered. Newly generated bone in the medulla was assessed by micro-CT and histology. To evaluate the function of newly generated bone, animals received intramedullary injury in tibiae followed by daily PTH. At day-14, implants were placed in the endocortical bone and the bone response to the implants was assessed. The fate of newly generated bone was compared with and without implants. We found that neither intramedullary injury nor medication alone resulted in bone formation. However, when combined, substantial bone was generated locally inside the diaphyseal medulla. Newly formed bone disappeared without implant placement but was retained with implants. Bone was especially retained around and between the implants. This study found that local bone marrow disruption followed by PTH or alendronate generated substantial cancellous bone locally in the diaphyseal medulla. This approach offers promise as a tissue engineering tool in medicine and dentistry.
Universal principles underlying segmental structures in parrot song and human speech
Authors: Mann Dan C. , Fitch W. Tecumseh , Tu Hsiao-Wei , Hoeschele Marisa 
Published: January 2021

AbstractDespite the diversity of human languages, certain linguistic patterns are remarkably consistent across human populations. While syntactic universals receive more attention, there is stronger evidence for universal patterns in the inventory and organization of segments: units that are separated by rapid acoustic transitions which are used to build syllables, words, and phrases. Crucially, if an alien researcher investigated spoken human language how we analyze non-human communication systems, many of the phonological regularities would be overlooked, as the majority of analyses in non-humans treat breath groups, or “syllables” (units divided by silent inhalations), as the smallest unit. Here, we introduce a novel segment-based analysis that reveals patterns in the acoustic output of budgerigars, a vocal learning parrot species, that match universal phonological patterns well-documented in humans. We show that song in four independent budgerigar populations is comprised of consonant- and vowel-like segments. Furthermore, the organization of segments within syllables is not random. As in spoken human language, segments at the start of a vocalization are more likely to be consonant-like and segments at the end are more likely to be longer, quieter, and lower in fundamental frequency. These results provide a new foundation for empirical investigation of language-like abilities in other species.