bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular detection and characterization of mutation on 23S rRNA gene associated with clarithromycin resistant in Helicobacter pylori
Authors: Abd albagi Sahar Obi , aldayem Altayeb Hisham Nour , Khalil Abuzeid Nadir Musa 
Published: May 2019

AbstractBackgroundHelicobacter pylori consider as pathogenic resistant bacterium was colonized mainly in stomach and causing a prolonged gastritis with gastric ulcers were progressing to gastric carcinoma. Also its resistance to antibiotic considered as the main reason for failure to eradicate of this pathogen has been difficult when this resistance occurred as mutant on protein binding site in 23s ribosomal RNA. The highest cure rates have required multidrug antimicrobial therapies including combinations of omeprazole, clarithromycin and metronidazole.ResultBacterial DNA sequence from gastritis patients with confirmed previous positive ICT samples (Stool and Bloo) were used to obtain co-related between phenotypic & genotypic variant outcome have been observed as SNPs carried on nucleotides which could be altered protein prediction as result of that caused chronic gastritis incline to gastric carcinoma due to abnormal consequence on genetic level in H. species (23s rRNA) was referred to clarithromycin resistance, was achieved on this cross-sectional studies by running two different primers were amplify in PCR machine, first one for urease producing gene (Glm as universal primer) and second one for 23s rRNA as specific primer (rp1/fp1). Two samples out of Four samples were amplified as final isolate in the first cycle and have a specific band in 23s rRNA (NO.11, NO.24) as further DNA samples investigation were sent to get our target sequence.ConclusionBioinformatics tools used to confirm a specific types of mutations give specific position responsible for bacteriostatic activity of macrolides such as clarithromycin depends on capacity to inhibit protein synthesis by binding to the 23S ribosomal subunit (23S rRNA) as resistant gene. The detection tools as MSA (multiple sequence alignment) for our nucleotides sequence to (11&24) samples with Genbank accession number 24_MK208582 and 11_MK208583. One type of mutation has been observed in nucleotide sequence (sample-24) in position 2516 (1344 _complementary) sequence result compared with reference sequence standard reference strain (H. pylori U27270) was confirmed which consider it as novel mutation in database for 23S rRNA Gene of H. pylori associated with Clarithromycin Resistance gene in Sudanese patients.
A comparative assessment of aging-related NADPH diaphorase positivity in the spinal cord and medullary oblongata between pigeon and murine
Authors: Jia Yunge , Hou Wei , Li Yinhua , Wen Xiaoxin , Rao Chenxu , Wei Zichun , Zhang Tianyi , Wang Xinghang , Li Xiuyuan , bai Lu , Zhang Weijin , Wang Pan , Bi Jing , Guo Anchen , Wang Jie , Tan Huibing 
Published: May 2019

AbstractNADPH diaphorase (N-d) positive neurons has been examined in many animals. N-d neurodegenerative neurites were detected in some animal models. However, detailed information of N-d positivity and aging related changes was still lack in the spinal cord and medulla oblongata of pigeons. In this study, we evaluated the N-d positivity and aging alterations in the spinal cord and medullary oblongata of the pigeon compared with rat and mouse. In pigeons, N-d neurons were more numerous in the dorsal horn, around the central canal and in the column of Terni in the thoracic and lumbar segments and scattered neurons occurred in the ventral horn of spinal segments. N-d neurons also occurred in the white matter of spinal cord. Morphometrical analysis demonstrated in the lumbosacral, cervical and thoracic regions. Compared with young pigeons, the size of N-d soma was significantly altered in aged pigeons. Meanwhile, the dramatic morphological changes occurred in the lumbar to sacral segments. The most important findings of this study were aging-related N-d positive bodies (ANB) in aged pigeons, mainly in the nucleus cuneatus externus (CuE), occasionally in the nuclei gracilis et cuneatus. ANBs were identified in the gracile nuclei in spinal cord in the aged rats and mice. ANBs were also detected in the CuE spinal nucleus in the aged rats. Immunohistochemistry also showed that the aging changes occurred in the cell types and neuropeptides in aged animals. The results suggested the weak inflammation and neuronal dysfunction in the spinal cord in aged pigeons. Our results suggested that the ANB could be considered as aging marker in the central nervous system.
Gated electron transport in rhodopsin and its relevance to GPCR activation
Authors: Gehrckens Angela S , Horsfield Andrew P , Skoulakis Efthimios M C , Turin Luca 
Published: May 2019

AbstractWe identify, by density-functional theory calculations, an electron donor-bridge-acceptor (DBA) complex within the highest resolution X-ray diffraction structures of rhodopsin. The donor is a conserved tryptophan, the acceptor is a zinc ion surrounded by a tryptophan, a histidine and a conserved glutamate. The unusual environment of the zinc ion confers high electron affinity on the zinc site. The bridge is the retinal which can exist either in the neutral aldimine (Schiff’s base) or aldiminium (protonated) state. When the retinal is unprotonated, no electron transfer occurs. Upon protonation of the aldimine, the DBA complex conducts and a full electron charge is transferred from donor tryptophan to the zinc complex. This gated electron transfer creates the molecular equivalent of a tunnel triode. Since rhodopsin is the ancestor of GPCRs, we discuss the possible relevance of this gated electron transport to other GPCRs, in particular to olfactory receptors which have been proposed to use an electron tunneling mechanism to detect molecular vibrations.
Next-generation in situ conservation and educational outreach in Madagascar using a mobile genetics lab
Authors: Blanco Marina B. , Greene Lydia K. , Williams Rachel C. , Andrianandrasana Lanto , Yoder Anne D. , Larsen Peter A. 
Published: May 2019

AbstractMadagascar is a biodiversity hotspot that is facing rapid rates of deforestation, habitat destruction and poverty. Urgent action is required to document the status of biodiversity to facilitate efficacious conservation plans. Within country, new generations of Malagasy scientists and conservationists are taking on leadership roles, although many lack access to modern genetic sequencing and are underrepresented in academic publications, when compared to international counterparts.With the recent advent of portable and affordable genetic technologies, it is now possible to tackle logistical considerations. Mobile genetics labs, with the capacity for in situ DNA extraction, amplification and sequencing, can produce scientifically reproducible data under field conditions, minimizing the time between sample collection and data analysis. Additionally, mobile labs offer powerful training opportunities for in-country scientists that enable local students and researchers to actively participate and contribute fully to the research enterprise, and that further empower these communities to contribute to the conservation dialog.Here, we show “proof of concept” by deploying a miniaturized thermal cycler alongside the Oxford Nanopore MinION DNA sequencer in Madagascar, including in the newly established Anjajavy Protected Area in northwestern Madagascar. We successfully extracted DNA from tissue samples collected using minimally-invasive techniques, amplified and sequenced a phylogenetically informative mitochondrial gene (cytochrome-b; cytb), and thereby confirmed the presence of Danfoss’ mouse lemur (M. danfossi) within the Anjajavy Reserve.To demonstrate the reproducibility of our methods, we successfully performed our established molecular and analytical pipeline at two additional locations in Madagascar, where we also conducted two-day workshops at local higher-education Institutions to demonstrate the process from tissue samples to DNA sequencing. Ultimately, we show that a mobile genetics lab can provide reliable and expeditious results, become a powerful educational tool, and allow scientists to conduct genetic analyses, potentially allowing for rapid interventions under emergency conditions in situ.
Exploiting codon usage identifies RpS21 as anin vivosignal strength-dependent Ras/MAPK regulator
Authors: Sawyer Jessica K. , Kabiri Zahra , Montague Ruth A. , Paramore Sarah V. , Cohen Erez , Zaribafzadeh Hamed , Counter Christopher M. , Fox Donald T. 
Published: May 2019

ABSTRACTSignal transduction pathways are intricately fine-tuned to accomplish diverse biological processes. An example is the conserved Ras/mitogen-activated-protein-kinase (MAPK) pathway, which exhibits context-dependent signaling output dynamics and regulation. Here, by altering codon usage as a novel platform to control signaling output, we screened theDrosophilagenome for modifiers specific to either weak or strong Ras-driven eye phenotypes. We mapped the underlying gene from one modifier to the ribosomal geneRpS21. RpS21 preferentially influences weak Ras/MAPK signaling outputs, and negatively regulates Ras/MAPK in multiple cell/tissue and signaling settings. In turn, MAPK signaling may regulate its own negative feedback by promoting RpS21 expression. These data show that codon usage manipulation can identify output-specific signaling regulators, and identify RpS21 as anin vivoRas/MAPK phenotypic regulator.
Species-specific oscillation periods of human and mouse segmentation clocks are due to cell autonomous differences in biochemical reaction parameters
Authors: Matsuda Mitsuhiro , Hayashi Hanako , Garcia-Ojalvo Jordi , Yoshioka-Kobayashi Kumiko , Kageyama Ryoichiro , Yamanaka Yoshihiro , Ikeya Makoto , Toguchida Junya , Alev Cantas , Ebisuya Miki 
Published: May 2019

AbstractWhile the mechanisms of embryonic development are similar between mouse and human, the tempo is in general slower in human. The cause of interspecies differences in developmental time remains a mystery partly due to lack of an appropriate model system1. Since murine and human embryos differ in their sizes, geometries, and nutrients, we usein vitrodifferentiation of pluripotent stem cells (PSCs) to compare the same type of cells between the species in similar culture conditions. As an example of well-defined developmental time, we focus on the segmentation clock, oscillatory gene expression that regulates the timing of sequential formation of body segments2–4. In this way we recapitulate the murine and human segmentation clocksin vitro, showing that the species-specific oscillation periods are derived from cell autonomous differences in the speeds of biochemical reactions. Presomitic mesoderm (PSM)-like cells induced from murine and human PSCs displayed the oscillatory expression of HES7, the core gene of the segmentation clock5,6, with oscillation periods of 2-3 hours (mouse PSM) and 5-6 hours (human PSM). Swapping HES7 loci between murine and human genomes did not change the oscillation periods dramatically, denying the possibility that interspecies differences in the sequences of HES7 loci might be the cause of the observed period difference. Instead, we found that the biochemical reactions that determine the oscillation period, such as the degradation of HES7 and delays in its expression, are slower in human PSM compared with those in mouse PSM. With the measured biochemical parameters, our mathematical model successfully accounted for the 2-3-fold period difference between mouse and human. We further demonstrate that the concept of slower biochemical reactions in human cells is generalizable to several other genes, as well as to another cell type. These results collectively indicate that differences in the speeds of biochemical reactions between murine and human cells give rise to the interspecies period difference of the segmentation clock and may contribute to other interspecies differences in developmental time.
Seasonal and spatial controls on N2O concentrations and emissions in low-nitrogen estuaries: Evidence from three tropical systems
Authors: Murray Rachel , Erler Dirk , Rosentreter Judith , Wells Naomi , Eyre Bradley 
Published: May 2019

AbstractEstuarine N2O emissions contribute to the atmospheric N2O budget, but little is known about estuary N2O fluxes under low dissolved inorganic nitrogen (DIN) conditions. We present high-resolution spatial surveys of N2O concentrations and water-air fluxes in three low-DIN (NO3−< 30µmol L−1) tropical estuaries in Queensland, Australia (Johnstone River, Fitzroy River, Constant Creek) during consecutive wet and dry seasons. Constant Creek had the lowest concentrations of dissolved inorganic nitrogen (DIN; 0.01 to 5.4µmol L−1of NO3−and 0.09 to 13.6µmol L−1of NH4+) and N2O (93–132% saturation), and associated lowest N2O emissions (– 1.4 to 8.4µmol m−2d−1) in both seasons. The other two estuaries exhibited higher DIN inputs and higher N2O emissions. The Johnstone River Estuary had the highest N2O concentrations (97–245% saturation) and emissions (– 0.03 to 25.7µmol m−2d−1), driven by groundwater inputs from upstream sources, with increased N2O input in the wet season. In the Fitzroy River Estuary, N2O concentrations (100–204% saturation) and emissions (0.03–19.5µmol m−2d−1) were associated with wastewater inputs, which had a larger effect during the dry season and were diluted during the wet season. Overall N2O emissions from the three tropical estuaries were low compared to previous studies, and at times water-air N2O fluxes were actually negative, indicating that N2O consumption occurred. Low water column NO3−concentration (i.e. < 5µmol L−1) appears to promote negative water-air N2O fluxes in estuary environments; considering the number of estuaries and mangrove creeks where DIN falls below this threshold, negative water-air N2O fluxes are likely common.
Immunogenicity assessment of PRRS polylactic acid glycolic acid DNA vaccine
Authors: Kowalski Sean , Smith John 
Published: May 2019

AbstractIn order to enhance the immune effect of DNA vaccine, poly(lactide-co-glycolide (PLGA)] microparticles were prepared by solvent evaporation method, and the porcine reproductive and respiratory syndrome (PRRS) DNA vaccine pCI-ORF5 was adsorbed to the porcine reproductive and respiratory syndrome (PRRS) DNA vaccine. The surface of the microparticles was used to detect the amount of DNA adsorbed by PLGA microparticles, in vitro release, and immunogenicity in mice. The results showed that the DNA adsorption capacity of PLGA particles could reach 0.9% within 6h, and the release in vitro was affected by many factors such as CTAB content, PLGA molecular weight, PLGA concentration and internal water phase volume. After immunizing mice with the naked DNA vaccine, PLGA microparticles were found to significantly enhance the humoral and cellular immunity induced by the adsorbed DNA vaccine, indicating that it has a good application prospect as a vector for delivering DNA vaccines.
Peptide Arrays of Three Collections of Human Sera from Patients Infected with Mosquito-Borne Viruses
Authors: Martinez Viedma Maria del Pilar , Kose Nurgun , Parham Leda , Balmaseda Angel , Kuan Guillermina , Lorenzana Ivette , Harris Eva , Crowe James E. , Pickett Brett E. 
Published: May 2019

ABSTRACTGlobal outbreaks and epidemics caused by emerging or re-emerging mosquito-borne viruses are becoming more common. These viruses belong to multiple genera including Flavivirus and Alphavirus and often cause non-specific or asymptomatic infection, which can confound viral prevalence studies. In addition, many acute phase diagnostic tests rely on the detection of viral components such as RNA or antigen. Standard serological tests are often not reliable for diagnosis after the acute phase due to cross-reactivity among viruses (e.g. flaviviruses). In order to contribute to development efforts for mosquito-borne serodiagnostics, we incubated 137 human sera on individual custom peptide arrays that consisted of over 866 unique peptides in quadruplicate. Our bioinformatics workflow to analyze these data incorporated machine learning, statistics, and B-cell epitope prediction. The unprocessed array data can be useful in separate meta-analyses that can be applicable to diverse efforts including the development of new pan-flavivirus antibodies, more accurate epitope mapping, and vaccine development against these viral pathogens.
A prediction method for wheel tread wear
Authors: Wang Xue Ping , Ma He , Zhang Jun 
Published: May 2019

Purpose
The increasing demands of high-speed railway transportation aggravate the wheel and rail surface wear. It is of great significance to repair the worn wheel timely by predicting the wheel and rail surface wear, which will improve both the service life of the wheel and rail and the safe operation of the train. The purpose of this study is to propose a new prediction method of wheel tread wear, which can provide some reference for selecting proper re-profiling period of wheel.

Design/methodology/approach
The standard and worn wheel profiles were first matched with the standard 60N rail profile, and then the wheel/rail finite element models (FEMs) were established for elastic-plastic contact calculation. A calculation method of the friction work was proposed based on contact analysis. Afterwards, a simplified method for calculating wheel tread wear was presented and the wear with different running mileages was predicted.

Findings
The wheel tread wear increased the relative displacement and friction of contact spots. There was obvious fluctuation in the wheel tread friction work curve of the worn model. The wear patterns predicted in the present study were in accordance with the actual situation, especially in the worn model.

Originality/value
In summary, the simplified method based on FEM presented in this paper could effectively calculate wheel tread wear and predict the wear patterns. It would provide valuable clews for the wheel repair work.
Segregostat: a novel concept to control phenotypic diversification dynamics on the example of Gram‐negative bacteria
Authors: Sassi Hosni , Nguyen Thai Minh , Telek Samuel , Gosset Guillermo , Grünberger Alexander , Delvigne Frank 
Published: May 2019

SummaryControlling and managing the degree of phenotypic diversification of microbial populations is a challenging task. This task not only requires detailed knowledge regarding diversification mechanisms but also advanced technical set‐ups for the real‐time analyses and control of population behaviour on single‐cell level. In this work, set‐up, design and operation of the so called segregostat are described which, in contrast to a traditional chemostat, allows the control of phenotypic diversification of microbial populations over time. Two exemplary case studies will be discussed, i.e. phenotypic diversification dynamics of Eschericia coli and Pseudomonas putida based on outer membrane permeabilization, emphasizing the applicability and versatility of the proposed approach. Upon nutrient limitation, cell population tends to diversify into several subpopulations exhibiting distinct phenotypic features (non‐permeabilized and permeabilized cells). Online analysis leads to the determination of the ratio between cells in these two states, which in turn triggers the addition of glucose pulses in order to maintain a predefined diversification ratio. These results prove that phenotypic diversification can be controlled by means of defined pulse‐frequency modulation within continuously running bioreactor set‐ups. This lays the foundation for systematic studies, not only of phenotypic diversification but also for all processes where dynamics single‐cell approaches are required, such as synthetic co‐culture processes.
In their own words: language preferences of individuals who use heroin
Authors: Pivovarova Ekaterina , Stein Michael D. 
Published: May 2019

ABSTRACTBackground and AimsUse of non‐judgmental, respectful and uniform language to describe individuals with substance use disorders (SUD) is recommended to reduce stigma. However, existing research concerning the use of labels for substance use has largely focused on perspectives of treatment providers and the general public, and to a lesser degree of those in long‐term recovery. This study aimed to examine and compare labels that individuals who use heroin and are initiating SUD treatment (1) use to describe themselves and when speaking with others who use drugs, with family and with treatment providers, and (2) prefer to be called and never want to be called.Design and SettingThis was a cross‐sectional survey study using a convenience sample of individuals initiating an in‐patient managed withdrawal program in Massachusetts, USA.ParticipantsBetween October 2017 and May 2018, 263 participants were enrolled.MeasuresParticipants completed a survey about (1) what labels they used to refer to self and when talking with others who use drugs, with providers, families and at 12‐Step meetings and (2) to identify which label they preferred least and most for others to use when referring to them.FindingsMore than 70% of participants used the term ‘addict’ to describe themselves and when speaking with others. However, use of ‘addict’ varied by context, and was most common at 12‐Step programs. Fewer than 15% reported using ‘user’ or slang terms, most commonly ‘junkie’, in any communications. The most‐preferred label for others to call them was ‘person who uses drugs’, while the most common label that participants never wanted to be called was ‘heroin misuser’ or ‘heroin‐dependent’.ConclusionLabel preferences by individuals who use heroin and are in early recovery are consistent with general guidelines about use of first‐person language and suggest avoidance of language indicative of drug misuse or dependence.
Transient left bundle branch block and intraventricular dyssynchrony as a cause of reversible left ventricular dysfunction: The “in vivo” documentation of spontaneous electrical remodeling
Authors: Moccia Eleonora , Sanna Giuseppe D. , Parodi Guido 
Published: May 2019

AbstractSpontaneous resolution of non‐rate‐dependent left bundle branch block (LBBB) has been rarely reported. We present the case of a 74‐year‐old woman admitted with pulmonary edema, a newly diagnosed LBBB and severe left ventricular (LV) dysfunction. Five months later, the patient was asymptomatic, the ECG recording showed complete regression of the LBBB to narrow QRS and LV function completely recovered. However, at one‐year follow‐up LBBB reappeared together with mild LV dysfunction. Spontaneous resolution of LBBB may be responsible for LV electrical and mechanical reverse remodeling in dyssynchronopathies.
Long term outcomes in monoclonal gammopathy of renal significance
Authors: Khera Akhil , Panitsas Fotios , Djebbari Faouzi , Kimberger Katja , Stern Simon , Quinn John , Rabin Neil , Kothari Jaimal , Alchi Bassam , Haynes Richard , Winearls Christopher , Roberts Ian , Ramasamy Karthik 
Published: May 2019

SummaryUnlike AL amyloid and cast nephropathy, the long‐term outcomes of monoclonal gammopathy of renal significance (MGRS) patients with other renal histopathologies remain unclear. It is uncertain if early intervention improves renal outcomes, because of a lack of evidence from prospective studies. In this retrospective study, we examined outcomes of 41 MGRS patients treated between 2004 and 2017 across five centres: four in the UK and one in the Republic of Ireland. The primary outcome measure was renal survival estimated by Kaplan–Meier product‐limit method. Thirty‐three patients (80·5%) were kappa light chain (LC) restricted. Twenty‐seven patients (65·9%) presented with LC deposition disease on renal histology. At 24 months follow‐up, estimated renal survival was 81·6% for the whole cohort. The estimated overall survival was 80·3% at 48 months. At 24 months, patients who had chronic kidney disease (CKD) stage 2–3b at diagnosis showed an estimated renal survival of 100% compared to 80·7% in those with CKD stage 4–5 at diagnosis (P = 0·04). Poorer outcomes in MGRS patients were historically attributed to delayed diagnosis due to small plasma cell clones, as well as the need for renal biopsy.