bluuebunny/crossref_metadata_2025 huggingface dataset:
Antimicrobial resistance: A multifaceted problem with multipronged solutions
Authors: Gil‐Gil Teresa , Laborda Pablo , Sanz‐García Fernando , Hernando‐Amado Sara , Blanco Paula , Martínez José Luis
Published: November 2019

Infectious diseases still stand as a major cause of morbidity and mortality, and this problem can be worsened with the current antimicrobial resistance crisis. To tackle this crisis more studies analyzing the causes, routes, and reservoirs where antimicrobial resistance can emerge and expand, together with new antimicrobials and strategies for fighting antimicrobial resistance are needed. In the current special issue of MicrobiologyOpen, a set of articles dealing with the multiple faces of antimicrobial resistance are presented. These articles provide new information for understanding and addressing this problem.
Combining culture and culture‐independent methods reveals new microbial composition of halitosis patients' tongue biofilm
Authors: Bernardi Sara , Karygianni Lamprini , Filippi Andreas , Anderson Annette Carola , Zürcher Andrea , Hellwig Elmar , Vach Kirstin , Macchiarelli Guido , Al‐Ahmad Ali
Published: November 2019

Background

Oral malodor is a very discomforting condition deriving from the presence of volatile sulfur compounds in the expired air. In halitosis of intraoral etiology, the volatile sulfur compounds are metabolic products of the oral microorganisms within the biofilm coating the tongue dorsum as well as other tissues in the oral cavity. The aim of this study was to characterize and compare the microbial composition of tongue biofilm in volunteers suffering from halitosis and healthy volunteers by means of both the culture method and culture‐independent cloning technique.

Results

A high bacterial variety (more than 80 different species) was detected using the combination of both methods. A distinct bacterial composition was revealed in the halitosis‐associated biofilms compared with the health‐associated biofilms. Actinomyces graevenitzii was shown to be significantly associated with the halitosis condition. The culture method identified 47 species, included Veillonella rogosae, never isolated from the tongue biofilm of halitosis patients so far. In the healthy condition, the culture‐dependent method showed that the most frequent species were Streptococcus parasanguinis among the aerobes and Veillonella spp. among the anaerobes. The culture‐independent cloning method detected more than 50 species. Streptococci, in particular S. mitis/oralis, S. pseudopneumoniae, and S. infantis as well as Prevotella spp., were found most frequently in halitosis patients. Streptococcus salivarius and Rothia mucilaginosa were found more frequently in the healthy condition.

Conclusions

The combination of the culture‐dependent and culture‐independent cloning techniques allowed for a widespread analysis of the tongue biofilm in halitosis patients. The results can support further pharmacological research for new antimicrobial agents and halitosis therapy strategies.
A scaffold‐free Bio 3D nerve conduit for repair of a 10‐mm peripheral nerve defect in the rats
Authors: Takeuchi Hisataka , Ikeguchi Ryosuke , Aoyama Tomoki , Oda Hiroki , Yurie Hirofumi , Mitsuzawa Sadaki , Tanaka Mai , Ohta Souichi , Akieda Shizuka , Miyazaki Yudai , Nakayama Koichi , Matsuda Shuichi
Published: November 2019

Introduction

A Bio 3D printed nerve conduit was reported to promote nerve regeneration in a 5 mm nerve gap model. The purpose of this study was to fabricate Bio 3D nerve conduits suitable for a 10 mm nerve gap and to evaluate their capacity for nerve regeneration in a rat sciatic nerve defect model.

Materials and Methods

Eighteen F344 rats with immune deficiency (9–10 weeks old; weight, 200–250 g) were divided into three groups: a Bio 3D nerve conduit group (Bio 3D, n = 6), a nerve graft group (NG, n = 6), and a silicon tube group (ST, n = 6). A 12‐mm Bio 3D nerve conduit or silicon tube was transplanted into the 10‐mm defect of the right sciatic nerve. In the nerve graft group, reverse autografting was performed with an excised 10‐mm nerve segment. Assessments were performed at 8 weeks after the surgery.

Results

In the region distal to the suture site, the number of myelinated axons in the Bio 3D group were significantly larger compared with the silicon group (2,548 vs. 950, p < .05). The myelinated axon diameter (MAD) and the myelin thickness (MT) of the regenerated axons in the Bio 3D group were significantly larger compared with those of the ST group (MAD: 3.09 vs. 2.36 μm; p < .01; MT: 0.59 vs. 0.40 μm, p < .01).

Conclusions

This study indicates that a Bio 3D nerve conduit can enhance peripheral nerve regeneration even in a 10 mm nerve defect model.
Low‐profile annular ring‐shaped continuous transverse stub antenna array with two‐dimensional beam scanning
Authors: Lou Tian , Yang Xue‐Xia , Qiu Houtong
Published: November 2019

A low profile two‐dimensional beam scanning antenna array formed by annular ring‐shaped continuous transverse stubs (CTS) is proposed. The annular ring‐shaped CTS array is constructed on two substrate layers by the substrate integrated waveguide (SIW) technique and fed by a planar SIW horn, which is located at the center of the antenna array. A 360° azimuth beam scanning could be achieved by rotating the feed SIW horn around the antenna axle, while the elevation beam scanning would be obtained with the frequency‐scanning. This SIW‐CTS array is designed, fabricated, and tested. The measured −10 dB reflection coefficient bandwidth is from 15.2 to 22 GHz (36.5%). The measured main beam scanning range in the elevation is 27.6° with the frequency varying, while the array gain is between 17 and 18.9 dBi.
Side‐to‐side supercharging nerve allograft enhances neurotrophic potential
Authors: Isaacs Jonathan , Feger Mark A. , Mallu Satya , Patel Gaurangkumar , Debkowska Monika , Yager Dorne , Ernst Brady , Chilukuri Sravya , Moser Matthew , Kurtz Camden
Published: November 2019

Introduction

Critical limitations of processed acellular nerve allograft (PNA) are linked to Schwann cell function. Side‐to‐side bridge grafting may enhance PNA neurotrophic potential.

Methods

Sprague–Dawley rats underwent tibial nerve transection and immediate repair with 20‐mm PNA (n = 33) or isograft (ISO; n = 9) or 40‐mm PNA (n = 33) or ISO (n = 9). Processed acellular nerve allograft groups received zero, one, or three side‐to‐side bridge grafts between the peroneal nerve and graft. Muscle weight, force generation, and nerve histomorphology were tested 20 weeks after repair. Selected animals underwent neuron back labeling with fluorescent dyes.

Results

Inner axon diameters, g‐ratios, and axon counts were smaller in the distal vs proximal aspect of each graft (P < .05). Schwann cell counts were greater, with a lower proportion of senescent cells for groups with bridges (P < .05). Retrograde labeling demonstrated that 6.6% to 17.7% of reinnervating neurons were from the peroneal pool.

Discussion

Bridge grafting positively influenced muscle recovery and Schwann cell counts and senescence after long PNA nerve reconstruction.
Outcome measures in a cohort of ambulatory adults with spinal muscular atrophy
Authors: Elsheikh Bakri , King Wendy , Peng Juan , Swoboda Kathy J. , Reyna Sandra P. , LaSalle Bernard , Prior Thomas W. , Arnold W. David , Kissel John T. , Kolb Stephen J.
Published: November 2019

Introduction

With the advent of disease‐altering therapies for spinal muscular atrophy (SMA), there is a requirement to better characterize outcome measures, particularly in milder forms of disease.

Methods

Maximal voluntary isometric contraction testing and 6‐minute walk test (6MWT) performed in ambulatory SMA adults as part of the SMA‐VALIANT trial were analyzed. Test–retest reliability and correlation with other candidate biomarkers and outcomes were investigated.

Results

Maximal voluntary isometric contraction testing and 6MWT showed good test–retest reliability (intraclass correlation coefficient = 0.98 and 0.85, respectively). Maximal voluntary isometric contraction testing and 6MWT demonstrated very strong correlation (r = 0.83, P <. 0001), and each correlated with the SMA Functional Rating Scale (r = 0.7, P < .0001 and r = 0.65, P = .0001, respectively), lean muscle mass (r = 0.68, P < .0001 and r = 0.56, P = .001, respectively), and ulnar compound muscle action potential (r = 0.57, P = .0008 and r = 0.47, P = .008, respectively).

Discussion

Maximal voluntary isometric contraction testing and 6MWT are suitable outcomes for use in ambulatory adults with SMA. Maximal voluntary isometric contraction testing may be preferable because of superior test–retest reliability and closer associations with other outcomes and biomarkers of neuromuscular function.
Bladder reinnervation by somatic nerve transfer to pelvic nerve vesical branches does not reinnervate the urethra
Authors: Barbe Mary F. , Braverman Alan S. , Salvadeo Danielle M. , Gomez‐Amaya Sandra M. , Lamarre Neil S. , Brown Justin M. , De Elise J. , McIntyre Brian S. , Day Emily P. , Cruz Geneva E. , Frara Nagat , Ruggieri Michael R.
Published: November 2019

Aims

We sought to determine whether somatic lumbar nerve transfer to the pelvic nerve's anterior vesical branch after sacral decentralization for detrusor muscle reinnervation also leads to aberrant innervation of the bladder outlet.

Methods

Twenty‐six female mongrel hound dogs underwent transection of sacral dorsal and ventral spinal roots (ie, sacral decentralization). Immediately afterward, 12 received genitofemoral nerve transfer and 9 received femoral nerve branch transfer. Five were left sacrally decentralized. Controls included 3 sham‐operated and 6 unoperated. Eight months postsurgery, the bladder and urethra were injected with retrograde tracing dyes cystoscopically. After 3 weeks, detrusor and urethral pressures were assayed electrophysiologically immediately before euthanasia and characterization of neural reinnervation.

Results

Electrical stimulation of spinal cords or roots did not lead to increased urethral sphincter pressure in nerve transfer animals, compared with decentralized animals, confirming a lack of functional reinnervation of the bladder outlet. In contrast, mean detrusor pressure increased after lumbar cord/root stimulation. In sham/unoperated animals, urethral and bladder dye injections resulted in labeled neurons in sacral level neural structures (dorsal root ganglia [DRG], sympathetic trunk ganglia [STG], and spinal cord ventral horns); labeling absent in decentralized animals. Urethral dye injections did not result in labeling in lumbar or sacral level neural structures in either nerve transfer group while bladder dye injections lead to increased labeled neurons in lumbar level DRG, STG, and ventral horns, compared to sacrally decentralized animals.

Conclusion

Pelvic nerve transfer for bladder reinnervation does not impact urethral sphincter innervation.
Whole brain 7T‐fMRI during pelvic floor muscle contraction in male subjects
Authors: Groenendijk Ilse M. , Luijten Sven P. R. , de Zeeuw Chris I. , Holstege Joan C. , Scheepe Jeroen R. , van der Zwaag Wietske , Blok Bertil F. M.
Published: November 2019

Aim

The primary aim of this study is to demonstrate that 7‐tesla functional magnetic resonance imaging (7T‐fMRI) can visualize the neural representations of the male pelvic floor in the whole brain of a single subject.

Methods

In total, 17 healthy male volunteers (age 20‐47) were scanned in a 7T‐MRI scanner (Philips Achieva). The scanning protocol consisted of two functional runs using a multiband echo planar imaging sequence and a T1‐weighted scan. The subjects executed two motor tasks, one involving consecutive pelvic floor muscle contractions (PFMC) and a control task with tongue movements.

Results

In single subjects, results of both tasks were visualized in the cortex, putamen, thalamus, and the cerebellum. Activation was seen during PFMC in the superomedial and inferolateral primary motor cortex (M1), supplementary motor area (SMA), insula, midcingulate gyrus (MCG), putamen, thalamus, and in the anterior and posterior lobes of the cerebellum. During tongue movement, activation was seen in the inferolateral M1, SMA, MCG, putamen, thalamus, and anterior and posterior lobes of the cerebellum. Tongue activation was found in the proximity of, but not overlapping with, the PFMC activation. Connectivity analysis demonstrated differences in neural networks involved in PFMC and tongue movement.

Conclusion

This study demonstrated that 7T‐fMRI can be used to visualize brain areas involved in pelvic floor control in the whole brain of single subjects and defined the specific brain areas involved in PFMC. Distinct differences between brain mechanisms controlling the pelvic floor and tongue movements were demonstrated using connectivity analysis.
Contribution of agriculture in economic growth: A case study of West Bengal (India)
Authors: Khan Waseem , Jamshed Mohammed , Fatima Sana
Published: November 2019

Economists have argued that role of agriculture is pivotal for economic development of the nation. Worldwide studies have shown that agriculture sector is more effective in reducing hunger and poverty than other sectors. This study is an attempt to ascertain the importance of agriculture in the economic growth of West Bengal. Agriculture, being the source of livelihood and supplier of raw material to various industries, triggers economic growth of the nation. This paper exhibits how agriculture has contributed to West Bengal's economic excellence using empirical data and a cointegration analysis. The role of agriculture is examined on four contributions: (a) product contribution (forward linkage), (b) market contribution (backward linkage), (c) factor contribution, and (d) foreign exchange contribution. The composition and growth of the sectors and its association with other sectors is analyzed using time series analysis. Findings of the study revealed that agriculture sector has appeared as an important contributor to drive West Bengal economic growth even after declining share in gross state domestic product over the years. Empirical analysis reveals that agriculture is having long run causal linkages with industry, services, and overall economic growth in West Bengal.
Interaction of real effective exchange rate with economic growth via openness of the economy: Empirical evidence from India
Authors: Jena Nihar Ranjan , Sethi Narayan
Published: November 2019

This paper examines the interaction between real effective exchange rate (REER) with select macroeconomic variables such as gross domestic product (GDP), foreign direct investment, foreign institutional investors (FII), fiscal deficits, terms of trade, trade openness, and foreign exchange reserves from 1981–2017. Autoregressive distributed lag bounds test results confirm the existence of long‐run relationships among the considered variables. The study finds that among the selected macroeconomic variables, GDP and remittances have positive and significant impact on REER. The study also reveals that although the variables official development assistance, FII, and fiscal deficit have positive impacts on REER, the results are not statistically significant. Further, our study indicated that the speed of convergence of REER towards long‐run equilibrium is 30% per annum, which is below standard in nature.
Emotional symptoms and family functioning in caregivers of children with newly diagnosed leukemia/lymphomas and solid tumors: Short‐term changes and related demographic factors
Authors: Peterson Rachel K. , Chung Joanna , Barrera Maru
Published: November 2019

Background

Pediatric oncology diagnoses are distressing to caregivers. However, researchers have not investigated the impact that the type of cancer diagnosis has on caregiver anxiety, depression, distress, and family functioning. The purpose of this study was to longitudinally investigate the early trajectory of caregiver psychological symptoms of anxiety, depression, distress, and family functioning near diagnosis and 6 months later by cancer type, and to examine the demographic factors that may be associated with caregiver emotional and family functioning outcomes.

Methods

Caregivers (n = 122) of children with a recent diagnosis of leukemia/lymphoma or solid tumor completed self‐report measures of psychological and family functioning (Hospital Anxiety and Depression Scale, Distress Thermometer, and Family Environment Scale).

Results

In general, caregivers endorsed elevated psychological symptoms at the time of diagnosis, which decreased 6 months later. Caregivers of children with solid tumors endorsed greater anxiety across time than caregivers of children with leukemia/lymphoma did. In addition to caring for a child with a solid tumor, female sex, non‐White ethnicity, and non‐English language spoken in the home were factors associated with anxious and depressive symptoms and poorer family functioning.

Conclusion

When creating psychosocial interventions for families of children with cancer, the unique demands of solid tumor treatments, the caregiver's sex, and cultural characteristics must be considered to promote coping, resiliency, and problem‐solving skills around the time of diagnosis, particularly in more vulnerable families.
Variation in hospital admission of sickle cell patients from the emergency department using the Pediatric Health Information System
Authors: Jacob Seethal A. , Mueller Emily L. , Cochrane Anneli R. , Carroll Aaron E. , Bennett William E.
Published: November 2019

Background

Universal newborn screening and improved treatment options have led to increased survival in sickle cell disease (SCD). However, patients with SCD still rely heavily on acute care services.

Objective

To determine the variation seen in hospitalizations for the top complaints for ED visits for children with SCD nationally.

Methods

We performed a retrospective review of the Pediatric Health Information Systems (PHIS) Database between October 2011 and September 2015. Emergency department (ED) encounters were selected by using International Classification of Diseases, Ninth Edition, Clinical Modification (ICD‐9‐CM) codes for SCD with and without crisis, fever, and pain. Univariate analyses were performed, as well as index of dispersion (ID) to assess variation by day of the week and region. ANOVA and t‐test were used to determine statistical significance.

Results

A total of 68 661 ED encounters at 36 hospitals met the criteria for inclusion. Of those encounters, 50.1% were admitted to the hospital. Pain and fever were the most common primary diagnoses among this population. Although variation in hospitalization was seen overall, as well as for a primary diagnosis of pain or fever, this variation was not explained by weekday/weekend designation.

Conclusion

The results of our study confirm pain and fever as the most common primary diagnoses for children with SCD who seek acute care, as well as demonstrate that while significant variation in hospitalization exists, it is not associated with day of the week. Further studies to elucidate patient‐ and hospital‐level factors that influence admission variation are necessary.
Novel variants in FERMT3 and RASGRP2—Genetic linkage in Glanzmann‐like bleeding disorders
Authors: Manukjan Georgi , Wiegering Verena A. , Reindl Tobias , Strauß Gabriele , Klopocki Eva , Schulze Harald , Andres Oliver
Published: November 2019

Defects of platelet intracellular signaling can result in severe platelet dysfunction. Several mutations in each of the linked genes FERMT3 and RASGRP2 on chromosome 11 causing a Glanzmann‐like bleeding phenotype have been identified so far. We report on novel variants in two unrelated pediatric patients with severe bleeding diathesis—one with leukocyte adhesion deficiency type III due to a homozygous frameshift in FERMT3 and the other with homozygous variants in both, FERMT3 and RASGRP2. We focus on the challenging genetic and functional variant assessment and aim to accentuate the risk of obtaining misleading results due to the phenomenon of genetic linkage.
Effectiveness of interventions to improve adverse drug reaction reporting by healthcare professionals over the last decade: A systematic review
Authors: Li Raymond , Zaidi Syed Tabish Razi , Chen Timothy , Castelino Ronald
Published: November 2019

Background

Various strategies have been studied in the literature to address the significant underreporting of adverse drug reactions (ADRs) in healthcare systems worldwide.

Objectives

We conducted a systematic review of the literature that assessed the impact of various strategies to improve ADR reporting published in the last decade and compared this with the strategies identified in a previous systematic review.

Methods

MEDLINE and EMBASE databases were used to retrieve papers published from 01 July 2010 to 17 June 2019. We included papers in the English language that investigated the quantitative impact of strategies used to improve ADR reporting.

Results

A total of 10,021 articles were retrieved using our search criteria, of which 13 met the inclusion criteria. Multifaceted strategies resulted in a point estimate increase in ADR reporting of 9.26‐fold (−2.21–17.11, 95% CI) versus 7.19‐fold (−5.29–32.68, 95% CI) for single interventions. Using electronic reporting tools was more commonly identified as an interventional strategy with a point estimate increase of 13.69‐fold (−5.29–32.68, 95%CI) versus 4.42‐fold (0.66–8.19, 95% CI) for traditional educational methods. The quality of the majority of publications included in this review was low.

Conclusions

Developments in digital technology in the last decade has led to the increased use of electronic reporting tools to improve ADR reporting. Higher quality studies investigating the impact of these electronic methods are needed to fully explore its role in improving ADR reporting.
Automated Precision Assembly of Optical Systems
Authors: Haag Sebastian , Müller Tobias
Published: November 2019

Manufacturing equipment for novel products needs to be operational within days to weeks, prototyping should be done in an instant and create a basis for consecutive quick implementation of small‐series production and the following scaling of production.
Improved Inspection Thanks to Machine Learning
Authors: Hess Patrick , Sudowe Patrick , Christ Tassilo
Published: November 2019

A pilot setup of different machine learning technologies for the real‐time identification of damaged medical containers puts deep learning for the classification of image contents in focus.
Reciprocal regulation of photosynthesis and mitochondrial respiration by TOR kinase in Chlamydomonas reinhardtii
Authors: Upadhyaya Shivani , Rao Basuthkar Jagadeeshwar
Published: November 2019

While the role of TOR kinase in the chloroplast biogenesis and transcriptional regulation of photosynthesis is well documented in Arabidopsis, the functional relevance of this metabolic sensor kinase in chloroplast–mitochondria cross talk is unknown. Using Chlamydomonas reinhardtii as the model system, we demonstrate the role of TOR kinase in the regulation of chloroplast and mitochondrial functions: We show that TOR kinase inhibition impairs the maintenance of high ETR associated with PSII and low NPQ and inhibits efficient state transitions between PSII and PSI. While compromised photosynthetic functions are observed in TOR kinase inhibited cells, same conditions lead to augmentation in mitochondrial basal respiration rate by twofold and concomitantly a rise in ATP production. Interestingly, such upregulated mitochondrial functions in TOR‐inhibited cells are mediated by fragmented mitochondria via upregulating COXIIb and downregulating Hxk1 and AOX1 protein levels. We propose that TOR kinase may act as a sensor that counter‐regulates chloroplast versus mitochondrial functions in a normal C. reinhardtii cell.
Relationship between edge roughness in mask pattern and charging in plasma etching
Authors: Zhang Peng
Published: November 2019

The edge roughness (ER) developed in the mask pattern during the plasma etching process harms the perfect pattern transformation from mask to substrate. To understand and ultimately manipulate plasma‐induced ER, this study investigated the interplay between charging and nanoscale roughness of an isolated rough mask hole in the plasma etching process using a modeling framework, which consisted of a surface etching module, a surface charging module, and a profile evolution module. Specifically, on the one hand, the distributions of the spatial electric field (E‐field) and etching rate were simulated for the rough mask surface being etched. It is revealed that the distribution of the etching rate is similar with that of E‐field clinging to the mask surface, and both of them reach their maximum strength around the mask hole edge and gradually becomes uniform/nonuniform with the decrease of the value of the dominant amplitude/wavelength of roughness; on the other hand, a string algorithm was used to simulate the evolution rule for a rough profile of a mask hole with etching time under various values of roughness parameters. The simulated evolution of the profile has good agreement with experimental observation. The charging effect contributes to the enhancement of the root mean square roughness. Additionally, the influence of roughness parameters on the charging time versus root mean square was also examined. The mechanism behind these results was analyzed systematically. This study will greatly contribute toward improving the physical and chemical properties of the mask or optimizing the etching technique.
New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink “waters,” and NGL Viewer to recapture online 3D graphics
Authors: Prisant Michael G. , Williams Christopher J. , Chen Vincent B. , Richardson Jane S. , Richardson David C.
Published: November 2019

The MolProbity web service provides macromolecular model validation to help correct local errors, for the structural biology community worldwide. Here we highlight new validation features, and also describe how we are fighting back against outside developments which compromise that mission. Our new tool called UnDowser analyzes the properties and context of clashing HOH “waters” to diagnose what they might actually represent; a dozen distinct scenarios are illustrated and described. We now treat alternate conformations more thoroughly, and switching to the Neo4j database (graphical rather than relational) enables cleaner, more comprehensive, and much larger reference datasets. A problematic outside change is that refinement software now increasingly restrains traditional validation criteria (geometry, clashes, rotamers, and even Ramachandran) in order to supplement the sparser experimental data at 3–4 Å resolutions typical of modern cryoEM. But unfortunately the broad density allows model optimization without fixing underlying problems, which means these structures often score much better on validation than they really are. CaBLAM, our tool designed for evaluating peptide orientations at lower resolutions, was described in the previous Tools issue, and here we demonstrate its effectiveness in diagnosing local errors even when other validation outliers have been artificially removed. Sophisticated hacking of the MolProbity server has required continual monitoring and various security measures short of restricting user access. The deprecation of Java applets now prevents KiNG interactive online display of outliers on the 3D model during a MolProbity run, but that important functionality has now been recaptured with a modified version of the Javascript NGL Viewer.
Facilities that make the PDB data collection more powerful
Authors: Lange Joanna , Baakman Coos , Pistorius Arthur , Krieger Elmar , Hooft Rob , Joosten Robbie P. , Vriend Gert
Published: November 2019

We describe a series of databases and tools that directly or indirectly support biomedical research on macromolecules, with focus on their applicability in protein structure bioinformatics research. DSSP, that determines secondary structures of proteins, has been updated to work well with extremely large structures in multiple formats. The PDBREPORT database that lists anomalies in protein structures has been remade to remove many small problems. These reports are now available as PDF‐formatted files with a computer‐readable summary. The VASE software has been added to analyze and visualize HSSP multiple sequence alignments for protein structures. The Lists collection of databases has been extended with a series of databases, most noticeably with a database that gives each protein structure a grade for usefulness in protein structure bioinformatics projects. The PDB‐REDO collection of reanalyzed and re‐refined protein structures that were solved by X‐ray crystallography has been improved by dealing better with sugar residues and with hydrogen bonds, and adding many missing surface loops. All academic software underlying these protein structure bioinformatics applications and databases are now publicly accessible, either directly from the authors or from the GitHub software repository.
Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins
Authors: Koike Ryotaro , Amano Mutsuki , Kaibuchi Kozo , Ota Motonori
Published: November 2019

Phosphorylation is a major post‐translational modification that plays a central role in signaling pathways. Protein kinases phosphorylate substrates (phosphoproteins) by adding phosphate at Ser/Thr or Tyr residues (phosphosites). A large amount of data identifying and describing phosphosites in phosphoproteins has been reported but the specificity of phosphorylation is not fully resolved. In this report, data of kinase‐substrate pairs identified by the Kinase‐Interacting Substrate Screening (KISS) method were used to analyze phosphosites in intrinsically disordered regions (IDRs) of intrinsically disordered proteins. We compared phosphorylated and nonphosphorylated IDRs and found that the phosphorylated IDRs were significantly longer than nonphosphorylated IDRs. The phosphorylated IDR is often the longest IDR (71%) in a phosphoprotein when only a single phosphosite exists in the IDR, and when the phosphoprotein has multiple phosphosites in an IDR(s), the phosphosites are primarily localized in a single IDR (78%) and this IDR is usually the longest one (81%). We constructed a stochastic model of phosphorylation to estimate the effect of IDR length. The model that accounted for IDR length produced more realistic results when compared with a model that excluded the IDR length. We propose that the IDR length is a significant determinant for locating kinase phosphorylation sites in phosphoproteins.
Effect of Nitrogen on the Amorphous Structure and Subthreshold Electrical Conduction of GeSeSb‐Based Ovonic Threshold Switching Thin Films
Authors: Verdy Anthonin , d'Acapito Francesco , Dory Jean-Baptiste , Navarro Gabriele , Bernard Mathieu , Noé Pierre
Published: November 2019

Herein, the amorphous structure of Ge–Se–Sb–N chalcogenide thin films is investigated through Raman, infrared, and X‐ray absorption spectroscopies in the light of the electrical performances of such materials once integrated in ovonic threshold switching (OTS) selector devices. In particular, it is shown that the presence of homopolar and wrong bonds in the amorphous structure has a detrimental impact on the subthreshold leakage current of the OTS devices. Although the presence of Sb–Sb and Ge–Sb bonds tends to increase the leakage current in pristine devices, the presence of Se–Se bonds is correlated to a significant device‐to‐device dispersion of subthreshold characteristics after the device initialization. Finally, the incorporation of a proper N concentration in Ge–Se–Sb glass permits to suppress the homopolar bonds, leading to a very low leakage current and a low device‐to‐device dispersion.
Extremal Wiener and Kirchhoff indices of globular caterpillars
Authors: Ye Luzhen
Published: November 2019

The Wiener and Kirchhoff indices of a graph G are two of the most important topological indices in mathematical chemistry. A graph G is called to be a globular caterpillar if G is obtained from a complete graph K
s with vertex set {v1,v2,…, v
s} by attaching n
i pendent edges to each vertex v
i of K
s for some positive integers s and n1,n2,…,n
s, denoted by . Let be the set of globular caterpillars with n vertices (). In this article, we characterize the globular caterpillars with the minimal and maximal Wiener and Kirchhoff indices among , respectively.
Random tree recursions: Which fixed points correspond to tangible sets of trees?
Authors: Johnson Tobias , Podder Moumanti , Skerman Fiona
Published: November 2019

Let be the set of rooted trees containing an infinite binary subtree starting at the root. This set satisfies the metaproperty that a tree belongs to it if and only if its root has children u and v such that the subtrees rooted at u and v belong to it. Let p be the probability that a Galton‐Watson tree falls in . The metaproperty makes p satisfy a fixed‐point equation, which can have multiple solutions. One of these solutions is p, but what is the meaning of the others? In particular, are they probabilities of the Galton‐Watson tree falling into other sets satisfying the same metaproperty? We create a framework for posing questions of this sort, and we classify solutions to fixed‐point equations according to whether they admit probabilistic interpretations. Our proofs use spine decompositions of Galton‐Watson trees and the analysis of Boolean functions.
Cyclocuneatol and Cuneatannin, New Cycloartane Triterpenoid and Ellagitannin Glycoside from Euphorbia cuneata
Authors: Elghamdi Amjad A. , Abdallah Hossam M. , Shehata Ibrahim A. , Mohamed Gamal A. , Shati Ali A. , Alfaifi Mohammad Y. , Elbehairi Serag Eldin I. , Koshak Abdulrahman E. , Ibrahim Sabrin R. M.
Published: November 2019

Phytochemical investigation of the aerial parts of Euphorbia cuneata Vahl. (Euphorbiaceae) revealed new cycloartane triterpenoid, cyclocuneatol (2) and new ellagitannin glycoside, cuneatannin (11), along with nine known metabolites: β‐sitosterol (1), 3β‐hydroxycycloart‐25‐ene‐24‐one (3), cycloart‐25‐ene‐3β,24β‐diol (4), cycloart‐23Z‐ene‐3β,25‐diol (5), 2R‐naringenin (6), β‐sitosterol‐3‐O‐β‐D‐glucopyranoside (7), quercetin (8), kaempferol‐7‐O‐β‐glucoside (9), and 2R‐naringenin‐7‐O‐β‐glucoside (10). Their chemical structures were identified by detailed analyses of physical, chemical, and spectral data as well as comparison with literature. Their cytotoxic activity was assessed towards HepG2, MCF7, and HCT116 cancer cell lines by sulphorhodamine B test (SRB). It is noteworthy that 3 and 4 demonstrated the most significant activity towards HepG2, MCF7, and HCT116 cells (IC50 2.6, 2.7, and 2.4 μM, respectively for 3 and 3.4, 4.1, and 5.3 μM, respectively for 4) in comparison with doxorubicin (IC50 0.18, 0.6, and 0.2 μM, respectively).
Non‐Aggregation‐Induced Colorimetric Detection of Ag+ by Tetrazine‐Capped Gold Nanoparticles Based on the Formation of Au‐Ag Core‐Shell Nanoparticles
Authors: Ray Shounak , Biswas Rima , Banerjee Rumeli , Ghosh Abhisek Brata , Biswas Papu
Published: November 2019

Recently, simple and rapid colorimetric sensing based on plasmonic nanoparticles has gained much attention as no expensive instrument required to achieve high sensitivity. In This study, 3,6‐di(pyridin‐2‐yl)‐1,2,4,5‐s‐tetrazine (pytz) and 3,6‐di(pyridin‐2‐yl)‐1,4‐dihydro‐1,2,4,5‐tetrazine (H2pytz) capped gold nanoparticles (TzAuNPs) were synthesized for the sensitive and selective colorimetric detection of Ag+. The synthesis of TzAuNPs was achieved by reaction of HAuCl4.3H2O in water with ethanolic solution of 3,6‐di(pyridin‐2‐yl)‐1,4‐dihydro‐1,2,4,5‐tetrazine (H2pytz) as reducing agent without the addition of any external stabilizing agent. As prepared TzAuNPs were characterized by FT‐IR, UV‐Vis, XRD and HRTEM techniques. The Ag+ sensing mechanism is based on the formation of Au−Ag core‐shell nanoparticles (NPs). The formation of Au−Ag core‐shell NPs has been achieved in absence of any external reducing agents to observe a distinct color change from red to brown. H2pytz molecules present on the surface of AuNPs as capping agent facilitate the reduction of Ag+. The formation of the core‐shell nanoparticles is confirmed from TEM and EDX‐particle mapping analysis. The detection limit (LOD) of the present assay is 0.56 ppb (considering signal/noise ratio=3.3) for Ag+ in absence of any external reducing agent. Significant reduction of response time and much lower LOD (0.0013 ppb) have also been achieved in presence of ascorbic acid (AA) as an external reducing agent.
l‐Glutamine Supported on Core–Shell Silica Iron Oxide Nanoparticles: A Highly Efficient Organocatalyst for Synthesis of Spirooxoindoles
Authors: Dutta Arup , Rahman Noimur , Khongriah Welfareson , Nongrum Ridaphun , Joshi Santa R. , Nongkhlaw Rishanlang
Published: November 2019

A novel, eco‐friendly super paramagnetic organo‐nano catalyst was fabricated by encapsulating ferrite@silica (Fe3O4@SiO2) nanoparticles with l‐Glutamine. The prepared catalyst was characterized by various analytical techniques viz., fourier transform infrared spectroscopy (FT‐IR), thermogravimetric analysis (TGA), transmission electron microscopy (TEM), Scanning electron microscopy (SEM), Energy Dispersive X‐ray analysis (EDX), powder X‐ray diffraction technique (XRD), vibrating sample magnetometer spectroscopy (VSM), Inductively coupled plasma optical emission spectroscopy (ICP‐OES) and its catalytic activity was investigated for the synthesis of spirooxindole derivatives. Utilizing the ferromagnetic nature of Fe3O4 nanoparticles, the prepared catalyst could be easily retrieved from the reaction mixture after completion of the reaction by using an external magnet. The catalyst was reused up to six runs with remarkable catalytic activity. The main advantages of this synthetic approach lie in its operational simplicity, cost effectiveness, higher yields, easy catalyst recyclability and reusability, eco‐friendly procedures and shorter reaction times. Also, the antimicrobial assay of the synthesized spirooxoindoles was evaluated against three bacterial isolates and one fungal isolate, and the results showed profound antimicrobial activities.
Syntheses and Properties of Three Types of 3,4‐Dichlorobenzoate‐based Ni(II)‐Ln(III) Heterometallic Clusters
Authors: Zhang Ju‐Wen , Liu Wen‐Hua , Wang Cen‐Ru , Xu Shuang , Liu Bin‐Qiu , Dong Yan‐Ping
Published: November 2019

The solvothermal reactions of NiCl2⋅6H2O, Ln(NO3)3⋅nH2O, 3,4‐dichlorobenzoic acid (3,4‐HDCB), and 2,2′‐bipyridine (2,2′‐bpy) yielded eight zero‐dimensional (0D) Ni(II)‐Ln(III) heterometallic complexes NdNi2(3,4‐DCB)7(2,2′‐bpy)2 (1) and Ln2Ni2(3,4‐DCB)10(2,2′‐bpy)2 [Ln=Sm (2), Eu (3), Gd (4), Tb (5), Dy (6), Er (7), and Yb (8)]. Complexes 1–8 display three types of linear heterometallic clusters. Complex 1 is a trinuclear cluster, whereas complexes 2–8 are tetranuclear clusters. Complexes 2–8 posssess the same formula, but the coordination number of Ln(III) in 2–6 is different from that in 7 and 8. In 1–8, the adjacent polynuclear clusters are linked by the π–π interactions into a one‐dimensional (1D) supramolecular chain. The size of Ln(III) ions and the position of halogen substituents have important effects on the formation and structures of 1–8. The properties of photoluminescence and magnetism of 1–8 were investigated.
Synthesis, Structures and Fluorescence Properties of Two Novel Cadmium MOFs Based on a Tetraphenylethene(TPE)‐Core Ligand
Authors: Xu Xiu‐Dian , Liang Yu , Mensah Abraham , Li Jun‐Feng , Zhou Lei , Chen Li‐Zhuang , Wang Fang‐Ming
Published: November 2019

Two novel Cadmium(II)‐based luminescent metal‐organic frameworks (LMOFs), namely, {[Cd(tipe)0.5(OBA)]⋅(H2O)5} [tipe=1,1,2,2‐tetrakis(4‐(1H‐imidazol‐1‐yl)phenyl)ethene, OBA=4,4‐oxoybis(benzoic acid)] (MOF‐1) and [Cd2(tipe)(SDC)2] (SDC=4,4′‐stilbenedicarboxylic acid) (MOF‐2), have been prepared by a tetraphenylethene (TPE)‐core ligand under hydrothermal condition. Results of single crystal X‐ray diffraction show that MOF‐1 crystallizes in monoclinic system and MOF‐2 crystallizes in the triclinic system. And two complexes all have blue emission with maximal peaks at 488 nm (MOF‐1) and 477 nm (MOF‐2), respectively. Solvent exchange experiments show that they are stable in most of organic solvents. As to MOF‐1, there exist different degrees of quenching or different stokes shifts in these solvents. It proves that MOF‐1 can have potential application in sensing organic solvents. Due to MOF‐2’s structural intercalation, the presence of organic solvents causes a large degree of quenching of fluorescence because they take part in photo‐induced electron transfer (PET) process.
Amine Functionalized Metal–Organic Framework Coordinated with Transition Metal Ions: d–d Transition Enhanced Optical Absorption and Role of Transition Metal Sites on Solar Light Driven H2 Production
Authors: Karthik P. , Shaheer A. R. Mahammed , Vinu Ajayan , Neppolian Bernaurdshaw
Published: November 2019

Design and development of efficient photocatalysts for H2 production from water and sunlight have gained significant attention as the solar assisted approach is considered to be a promising approach for the generation of clean fuel. However, the poor charge carrier separation and light harvesting ability of existing photocatalysts limits the efficiency of photoconversion of water. In this work, the synthesis of transition metal ions (M2+ = Co2+, Cu2+, and Ni2+) coordinated with Ti‐metal organic frameworks (Ti‐MOFs) through a simple post‐synthetic coordination method for efficient solar light‐driven H2 production is reported. Notably, coordination of M2+ ions with Ti‐MOF significantly improves the optical absorption by d–d transitions and the multimetal sites facilitate the fast charge carrier separation, thereby enhancing the solar light‐driven H2 production activity. Very interestingly, the rate of solar light‐driven H2 production is varied with respect to different metal ions coordination due to the position of d–d bands absorption in the solar spectrum, and the complexing tendency of M2+ ions with sacrificial electron donors. A maximum solar H2 production rate of 1583.55 µmol h−1 g−1 is achieved with a Cu2+ coordinated Ti‐MOF, which is ≈13 fold higher than that of the pristine Ti‐MOF.
The Impact of Housing Prices on Health in the United States Before, During, and After the Great Recession
Authors: Sung Jaesang , Qiu Qihua
Published: November 2019

We estimate the effects of U.S. Metropolitan Statistical Area housing prices on a variety of health outcomes and health‐related behaviors separately for homeowners and tenants. The constructed data set consists of information on individuals from the 2002–2012 Behavioral Risk Factor Surveillance System combined with homeownership data from the March Current Population Survey and housing prices from Freddie Mac. We estimate positive effects on homeowners' mental health when housing prices increase. We also find negative effects on tenants' health and health‐related behaviors with increases in housing prices. These estimated contemporaneous effects are concentrated among low‐income homeowners and tenants, and the effects for tenants are not persistent in the long run. However, the cumulative effects of an increase in housing prices on obesity become more pronounced for homeowners in the long run, resulting in worse self‐reported health.
UHPLC assay and impurity methods for diphenhydramine and phenylephrine hydrochloride oral solution
Authors: Kirkpatrick Douglas , Fain Margaret , Yang Jingyue , Santos Leonel , Anthony Clydewyn
Published: November 2019

Many over‐the‐counter drug products lack official compendial analytical methods. As a result, the United States Pharmacopeia and the United States Food and Drug Administration are seeking to develop and validate new methods to establish analysis standards for the assessment of the pharmaceutical quality of over‐the‐counter drug products. Diphenhydramine and phenylephrine hydrochloride oral solution, a combination drug product, was identified as needing a compendial standard. Therefore, an ultra‐high‐performance liquid chromatography method was developed to separate and quantify the two drug compounds and eleven related organic impurities. As part of a robustness study, the separation was demonstrated using different high‐performance liquid chromatography systems and columns from different manufacturers, and showed little dependence with changes in flow rate, column temperature, detection wavelength, injection volume and mobile phase gradient. The method was then validated conformant with the International Council for Harmonisation guidelines. For impurities, adequate specificity, linearity, accuracy and precision were demonstrated. For assay, a slight modification to the injection volume was necessary to achieve adequate analytical performance. With successful development and validation, these methods were shown to be suitable for their intended purpose and may be considered for adoption as compendial procedures.
Density‐Dependent Effects of Invasive Red Swamp Crayfish Procambarus clarkii on Experimental Populations of the Amargosa Pupfish
Authors: Paulson Brandon L. , Stockwell Craig A.
Published: November 2019

The adverse effects of invasive species are expected to be proportional to their relative densities. However, interference competition among conspecifics when invasive species are at high densities could limit such effects. These alternative hypotheses inspired us to test the density‐specific effects of red swamp crayfish Procambarus clarkii on experimental populations of the Amargosa Pupfish Cyprinodon nevadensis amargosae. The presence of crayfish had a significant influence on the survival of adult pupfish. In allopatry, adult pupfish survival was nearly 100%. However, the presence of crayfish resulted in significantly lower survival rates for adult pupfish, 84% and 69% survival for the low‐ and high‐density crayfish treatments, respectively. Crayfish also significantly affected the production of juvenile pupfish, with high juvenile production in the allopatric (705 juveniles/mesocosm) and low‐density crayfish treatments (705 juveniles/mesocosm). Juvenile production in both of these groups was significantly higher than that in the groups sympatric with high‐density crayfish (271 juveniles/mesocosm). The same pattern was observed when we evaluated the number of juvenile pupfish that were produced per adult female. We tested the hypothesis that interference competition among the crayfish would decrease predator efficacy by comparing the high‐density crayfish treatment with a fourth high‐density crayfish treatment wherein the crayfish were tethered. There was no significant difference in the rate of adult survivorship of the Amargosa Pupfish in the tethered and untethered high‐density treatment groups (70% and 69%, respectively). However, tethering resulted in a significant increase in juvenile production in the high‐density crayfish treatments (493 and 271 juveniles per mesocosm were produced in the tethered and untethered groups, respectively). The same patterns were observed when we examined the number of juvenile pupfish that was produced per adult female. These findings are inconsistent with the interference competition hypothesis, while supporting the hypothesis of density‐dependent effects of crayfish on Amargosa Pupfish populations. These findings suggest that reducing crayfish density will be a beneficial management tool for reducing the effects of crayfish on benthic fish populations.