bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutations in the prostate specific antigen (PSA/KLK3) correlate with male infertility
Authors: Gupta Nishi , Sudhakar Digumarthi V. S. , Gangwar Pravin Kumar , Sankhwar Satya Narayan , Gupta Nalini J. , Chakraborty Baidyanath , Thangaraj Kumarasamy , Gupta Gopal , Rajender Singh 
Published: September 2017

AbstractProstate specific antigen (PSA/KLK3) is known to be the chief executor of the fragmentation of semenogelins, dissolution of semen coagulum, thereby releasing sperm for active motility. Recent research has found that semenogelins also play significant roles in sperm fertility by affecting hyaluronidase activity, capacitation and motility, thereby making PSA important for sperm fertility beyond simple semen liquefaction. PSA level in semen has been shown to correlate with sperm motility, suggesting that PSA level/activity can affect fertility. However, no study investigating the genetic variations in theKLK3/PSAgene in male fertility has been undertaken. We analyzed the complete coding region of theKLK3gene in ethnically matched 875 infertile and 290 fertile men to find if genetic variations inKLK3correlate with infertility. Interestingly, this study identified 28 substitutions, of which 8 were novel (not available in public databases). Statistical comparison of the genotype frequencies showed that five SNPs, rs266881 (OR = 2.92, P < 0.0001), rs174776 (OR = 1.91, P < 0.0001), rs266875 (OR = 1.44, P = 0.016), rs35192866 (OR = 4.48, P = 0.025) and rs1810020 (OR = 2.08, P = 0.034) correlated with an increased risk of infertility. On the other hand, c.206 + 235 T > C, was more freuqent in the control group, showing protective association. Our findings suggest that polymorphisms in theKLK3gene correlate with infertility risk.
Human-to-human closed-loop control based on brain-to-brain interface and muscle-to-muscle interface
Authors: Mashat M. Ebrahim M. , Li Guangye , Zhang Dingguo 
Published: September 2017

AbstractNovel communication techniques have always been fascinating for humankind. This pilot study presents an approach to human interaction by combining direct brain-to-brain interface (BBI) and muscle-to-muscle interface (MMI) in a closed-loop pattern. In this system, artificial paths (data flows) functionally connect natural paths (nerves). The intention from one subject (sender) is recognized using electroencephalography (EEG) based brain-computer interface (BCI), which is sent out to trigger transcranial magnetic stimulation (TMS) on the other subject (receiver) and induce hand motion; meanwhile TMS results in a significant change on the motor evoked potentials (MEP) recorded by electromyography (EMG) of the receiver’s arm, which triggers functional electrical stimulation (FES) applied to the sender’s arm and generates hand motion. Human-controlled loop and automatic control loop experiments were performed with 6 pairs of healthy subjects to evaluate the performance of the introduced mechanism. The results indicated that response accuracy during human-controlled experiments was 85% which demonstrates the feasibility of the proposed method. During the automatic control test, two subjects could accomplish repetitive and reciprocal hand motion control up to 85 times consecutively.
HPLC-based quantification of bacterial housekeeping nucleotides and alarmone messengers ppGpp and pppGpp
Authors: Varik Vallo , Oliveira Sofia Raquel Alves , Hauryliuk Vasili , Tenson Tanel 
Published: September 2017

AbstractHere we describe an HPLC-based method to quantify bacterial housekeeping nucleotides and the signaling messengers ppGpp and pppGpp. We have replicated and tested several previously reported HPLC-based approaches and assembled a method that can process 50 samples in three days, thus making kinetically resolved experiments feasible. The method combines cell harvesting by rapid filtration, followed by acid extraction, freeze-drying with chromatographic separation. We use a combination of C18 IPRP-HPLC (GMP unresolved and co-migrating with IMP; GDP and GTP; AMP, ADP and ATP; CTP; UTP) and SAX-HPLC in isocratic mode (ppGpp and pppGpp) with UV detection. The approach is applicable to bacteria without the requirement of metabolic labelling with 32P-labelled radioactive precursors. We applied our method to quantify nucleotide pools in Escherichia coli BW25113 K12-strain both throughout the growth curve and during acute stringent response induced by mupirocin. While ppGpp and pppGpp levels vary drastically (40- and ≥8-fold, respectively) these changes are decoupled from the quotients of the housekeeping pool and guanosine and adenosine housekeeping nucleotides: NTP/NDP/NMP ratio remains stable at 6/1/0.3 during both normal batch culture growth and upon acute amino acid starvation.
Sacral Neuromodulation for Refractory Bladder Pain Syndrome/Interstitial Cystitis: a Global Systematic Review and Meta-analysis
Authors: Wang Junpeng , Chen Yang , Chen Jiawei , Zhang Guihao , Wu Peng 
Published: September 2017

AbstractBladder pain syndrome/interstitial cystitis (BPS/IC) is a common debilitating disease and there has not been consistently effective treatment. We aimed to evaluate all available literature regarding the efficacy and safety of sacral neuromodulation (SNM) for refractory BPS/IC. A comprehensive search of Pubmed, Web of Science and Cochrane Library through May 2016 was conducted. A total of 17 studies enrolling 583 patients were identified. Pooled analyses demonstrated that SNM was associated with great reduction in pelvic pain (weighted mean difference [WMD] −3.99; 95% confidence interval [CI] −5.22 to −2.76;p < 0.00001), Interstitial Cystitis Problem and Symptom Index scores (WMD −6.34; 95% CI −9.57 to −3.10;p = 0.0001; and WMD −7.17; 95% CI −9.90 to −4.45;p < 0.00001, respectively), daytime frequency (WMD −7.45; 95% CI −9.68 to −5.22;p < 0.00001), nocturia (WMD −3.01; 95% CI −3.56 to −2.45;p < 0.00001), voids per 24 hours (WMD −9.32; 95% CI −10.90 to −7.74;p < 0.00001) and urgency (WMD −1.08; 95% CI −1.79 to −0.37;p = 0.003) as well as significant improvement in average voided volume (WMD 95.16 ml; 95% CI 63.64 to 126.69;p < 0.0001). The pooled treatment success rate was 84% (95% CI 76% to 91%). SNM-related adverse events were minimal. Current evidence indicates that SNM might be effective and safe for treating refractory BPS/IC.
Densification of the interlayer spacing governs the nanomechanical properties of calcium-silicate-hydrate
Authors: Geng Guoqing , Myers Rupert J. , Qomi Mohammad Javad Abdolhosseini , Monteiro Paulo J. M. 
Published: September 2017

AbstractCalciuam-silicate-hydrate (C-S-H) is the principal binding phase in modern concrete. Molecular simulations imply that its nanoscale stiffness is ‘defect-driven’, i.e., dominated by crystallographic defects such as bridging site vacancies in its silicate chains. However, experimental validation of this result is difficult due to the hierarchically porous nature of C-S-H down to nanometers. Here, we integrate high pressure X-ray diffraction and atomistic simulations to correlate the anisotropic deformation of nanocrystalline C-S-H to its atomic-scale structure, which is changed by varying the Ca-to-Si molar ratio. Contrary to the ‘defect-driven’ hypothesis, we clearly observe stiffening of C-S-H with increasing Ca/Si in the range 0.8 ≤ Ca/Si ≤ 1.3, despite increasing numbers of vacancies in its silicate chains. The deformation of these chains along the b-axis occurs mainly through tilting of the Si-O-Si dihedral angle rather than shortening of the Si-O bond, and consequently there is no correlation between the incompressibilities of the a- and b-axes and the Ca/Si. On the contrary, the intrinsic stiffness of C-S-H solid is inversely correlated with the thickness of its interlayer space. This work provides direct experimental evidence to conduct more realistic modelling of C-S-H-based cementitious material.
The unexpected role of bioaerosols in the Oxidative Potential of PM
Authors: Samake A. , Uzu G. , Martins J. M. F. , Calas A. , Vince E. , Parat S. , Jaffrezo J. L. 
Published: September 2017

AbstractBioaerosols represent up to 15–25% of PM by mass, but there is currently no assessment of their impact on Oxidative Potential (OP), or capacity of particulate matter (PM) to produce damaging oxidative reactions in the human lungs. Here, the OP of selected bioaerosols (bacteria cells vs fungal spores) was assessed through the cell-free DTT assay. Results show that bioaerosols induce Reactive Oxygen Species (ROS) production, varying along the microorganism type, species, and concentration. Fungal spores show up to 10 times more ROS generation than bacterial cells. At the highest concentrations, fungal spores present as much oxidative reactivity as the most redox-active airborne chemicals (Copper, Naphtoquinone). Moreover, bioaerosols substantially influence OP of ambient PM and that of its chemical constituents: in presence of A. fumigatus spores, the OP of Cu/NQ is increased by a factor of 2 to 5, whereas, 104 and 105
S. epidermidis bacterial cells.mL−1 halves the OP of Cu/NQ. Finally, viable and gamma-rays-killed model bioaerosols present similar oxidative reactivity, suggesting a metabolism-independent cellular mechanism. These results reveal the importance of bioaerosols for PM reactivity. PM toxicity can be modified due to bioaerosols contribution or by their ability to modulate the OP of toxic chemicals present in PM.
Propagation of superconducting coherence via chiral quantum-Hall edge channels
Authors: Park Geon-Hyoung , Kim Minsoo , Watanabe Kenji , Taniguchi Takashi , Lee Hu-Jong 
Published: September 2017

AbstractRecently, there has been significant interest in superconducting coherence via chiral quantum-Hall (QH) edge channels at an interface between a two-dimensional normal conductor and a superconductor (N–S) in a strong transverse magnetic field. In the field range where the superconductivity and the QH state coexist, the coherent confinement of electron- and hole-like quasiparticles by the interplay of Andreev reflection and the QH effect leads to the formation of Andreev edge states (AES) along the N–S interface. Here, we report the electrical conductance characteristics via the AES formed in graphene–superconductor hybrid systems in a three-terminal configuration. This measurement configuration, involving the QH edge states outside a graphene–S interface, allows the detection of the longitudinal and QH conductance separately, excluding the bulk contribution. Convincing evidence for the superconducting coherence and its propagation via the chiral QH edge channels is provided by the conductance enhancement on both the upstream and the downstream sides of the superconducting electrode as well as in bias spectroscopy results below the superconducting critical temperature. Propagation of superconducting coherence via QH edge states was more evident as more edge channels participate in the Andreev process for high filling factors with reduced valley-mixing scattering.
Differential degeneration of the ACTAGT sequence among Salmonella: a reflection of distinct nucleotide amelioration patterns during bacterial divergence
Authors: Tang Le , Mastriani Emilio , Zhou Yu-Jie , Zhu Songling , Fang Xin , Liu Yang-Peng , Liu Wei-Qiao , Li Yong-Guo , Johnston Randal N. , Guo Zheng , Liu Gui-Rong , Liu Shu-Lin 
Published: September 2017

AbstractWhen bacteria diverge, they need to adapt to the new environments, such as new hosts or different tissues of the same host, by accumulating beneficial genomic variations, but a general scenario is unknown due to the lack of appropriate methods. Here we profiled the ACTAGT sequence and its degenerated forms (i.e., hexa-nucleotide sequences with one of the six nucleotides different from ACTAGT) in Salmonella to estimate the nucleotide amelioration processes of bacterial genomes. ACTAGT was mostly located in coding sequences but was also found in several intergenic regions, with its degenerated forms widely scattered throughout the bacterial genomes. We speculated that the distribution of ACTAGT and its degenerated forms might be lineage-specific as a consequence of different selection pressures imposed on ACTAGT at different genomic locations (in genes or intergenic regions) among different Salmonella lineages. To validate this speculation, we modelled the secondary structures of the ACTAGT-containing sequences conserved across Salmonella and many other enteric bacteria. Compared to ACTAGT at conserved regions, the degenerated forms were distributed throughout the bacterial genomes, with the degeneration patterns being highly similar among bacteria of the same phylogenetic lineage but radically different across different lineages. This finding demonstrates biased amelioration under distinct selection pressures among the bacteria and provides insights into genomic evolution during bacterial divergence.
The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation
Authors: Grzela Renata , Nusbaum Julien , Fieulaine Sonia , Lavecchia Francesco , Bienvenut Willy V. , Dian Cyril , Meinnel Thierry , Giglione Carmela 
Published: September 2017

AbstractProkaryotic proteins must be deformylated before the removal of their first methionine. Peptide deformylase (PDF) is indispensable and guarantees this mechanism. Recent metagenomics studies revealed new idiosyncratic PDF forms as the most abundant family of viral sequences. Little is known regarding these viral PDFs, including the capacity of the corresponding encoded proteins to ensure deformylase activity. We provide here the first evidence that viral PDFs, including the shortest PDF identified to date, Vp16 PDF, display deformylase activity in vivo, despite the absence of the key ribosome-interacting C-terminal region. Moreover, characterization of phage Vp16 PDF underscores unexpected structural and molecular features with the C-terminal Isoleucine residue significantly contributing to deformylase activity both in vitro and in vivo. This residue fully compensates for the absence of the usual long C-domain. Taken together, these data elucidate an unexpected mechanism of enzyme natural evolution and adaptation within viral sequences.
Evolution analysis of heterogeneous non-small cell lung carcinoma by ultra-deep sequencing of the mitochondrial genome
Authors: Amer Wafa , Toth Csaba , Vassella Erik , Meinrath Jeannine , Koitzsch Ulrike , Arens Anne , Huang Jia , Eischeid Hannah , Adam Alexander , Buettner Reinhard , Scheel Andreas , Schaefer Stephan C. , Odenthal Margarete 
Published: September 2017

AbstractAccurate assessment of tumour heterogeneity is an important issue that influences prognosis and therapeutic decision in molecular pathology. Due to the shortage of protective histones and a limited DNA repair capacity, the mitochondrial (mt)-genome undergoes high variability during tumour development. Therefore, screening of mt-genome represents a useful molecular tool for assessing precise cell lineages and tracking tumour history. Here, we describe a highly specific and robust multiplex PCR-based ultra-deep sequencing technology for analysis of the whole mt-genome (wmt-seq) on low quality-DNA from formalin-fixed paraffin-embedded tissues. As a proof of concept, we applied the wmt-seq technology to characterize the clonal relationship of non-small cell lung cancer (NSCLC) specimens with multiple lesions (N = 43) that show either different histological subtypes (group I) or pulmonary adenosquamous carcinoma as striking examples of a mixed-histology tumour (group II). The application of wmt-seq demonstrated that most samples bear common mt-mutations in each lesion of an individual patient, indicating a single cell progeny and clonal relationship. Hereby we show the monoclonal origin of histologically heterogeneous NSCLC and demonstrate the evolutionary relation of NSCLC cases carrying heteroplasmic mt-variants.
Transcriptional analysis of genes involved in competitive nodulation in Bradyrhizobium diazoefficiens at the presence of soybean root exudates
Authors: Liu Yao , Jiang Xin , Guan Dawei , Zhou Wei , Ma Mingchao , Zhao Baisuo , Cao Fengming , Li Li , Li Jun 
Published: September 2017

AbstractNodulation competition is a key factor that limits symbiotic nitrogen fixation between rhizobia and their host legumes. Soybean root exudates (SREs) are thought to act as signals that influence Bradyrhizobium ability to colonize roots and to survive in the rhizosphere, and thus they act as a key determinant of nodulation competitiveness. In order to find the competitiveness-related genes in B. diazoefficiens, the transcriptome of two SREs treated B. diazoefficiens with completely different nodulation abilities (B. diazoefficiens 4534 and B. diazoefficiens 4222) were sequenced and compared. In SREs treated strain 4534 (SREs-4534), 253 unigenes were up-regulated and 204 unigenes were down-regulated. In SREs treated strain 4534 (SREs-4222), the numbers of up- and down-regulated unigenes were 108 and 185, respectively. There were considerable differences between the SREs-4534 and SREs-4222 gene expression profiles. Some differentially expressed genes are associated with a two-component system (i.g., nodW, phyR-σEcfG), bacterial chemotaxis (i.g., cheA, unigene04832), ABC transport proteins (i.g., unigene02212), IAA (indole-3-acetic acid) metabolism (i.g., nthA, nthB), and metabolic fitness (i.g., put.), which may explain the higher nodulation competitiveness of B. diazoefficiens in the rhizosphere. Our results provide a comprehensive transcriptomic resource for SREs treated B. diazoefficiens and will facilitate further studies on competitiveness-related genes in B. diazoefficiens.
Creation and Initial Characterization of Isogenic Helicobacter pylori CagA EPIYA Variants Reveals Differential Activation of Host Cell Signaling Pathways
Authors: Bridge Dacie R. , Blum Faith C. , Jang Sungil , Kim Jinmoon , Cha Jeong-Heon , Merrell D. Scott 
Published: September 2017

AbstractThe polymorphic CagA toxin is associated withHelicobacter pylori-induced disease. Previous data generated using non-isogenic strains and transfection models suggest that variation surrounding the C-terminal Glu-Pro-Ile-Tyr-Ala (EPIYA) motifs as well as the number of EPIYA motifs influence disease outcome. To investigate potential CagA-mediated effects on host cell signaling, we constructed and characterized a large panel of isogenicH. pyloristrains that differ primarily in the CagA EPIYA region. The number of EPIYA-C motifs or the presence of an EPIYA-D motif impacted early changes in host cell elongation; however, the degree of elongation was comparable across all strains at later time points. In contrast, the strain carrying the EPIYA-D motif induced more IL-8 secretion than any other EPIYA type, and a single EPIYA-C motif induced comparable IL-8 secretion as isolates carrying multiple EPIYA-C alleles. Similar levels of ERK1/2 activation were induced by all strains carrying a functional CagA allele. Together, our data suggest that polymorphism in the CagA C-terminus is responsible for differential alterations in some, but not all, host cell signaling pathways. Notably, our results differ from non-isogenic strain studies, thus highlighting the importance of using isogenic strains to study the role of CagA toxin polymorphism in gastric cancer development.
Label-free and real-time monitoring of single cell attachment on template-stripped plasmonic nano-holes
Authors: Tu Long , Li Xuzhou , Bian Shengtai , Yu Yingting , Li Junxiang , Huang Liang , Liu Peng , Wu Qiong , Wang Wenhui 
Published: September 2017

AbstractLeveraging microfluidics and nano-plasmonics, we present in this paper a new method employing a micro-nano-device that is capable of monitoring the dynamic cell-substrate attachment process at single cell level in real time without labeling. The micro-nano-device essentially has a gold thin film as the substrate perforated with periodic, near-cm2-area, template-stripped nano-holes, which generate plasmonic extraordinary optical transmission (EOT) with a high sensitivity to refractive index changes at the metal-dielectric interface. Using this device, we successfully demonstrated label-free and real-time monitoring of the dynamic cell attachment process for single mouse embryonic stem cell (C3H10) and human tumor cell (HeLa) by collecting EOT spectrum data during 3-hour on-chip culture. We further collected the EOT spectral shift data at the start and end points of measurement during 3-hour on-chip culture for 50 C3H10 and 50 HeLa cells, respectively. The experiment results show that the single cell attachment process of both HeLa and C3H10 cells follow the logistic retarded growth model, but with different kinetic parameters. Variations in spectral shift during the same culture period across single cells present new evidence for cell heterogeneity. The micro-nano-device provides a new, label-free, real-time, and sensitive, platform to investigate the cell adhesion kinetics at single cell level.
The Oxidative State of Cysteine Thiol 144 Regulates the SIRT6 Glucose Homeostat
Authors: Long David , Wu Hanzhi , Tsang Allen W. , Poole Leslie B. , Yoza Barbara K. , Wang Xianfeng , Vachharajani Vidula , Furdui Cristina M. , McCall Charles E. 
Published: September 2017

AbstractControl of glucose homeostasis plays a critical role in health and lifespan and its dysregulation contributes to inflammation, cancer and aging. NAD + dependent Sirtuin 6 (SIRT6) is a glucose homeostasis regulator in animals and humans and its regulation at the molecular level is unknown. Here, we report that a cysteine thiol redox sensor contributes to the role of SIRT6 in controlling glucose homeostasis. Sulfenylation of SIRT6 occurs in THP1 cells and primary human promonocytes during inflammation and in splenocytes from mice with sepsis. Inhibiting xanthine oxidase, a major reactive oxygen species (ROS) contributor during acute inflammation, reduces sulfenylation of SIRT6, glucose transporter Glut1 expression, glucose uptake, and glycolysis. A block in glycolysis associated with monocyte deactivation by endotoxin, a process contributing to immunometabolic paralysis in human and mouse sepsis monocytes, can be reversed by increasing H2O2 and sulfenylating SIRT6. Mutation analysis of SIRT6 Cys144, which lies in its phylogenetically conserved zinc-associated Cys-X-X-Cys motif near the catalytic domain of the protein, decreases SIRT6 deacetylase activity and promotes glycolysis. These results suggest that direct and reversible cysteine thiol 144 may play a functional role in SIRT6-dependent control over monocyte glycolysis, an important determinant of effector innate immune responses.
Simulation of head and neck cancer oxygenation and doubling time in a 4D cellular model with angiogenesis
Authors: Forster Jake C. , Douglass Michael J. J. , Harriss-Phillips Wendy M. , Bezak Eva 
Published: September 2017

AbstractTumor oxygenation has been correlated with treatment outcome for radiotherapy. In this work, the dependence of tumor oxygenation on tumor vascularity and blood oxygenation was determined quantitatively in a 4D stochastic computational model of head and neck squamous cell carcinoma (HNSCC) tumor growth and angiogenesis. Additionally, the impacts of the tumor oxygenation and the cancer stem cell (CSC) symmetric division probability on the tumor volume doubling time and the proportion of CSCs in the tumor were also quantified. Clinically relevant vascularities and blood oxygenations for HNSCC yielded tumor oxygenations in agreement with clinical data for HNSCC. The doubling time varied by a factor of 3 from well oxygenated tumors to the most severely hypoxic tumors of HNSCC. To obtain the doubling times and CSC proportions clinically observed in HNSCC, the model predicts a CSC symmetric division probability of approximately 2% before treatment. To obtain the doubling times clinically observed during treatment when accelerated repopulation is occurring, the model predicts a CSC symmetric division probability of approximately 50%, which also results in CSC proportions of 30–35% during this time.