bluuebunny/crossref_metadata_2025_split huggingface dataset:
Staphylococcus aureus-dependent septic arthritis in murine knee joints: local immune response and beneficial effects of vaccination
Authors: Corrado Alessia , Donato Paolo , Maccari Silvia , Cecchi Raffaella , Spadafina Tiziana , Arcidiacono Letizia , Tavarini Simona , Sammicheli Chiara , Laera Donatello , Manetti Andrea Guido Oreste , Ruggiero Paolo , Galletti Bruno , Nuti Sandra , De Gregorio Ennio , Bertholet Sylvie , Seubert Anja , Bagnoli Fabio , Bensi Giuliano , Chiarot Emiliano 
Published: November 2016

AbstractStaphylococcus aureus is the major cause of human septic arthritis and osteomyelitis, which deserve special attention due to their rapid evolution and resistance to treatment. The progression of the disease depends on both bacterial presence in situ and uncontrolled disruptive immune response, which is responsible for chronic disease. Articular and bone infections are often the result of blood bacteremia, with the knees and hips being the most frequently infected joints showing the worst clinical outcome. We report the development of a hematogenous model of septic arthritis in murine knees, which progresses from an acute to a chronic phase, similarly to what occurs in humans. Characterization of the local and systemic inflammatory and immune responses following bacterial infection brought to light specific signatures of disease. Immunization of mice with the vaccine formulation we have recently described (4C-Staph), induced a strong antibody response and specific CD4+ effector memory T cells, and resulted in reduced bacterial load in the knee joints, a milder general inflammatory state and protection against bacterial-mediated cellular toxicity. Possible correlates of protection are finally proposed, which might contribute to the development of an effective vaccine for human use.
Genome-wide Diversity and Association Mapping for Capsaicinoids and Fruit Weight in Capsicum annuum L
Authors: Nimmakayala Padma , Abburi Venkata L. , Saminathan Thangasamy , Alaparthi Suresh B. , Almeida Aldo , Davenport Brittany , Nadimi Marjan , Davidson Joshua , Tonapi Krittika , Yadav Lav , Malkaram Sridhar , Vajja Gopinath , Hankins Gerald , Harris Robert , Park Minkyu , Choi Doil , Stommel John , Reddy Umesh K. 
Published: November 2016

AbstractAccumulated capsaicinoid content and increased fruit size are traits resulting fromCapsicum annuumdomestication. In this study, we used a diverse collection ofC. annuumto generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome. PCA and IBS were used in a mixed linear model of capsaicin and dihydrocapsaicin content and fruit weight to reduce spurious associations because of confounding effects of subpopulations in genome-wide association study (GWAS). Our GWAS results showed SNPs in Ankyrin-like protein, IKI3 family protein, ABC transporter G family and pentatricopeptide repeat protein are the major markers for capsaicinoids and of 16 SNPs strongly associated with FW in both years of the study, 7 are located in known fruit weight controlling genes.
Development of mouthparts in the cicada Meimuna mongolica (Distant): successive morphological patterning and sensilla differentiation from nymph to adult
Authors: Hao Yanan , Dietrich Christopher H. , Dai Wu 
Published: November 2016

AbstractDevelopment of the mouthparts in the cicadaMeimuna mongolica(Distant) is investigated here for the first time using scanning electron microscopy in order to document changes occurring in different nymphal instars and from nymph to adult, during which a shift from subterranean root-feeding to feeding on aboveground parts of the host plant occurs. The structure and component of mouthparts is similar to those found in other hemipteran insects. Fourteen types of sensilla and five types of cuticular processes were found on the mouthparts of nymphs and adults. Significant general transformations during development include changes in: (a) the size and shape of the labrum from square to long and shovel-shaped; (b) increases in type and quantity of sensilla with the stage of development; (c) the ridges at the tips of the mandiblar stylets become more prominent in later stages of nymphal development, while odontoid protrusions more prominent in the female than in the male of the adult; and (d) the cross section of the stylets is subcircular in nymphal stages but oblong elliptical in the adult. The implications of these mouthpart transformations on the feeding ability of nymphs and adults and their possible relationship to the feeding niche are discussed.
Input graph: the hidden geometry in controlling complex networks
Authors: Zhang Xizhe , Lv Tianyang , Pu Yuanyuan 
Published: November 2016

AbstractThe ability to control a complex network towards a desired behavior relies on our understanding of the complex nature of these social and technological networks. The existence of numerous control schemes in a network promotes us to wonder: what is the underlying relationship of all possible input nodes? Here we introduce input graph, a simple geometry that reveals the complex relationship between all control schemes and input nodes. We prove that the node adjacent to an input node in the input graph will appear in another control scheme, and the connected nodes in input graph have the same type in control, which they are either all possible input nodes or not. Furthermore, we find that the giant components emerge in the input graphs of many real networks, which provides a clear topological explanation of bifurcation phenomenon emerging in dense networks and promotes us to design an efficient method to alter the node type in control. The findings provide an insight into control principles of complex networks and offer a general mechanism to design a suitable control scheme for different purposes.
Gap Shape Classification using Landscape Indices and Multivariate Statistics
Authors: Wu Chih-Da , Cheng Chi-Chuan , Chang Che-Chang , Lin Chinsu , Chang Kun-Cheng , Chuang Yung-Chung 
Published: November 2016

AbstractThis study proposed a novel methodology to classify the shape of gaps using landscape indices and multivariate statistics. Patch-level indices were used to collect the qualified shape and spatial configuration characteristics for canopy gaps in the Lienhuachih Experimental Forest in Taiwan in 1998 and 2002. Non-hierarchical cluster analysis was used to assess the optimal number of gap clusters and canonical discriminant analysis was used to generate the discriminant functions for canopy gap classification. The gaps for the two periods were optimally classified into three categories. In general, gap type 1 had a more complex shape, gap type 2 was more elongated and gap type 3 had the largest gaps that were more regular in shape. The results were evaluated using Wilks’ lambda as satisfactory (p < 0.001). The agreement rate of confusion matrices exceeded 96%. Differences in gap characteristics between the classified gap types that were determined using a one-way ANOVA showed a statistical significance in all patch indices (p = 0.00), except for the Euclidean nearest neighbor distance (ENN) in 2002. Taken together, these results demonstrated the feasibility and applicability of the proposed methodology to classify the shape of a gap.
Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation
Authors: Zhu Yueming , Chen Peng , Bao Yunjuan , Men Yan , Zeng Yan , Yang Jiangang , Sun Jibin , Sun Yuanxia 
Published: November 2016

AbstractA novel marine strain representing efficient degradation ability toward brown algae was isolated, identified, and assigned to Bacillus weihaiensis Alg07. The alga-associated marine bacteria promote the nutrient cycle and perform important functions in the marine ecosystem. The de novo sequencing of the B. weihaiensis Alg07 genome was carried out. Results of gene annotation and carbohydrate-active enzyme analysis showed that the strain harbored enzymes that can completely degrade alginate and laminarin, which are the specific polysaccharides of brown algae. We also found genes for the utilization of mannitol, the major storage monosaccharide in the cell of brown algae. To understand the process of brown algae decomposition by B. weihaiensis Alg07, RNA-seq transcriptome analysis and qRT-PCR were performed. The genes involved in alginate metabolism were all up-regulated in the initial stage of kelp degradation, suggesting that the strain Alg07 first degrades alginate to destruct the cell wall so that the laminarin and mannitol are released and subsequently decomposed. The key genes involved in alginate and laminarin degradation were expressed in Escherichia coli and characterized. Overall, the model of brown algae degradation by the marine strain Alg07 was established, and novel alginate lyases and laminarinase were discovered.
In vitro skin models and tissue engineering protocols for skin graft applications
Authors: Naves Lucas B. , Dhand Chetna , Almeida Luis , Rajamani Lakshminarayanan , Ramakrishna Seeram 
Published: November 2016

In this review, we present a brief introduction of the skin structure, a concise compilation of skin-related disorders, and a thorough discussion of different in vitro skin models, artificial skin substitutes, skin grafts, and dermal tissue engineering protocols. The advantages of the development of in vitro skin disorder models, such as UV radiation and the prototype model, melanoma model, wound healing model, psoriasis model, and full-thickness model are also discussed. Different types of skin grafts including allografts, autografts, allogeneic, and xenogeneic are described in detail with their associated applications. We also discuss different tissue engineering protocols for the design of various types of skin substitutes and their commercial outcomes. Brief highlights are given of the new generation three-dimensional printed scaffolds for tissue regeneration applications.
Predicting Tissue Breaking Strengths in the Epileptic Brain with T2 Relaxometry: Application of Pulsed Water Jet Dissection System for Epilepsy Surgery
Authors: Takahashi Yoko , Nakagawa Atsuhiro , Sato Shiho , Nakasato Nobukazu , Tominaga Teiji , Iwasaki Masaki 
Published: November 2016

Background The piezo actuator-driven pulsed water jet (ADPJ) system is a novel surgical instrument that enables dissection of tissue without thermal damage. Using the ADPJ system in epilepsy surgery requires prediction of the tissue breaking strength of the epileptic brain. The aim of this study was to elucidate whether magnetic resonance imaging T2 relaxometry could predict the breaking strength.
Methods A total of 12 patients with drug-resistant temporal lobe epilepsy who received surgical treatment were included in the study. All the patients qualified for surgery after a comprehensive preoperative evaluation for the treatment of epilepsy. T2 relaxation time, breaking strength of the hippocampus, and an anterior temporal lobe specimen obtained from surgery with dissection depth determined by the ADPJ system were examined.
Results Preoperative T2 relaxation times of the anterior temporal lobe and hippocampus showed mild positive correlation with breaking strength (R2 = 0.60). The hippocampus showed higher T2 relaxation time than the temporal lobe. Hippocampal sclerosis seemed to have higher breaking strength than other pathologies, suggesting the correlation depends on the anatomical location and histopathology. The dissection depth of the extirpated lesion was negatively correlated with the breaking strength at input voltages of 10 V (R2 = − 0.34) and 20 V (R2 = − 0.20).
Conclusions T2 relaxometry may be useful to predict tissue breaking strength in the epileptic brain that allows safe application of the ADPJ system in epilepsy surgery.
Spatiotemporal imaging of small GTPases activity in live cells
Authors: Voss Stephanie , Krüger Dennis M. , Koch Oliver , Wu Yao-Wen 
Published: November 2016

Significance
Ras-like small GTPases regulate a wide range of cellular processes involving signal transduction, cytoskeleton rearrangement, and membrane trafficking by switching between an active GTP-bound and an inactive GDP-bound form. In this study, we developed conformational sensors for GTPase activity (COSGAs) by combining protein engineering and chemical labeling. The COSGAs enable quantitative detection of the GDP/GTP binding state of Rab1 and K-Ras in living cells with spatiotemporal resolution to gain insights into Rab membrane cycling and Ras signaling at the plasma membrane. This approach paves a new avenue for imaging activity of signaling molecules in the cell, which could deliver valuable information regarding their function and dynamics.
Elucidating the druggable interface of protein−protein interactions using fragment docking and coevolutionary analysis
Authors: Bai Fang , Morcos Faruck , Cheng Ryan R. , Jiang Hualiang , Onuchic José N. 
Published: November 2016

Significance
Protein−protein interfaces have become an emerging class of molecular targets for the design of therapeutic drugs. However, major challenges exist for the correct identification of binding sites on the protein surface as well as drug-like modulators of protein−protein interaction. An integrated approach using molecular fragment docking and coevolutionary analysis is presented to face these challenges. This approach can accurately predict and characterize the binding sites for protein−protein interactions as well as provide clusters of bound, fragment-sized molecules on the druggable regions of the predicted binding site. These bound, molecular fragments can be chemically combined to create candidate drugs.
Using the CRISPR/Cas9 system to eliminate native plasmids of Zymomonas mobilis ZM4
Authors: Cao Qing-Hua , Shao Huan-Huan , Qiu Hui , Li Tao , Zhang Yi-Zheng , Tan Xue-Mei 
Published: November 2016

Abstract
The CRISPR/Cas system can be used to simply and efficiently edit the genomes of various species, including animals, plants, and microbes. Zymomonas mobilis ZM4 is a highly efficient, ethanol-producing bacterium that contains five native plasmids. Here, we constructed the pSUZM2a-Cas9 plasmid and a single-guide RNA expression plasmid. The pSUZM2a-Cas9 plasmid was used to express the Cas9 gene cloned from Streptococcus pyogenes CICC 10464. The single-guide RNA expression plasmid pUC-T7sgRNA, with a T7 promoter, can be used for the in vitro synthesis of single-guide RNAs. This system was successfully employed to knockout the upp gene of Escherichia coli and the replicase genes of native Z. mobilis plasmids. This is the first study to apply the CRISPR/Cas9 system of S. pyogenes to eliminate native plasmids in Z. mobilis. It provides a new method for plasmid curing and paves the way for the genomic engineering of Z. mobilis.
Clinical Impact and Cost-effectiveness of Xpert MTB/RIF Testing in Hospitalized Patients With Presumptive Pulmonary Tuberculosis in the United States
Authors: Cowan James F. , Chandler Aldine S. , Kracen Elizabeth , Park David R. , Wallis Carolyn K. , Liu Emelline , Song Chao , Persing David H. , Fang Ferric C. 
Published: November 2016

Abstract

Background.
Microscopic examination of acid-fast-stained sputum smears is the current standard of care in the United States to determine airborne infection isolation (AII) of inpatients with presumptive pulmonary tuberculosis (PTB). However, nucleic acid amplification testing (NAAT) with the Xpert MTB/RIF assay (Xpert) may be more efficient and less costly.

Methods.
This prospective observational cohort study enrolled a consecutive sample of 318 AII-eligible inpatients from a public hospital in Seattle, Washington, from March 2012 to October 2013. Sputum samples were collected from each inpatient and analyzed using smear microscopy, culture, drug susceptibility testing, and NAAT. The performance, clinical utility (AII duration and survival), and cost-effectiveness from an institutional perspective were compared for 5 testing strategies.

Results.
Among the 318 admissions with presumptive PTB, 20 (6.3%) were culture-positive for Mycobacterium tuberculosis. The sensitivity of 1 Xpert, 2 Xperts, 2 smears, or 3 smears compared to culture was 0.85 (95% confidence interval [CI], .61–.96), 0.95 (95% CI, .73–1.0), 0.70 (95% CI, .46–.88), and 0.80 (95% CI, .56–.93), respectively. A cost-effectiveness analysis of the study results demonstrated that an Xpert test on 1 unconcentrated sputum sample (assuming equivalent results for unconcentrated and concentrated sputum samples) is the most cost-effective strategy (99.9% preferred at willingness-to-pay of US$50000) and on average would save 51.5 patient-hours in AII and up to $11466 relative to microscopy without a compromise in sensitivity.

Conclusions.
In hospitalized patients with presumptive PTB in a low-burden setting, NAAT can reduce AII and is comparably sensitive, more specific, and more cost-effective than smear microscopy.
Treatment options in immune thrombocytopenia
Authors: Dubis Laura , Collins Miranda 
Published: November 2016

ABSTRACT
Immune thrombocytopenia (ITP) is an autoimmune condition that can cause life-threatening bleeding. ITP may develop idiopathically, after an infection or administration of a medication, or as a comorbid condition. Treatment depends on whether life-threatening, active bleeding is occurring. Although corticosteroids remain a standard of care, new medications offer patients an alternative to splenectomy when other pharmacologic treatments fail.
A young woman with numbness in her feet
Authors: Pavlik Daniel , Huber Michael , Justice Melissa 
Published: November 2016

ABSTRACT
This article describes a young, otherwise healthy woman who presented to the ED with numbness in her feet and was discharged. Twenty-four hours later, she returned because of difficulty walking; in 48 hours she could not walk without assistance. Although Guillain-Barré syndrome was suspected initially, the patient's weakness, sensory loss, and autonomic dysfunction eventually were diagnosed as transverse myelitis, a myelopathy often associated with infectious or autoimmune diseases. The article describes the presentation, diagnostic evaluation and criteria, treatment, and prognosis of transverse myelitis.
Enhancing Student Empathetic Engagement, History-Taking, and Communication Skills During Electronic Medical Record Use in Patient Care
Authors: LoSasso Alisa Alfonsi , Lamberton Courtney E. , Sammon Mary , Berg Katherine T. , Caruso John W. , Cass Jonathan , Hojat Mohammadreza 
Published: November 2016

Purpose
To examine whether an intervention on proper use of electronic medical records (EMRs) in patient care could help improve medical students’ empathic engagement, and to test the hypothesis that the training would reduce communication hurdles in clinical encounters.

Method
Seventy third-year medical students from the Sidney Kimmel Medical College at Thomas Jefferson University were randomly divided into intervention and control groups during their six-week pediatric clerkship in 2012–2013. The intervention group received a one-hour training session on EMR-specific communication skills, including discussion of EMR use, the SALTED mnemonic and technique (Set-up, Ask, Listen, Type, Exceptions, Documentation), and role-plays. Both groups completed the Jefferson Scale of Empathy (JSE) at the clerkship’s start and end. At clerkship’s end, faculty and standardized patients (SPs) rated students’ empathic engagement in SP encounters, using the Jefferson Scale of Patient Perceptions of Physician Empathy (JSPPPE), and their history-taking and communication skills.

Results
Faculty mean ratings on the JSPPPE, history-taking skills, and communication skills were significantly higher for the intervention group than the control group. SP mean ratings on history-taking skills were significantly higher for the intervention group than the control group. Both groups’ JSE mean scores increased pretest to posttest, but the changes were not significant. The intervention group’s posttest JSE mean score was higher than the control group’s, but the difference was not significant.

Conclusions
The findings suggest that a simple intervention providing specialized training in EMR-specific communication can improve medical students’ empathic engagement in patient care, history-taking skills, and communication skills.
The Drivers of Discretionary Utilization: Clinical History Versus Physician Supply
Authors: Ruhnke Gregory W. , Manning Willard G. , Rubin David T. , Meltzer David O. 
Published: November 2016

Purpose
Because the effect of physician supply on utilization remains controversial, literature based on non-Medicare populations is sparse, and a physician supply expansion is under way, the potential for physician-induced demand across diverse populations is important to understand. A substantial proportion of gastrointestinal endoscopies may be inappropriate. The authors analyzed the impact of physician supply, practice patterns, and clinical history on esophagogastroduodenoscopy (EGD, defined as discretionary) among patients hospitalized with lower gastrointestinal bleeding (LGIB).

Method
Among 34,344 patients hospitalized for LGIB from 2004 to 2009, 43.1% and 21.3% had a colonoscopy or EGD, respectively, during the index hospitalization or within 6 months after. Linking to the Dartmouth Atlas via patients’ hospital referral region, gastroenterologist density and hospital care intensity (HCI) index were ascertained. Adjusting for age, gender, comorbidities, and race/education indicators, the association of gastroenterologist density, HCI index, and history of upper gastrointestinal disease with EGD was estimated using logistic regression.

Results
EGD was not associated with gastroenterologist density or HCI index, but was associated with a history of upper gastrointestinal disease (OR 2.30; 95% CI 2.17–2.43), peptic ulcer disease (OR 4.82; 95% CI 4.26–5.45), and liver disease (OR 1.34; 95% CI 1.18–1.54).

Conclusions
Among patients hospitalized with LGIB, large variation in gastroenterologist density did not predict EGD, but relevant clinical history did, with association strengths commensurate with risk for upper gastrointestinal bleeding. In the scenario studied, no evidence was found that specialty physician supply increases will result in more discretionary care within commercially insured populations.