bluuebunny/crossref_metadata_2025_split huggingface dataset:
Campylobacter concisus pathotypes induce distinct global responses in intestinal epithelial cells
Authors: Deshpande Nandan P. , Wilkins Marc R. , Castaño-Rodríguez Natalia , Bainbridge Emily , Sodhi Nidhi , Riordan Stephen M. , Mitchell Hazel M. , Kaakoush Nadeem O. 
Published: September 2016

AbstractThe epithelial response to the opportunistic pathogen Campylobacter concisus is poorly characterised. Here, we assessed the intestinal epithelial responses to two C. concisus strains with different virulence characteristics in Caco-2 cells using RNAseq, and validated a subset of the response using qPCR arrays. C. concisus strains induced distinct response patterns from intestinal epithelial cells, with the toxigenic strain inducing a significantly more amplified response. A range of cellular functions were significantly regulated in a strain-specific manner, including epithelial-to-mesenchymal transition (NOTCH and Hedgehog), cytoskeletal remodeling, tight junctions, inflammatory responses and autophagy. Pattern recognition receptors were regulated, including TLR3 and IFI16, suggesting that nucleic acid sensing was important for epithelial recognition of C. concisus. C. concisus zonula occludens toxin (ZOT) was expressed and purified, and the epithelial response to the toxin was analysed using RNAseq. ZOT upregulated PAR2 expression, as well as processes related to tight junctions and cytoskeletal remodeling. C. concisus ZOT also induced upregulation of TLR3, pro-inflammatory cytokines IL6, IL8 and chemokine CXCL16, as well as the executioner caspase CASP7. Here, we characterise distinct global epithelial responses to C. concisus strains, and the virulence factor ZOT, and provide novel information on mechanisms by which this bacterium may affect the host.
Unravelling molecular mechanisms from floral initiation to lipid biosynthesis in a promising biofuel tree species, Pongamia pinnata using transcriptome analysis
Authors: Sreeharsha Rachapudi V. , Mudalkar Shalini , Singha Kambam T. , Reddy Attipalli R. 
Published: September 2016

AbstractPongamia pinnata (L.) (Fabaceae) is a promising biofuel tree species which is underexploited in the areas of both fundamental and applied research, due to the lack of information either on transcriptome or genomic data. To investigate the possible metabolic pathways, we performed whole transcriptome analysis of Pongamia through Illumina NextSeq platform and generated 2.8 GB of paired end sequence reads. The de novo assembly of raw reads generated 40,000 contigs and 35,000 transcripts, representing leaf, flower and seed unigenes. Spatial and temporal expression profiles of photoperiod and floral homeotic genes in Pongamia, identified GIGANTEA (GI) - CONSTANS (CO) - FLOWERING LOCUS T (FT) as active signal cascade for floral initiation. Four prominent stages of seed development were selected in a high yielding Pongamia accession (TOIL 1) to follow the temporal expression patterns of key fatty acid biosynthetic genes involved in lipid biosynthesis and accumulation. Our results provide insights into an array of molecular events from flowering to seed maturity in Pongamia which will provide substantial basis for modulation of fatty acid composition and enhancing oil yields which should serve as a potential feedstock for biofuel production.
Cross-talk between Human Papillomavirus Oncoproteins and Hedgehog Signaling Synergistically Promotes Stemness in Cervical Cancer Cells
Authors: Vishnoi Kanchan , Mahata Sutapa , Tyagi Abhishek , Pandey Arvind , Verma Gaurav , Jadli Mohit , Singh Tejveer , Singh Sukh Mahendra , Bharti Alok C. 
Published: September 2016

AbstractViral oncoproteins E6/E7 play key oncogenic role in human papillomavirus (HPV)-mediated cervical carcinogenesis in conjunction with aberrant activation of cellular signaling events. GLI-signaling has been implicated in metastasis and tumor recurrence of cervical cancer. However, the interaction of GLI-signaling with HPV oncogenes is unknown. We examined this relationship in established HPV-positive and HPV-negative cervical cancer cell lines using specific GLI inhibitor, cyclopamine and HPVE6/E7 siRNAs. Cervical cancer cell lines showed variable expression of GLI-signaling components. HPV16-positive SiHa cells, overexpressed GLI1, Smo and Patch. Inhibition by cyclopamine resulted in dose-dependent reduction of Smo and GLI1 and loss of cell viability with a higher magnitude in HPV-positive cells. Cyclopamine selectively downregulated HPVE6 expression and resulted in p53 accumulation, whereas HPVE7 and pRb level remained unaffected. siRNA-mediated silencing of HPV16E6 demonstrated reduced GLI1 transcripts in SiHa cells. Cervical cancer stem-like cells isolated by side population analysis, displayed retention of E6 and GLI1 expression. Fraction of SP cells was reduced in cyclopamine-treated cultures. When combined with E6-silencing cyclopamine resulted in loss of SP cell’s sphere-forming ability. Co-inhibition of GLI1 and E6 in cervical cancer cells showed additive anti-cancer effects. Overall, our data show existence of a cooperative interaction between GLI signaling and HPVE6.
Neoadjuvant Chemoradiotherapy vesus Chemotherapy alone Followed by Surgery for Resectable Stage III Non-Small-Cell Lung Cancer: a Meta-Analysis
Authors: Guo Shan xian , Jian Yan , Chen Ying lan , Cai Yun , Zhang Qing yuan , Tou Fang fang 
Published: September 2016

AbstractNeoadjuvant Chemotherapy has been used for the stage III of non-small cell lung cancer (NSCLC) and has shown good clinical effects. However, the survival benefits of radiation therapy added in induction regimens remains controversial. We therefore conducted a meta-analysis of the published clinical trials to quantitatively evaluate the benefit of preoperative chemoradiotherapy. After searching the database of Pubmed, CNKI, EMBASE, ESMO, The Cochrane Library databases, The American Society of Clinical Oncology and Clinical Trials.gov. Trials were selected for meta-analysis if they provided an independent assessment of neoadjuvant chemoradiation and neoadjuvant chemotherapy, odds ratio(OR) for tumor downstaging, mediastinal lymph nodes pathological complete response and local control, hazard ratios (HRs) for 5-year survival and progression-free survival were pooled by the stata software version 12.0. Twelve studies involving 2,724 patients were identified, tumor downstaging (p = 0.01), mediastinal lymph nodes pathological complete responses (p = 0.028) and local control (P = 0.002) were achieved, when compared with neoadjuvant chemotherapy. The meta-analysis demonstrated neither 5-year survival nor progression-free-survival benefit in survival from adding radiation. In conclusion, the addition of radiotherapy into chemotherapy was not superior to neoadjuvant chemotherapy. The higher quality of trials need be investigated combining with the histopathological type and genotyping of lung cancer by clinicians.
Allosteric Inhibitory Molecular Recognition of a Photochromic Dye by a Digestive Enzyme: Dihydroindolizine makes α-chymotrypsin Photo-responsive
Authors: Bagchi Damayanti , Ghosh Abhijit , Singh Priya , Dutta Shreyasi , Polley Nabarun , Althagafi Ismail.I. , Jassas Rabab S. , Ahmed Saleh A. , Pal Samir Kumar 
Published: September 2016

AbstractThe structural-functional regulation of enzymes by the administration of an external stimulus such as light could create photo-switches that exhibit unique biotechnological applications. However, molecular recognition of small ligands is a central phenomenon involved in all biological processes. We demonstrate herein that the molecular recognition of a photochromic ligand, dihydroindolizine (DHI), by serine protease α-chymotrypsin (CHT) leads to the photo-control of enzymatic activity. We synthesized and optically characterized the photochromic DHI. Light-induced reversible pyrroline ring opening and a consequent thermal back reaction via 1,5-electrocyclization are responsible for the photochromic behavior. Furthermore, DHI inhibits the enzymatic activity of CHT in a photo-controlled manner. Simultaneous binding of the well-known inhibitors 4-nitrophenyl anthranilate (NPA) or proflavin (PF) in the presence of DHI displays spectral overlap between the emission of CHT-NPA or CHT-PF with the respective absorption of cis or trans DHI. The results suggest an opportunity to explore the binding site of DHI using Förster resonance energy transfer (FRET). Moreover, to more specifically evaluate the DHI binding interactions, we employed molecular docking calculations, which suggested binding near the hydrophobic site of Cys-1-Cys-122 residues. Variations in the electrostatic interactions of the two conformers of DHI adopt unfavorable conformations, leading to the allosteric inhibition of enzymatic activity.
Conditional abrogation of Atm in osteoclasts extends osteoclast lifespan and results in reduced bone mass
Authors: Hirozane Toru , Tohmonda Takahide , Yoda Masaki , Shimoda Masayuki , Kanai Yae , Matsumoto Morio , Morioka Hideo , Nakamura Masaya , Horiuchi Keisuke 
Published: September 2016

AbstractAtaxia-telangiectasia mutated (ATM) kinase is a central component involved in the signal transduction of the DNA damage response (DDR) and thus plays a critical role in the maintenance of genomic integrity. Although the primary functions of ATM are associated with the DDR, emerging data suggest that ATM has many additional roles that are not directly related to the DDR, including the regulation of oxidative stress signaling, insulin sensitivity, mitochondrial homeostasis and lymphocyte development. Patients and mice lacking ATM exhibit growth retardation and lower bone mass; however, the mechanisms underlying the skeletal defects are not fully understood. In the present study, we generated mutant mice in which ATM is specifically inactivated in osteoclasts. The mutant mice did not exhibit apparent developmental defects but showed reduced bone mass due to increased osteoclastic bone resorption. Osteoclasts lacking ATM were more resistant to apoptosis and showed a prolonged lifespan compared to the controls. Notably, the inactivation of ATM in osteoclasts resulted in enhanced NF-κB signaling and an increase in the expression of NF-κB-targeted genes. The present study reveals a novel function for ATM in regulating bone metabolism by suppressing the lifespan of osteoclasts and osteoclast-mediated bone resorption.
Fractal zone plate beam based optical tweezers
Authors: Cheng Shubo , Zhang Xinyu , Ma Wenzhuo , Tao Shaohua 
Published: September 2016

AbstractWe demonstrate optical manipulation with an optical beam generated by a fractral zone plate (FZP). The experimental results show that the FZP beam can simultaneously trap multiple particles positioned in different focal planes of the FZP beam, owing to the multiple foci and self-reconstruction property of the FZP beam. The FZP beam can also be used to construct three-dimensional optical tweezers for potential applications.
Survey on the Effectiveness of Dietary Supplements to Treat Tinnitus
Authors: Coelho Claudia , Tyler Richard , Ji Haihong , Rojas-Roncancio Eveling , Witt Shelley , Tao Pan , Jun Hyung-Jin , Wang Tang Chuan , Hansen Marlan R. , Gantz Bruce J. 
Published: September 2016

Purpose
We surveyed the benefit of dietary supplements to treat tinnitus and reported adverse effects.

Method
A website was created for people with tinnitus to complete a variety of questions.

Results

The 1,788 subjects who responded to questionnaires came from 53 different countries; 413 (23.1%) reported taking supplements. No effect on tinnitus was reported in 70.7%, improvement in 19.0%, and worsening in 10.3%. Adverse effects were reported in 6% (
n
= 36), including bleeding, diarrhea, headache, and others. Supplements were reported to be helpful for sleep: melatonin (effect size,
d
= 1.228) and lipoflavonoid (
d
= 0.5244); emotional reactions: melatonin (
d
= 0.6138) and lipoflavonoid (
d
= 0.457); hearing:
Ginkgo biloba
(
d
= 0.3758); and concentration
Ginkgo biloba
(
d
= 0.3611). The positive, subjective reports should be interpreted cautiously; many might have reported a positive effect because they were committed to treatment and expected a benefit. Users of supplements were more likely to have loudness hyperacusis and to have a louder tinnitus.

Conclusions

The use of dietary supplements to treat tinnitus is common, particularly with
Ginkgo biloba
, lipoflavonoids, magnesium, melatonin, vitamin B12, and zinc. It is likely that some supplements will help with sleep for some patients. However, they are generally not effective, and many produced adverse effects. We concluded that dietary supplements should not be recommended to treat tinnitus but could have a positive outcome on tinnitus reactions in some people.
Referral Patterns as a Contextual Variable in Pediatric Brain Injury: A Retrospective Analysis
Authors: Ciccia Angela Hein , Lundine Jennifer P. , Coreno Alyssa 
Published: September 2016

Purpose
Access to speech-language pathology (SLP) services is a critical variable in the rehabilitation of pediatric brain injury. In this study, we examined patterns of SLP referral and factors affecting referral during the acute period following brain injury in 2 large pediatric specialty hospitals.

Method

In a retrospective, cohort chart review study, data collection focused on referrals made during the acute period using
International Classification of Diseases, Ninth Revision, Clinical Modification
codes for primary diagnoses of brain injury between 2007 and 2014 (Centers for Disease Control and Prevention [CDC], 2014). A total of 200 charts were reviewed. Data extraction included demographic and injury-related variables, referral for rehabilitation across disciplines, and plans of care following assessment.

Results
Samples for both facilities were similar except for primary mechanism of traumatic brain injuries and severity. SLP referral rate at Hospital 1 was 36% and only 2% at Hospital 2. Regression revealed that individuals were less likely to receive an SLP referral if injury severity was classified as unknown or mild or if they were younger in age.

Conclusion
SLP referral rates in the early acute period for children with brain injury were poor, creating a barrier to rehabilitation. This not only limits access to SLP services, but also may have broader and long-term impact.
Underestimation of measured self‐heating in nanowires by using gate resistance technique
Authors: Mariniello G. , Cassé M. , Reimbold G. , Pavanello M.A. 
Published: September 2016

The channel temperature rise is demonstrated due to self‐heating in narrow tri‐gate fully depleted silicon‐on‐insulator devices becomes inaccurate when extracted using the gate resistance thermometry. Thermal resistance and channel temperature have been extracted by both gate resistance measurements and 3D TCAD electrothermal simulations for tri‐gate wide and nanowire MOSFETs down to 12.5 nm fin width. A critical fin width around 500 nm the extracted channel temperature accessed by the gate resistance thermometry differs significantly from the actual channel temperature due to heat dissipation through the gate contacts is shown below, leading to significantly underestimated values.
Wideband low‐profile planar square segmented loop antenna for UAV applications
Authors: Kang D. , Tak J. , Choi J. 
Published: September 2016

A wideband low‐profile planar square segmented loop antenna for unmanned aerial vehicle (UAV) applications is proposed. The antenna consists of a square segmented loop, a patch element, and a shorting strip. The antenna operates at 956 MHz because the eight segments of the loop are electrically connected by capacitive coupling. By adding the patch element and shorting strip, the antenna has a wideband covering GPS L1, GSM1800, GSM1900, UMTS, LTE2300, LTE2500, and 2400 MHz ISM bands due to improved impedance matching. The antenna has omnidirectional radiation at 956 MHz and quasi‐omnidirectional radiation over the broad bandwidth.
Isabella d’Este
Authors: Shemek Deanna 
Published: September 2016

Isabella d’Este (b. 1474–d. 1539) was the eldest child of Ercole I d’Este (b. 1431–d. 1505), second duke of Ferrara, and Duchess Eleonora d’Aragona (b. 1450–d. 1493). Raised in luxury and privilege, she was educated by humanists in a city that boasted an exceptionally refined court culture and one of Europe’s greatest universities. In 1490 she married Francesco II Gonzaga (b. 1466–d. 1519), Marchese of Mantua, and entered that city in triumph as its new princess. As Marchesa, she displayed extraordinary skills in management, diplomacy, and Politics, often counseling her husband and at times assuming the reins of government. All of Isabella and Francesco’s six children attained important positions among the European elite (See Family Relations). She is mainly remembered for her achievements not as a ruler, however, but as a collector of art and antiquities and the first woman in Europe to fashion a personalized gallery space in which to display her acquisitions. She called these rooms her studiolo and grotta, or her camerini. Her apartments also housed an impressive book collection, the musical instruments she was adept at playing, and other luxury items she collected (See Patronage, Collecting, Studiolo and Exhibition Catalogues). Her portraitists include Andrea Mantegna, Francesco Francia, Leonardo da Vinci, Titian, and Rubens. A woman of tremendous energies and intelligence, Isabella cultivated relationships with many writers and composers of her time. She also devoted notable attention to fashion, travel, gardening, food production and exchange, and the keeping of animals. Given her wide range of interests, her keen intelligence, and her extraordinarily active public profile, Isabella d’Este has often been regarded as a female version of the period’s “Renaissance men.” Her multifaceted life is recorded most visibly in the archive of her correspondence, now housed in the Archivio di Stato di Mantova (ASMn), where many thousands of her letters survive along with a wealth of official documents related to her court. Isabella d’Este’s art collections now reside in museums around the world, chief among these the Paris Louvre and the Vienna Kunsthistorisches Museum.
Flipping the Quality Improvement Classroom in Residency Education
Authors: Bonnes Sara L. , Ratelle John T. , Halvorsen Andrew J. , Carter Kimberly J. , Hafdahl Luke T. , Wang Amy T. , Mandrekar Jayawant N. , Oxentenko Amy S. , Beckman Thomas J. , Wittich Christopher M. 
Published: September 2016

Purpose
The flipped classroom (FC), in which instructional content is delivered before class with class time devoted to knowledge application, has the potential to engage residents. A Mayo Clinic Internal Medicine Residency Program study was conducted to validate an FC perception instrument (FCPI); determine whether participation improved FC perceptions; and determine associations between resident characteristics, change in quality improvement (QI) knowledge, and FC perception scores.

Method
All 143 internal medicine residents at Mayo Clinic, Rochester participated from 2014 to 2015; some experienced a flipped QI curriculum and others completed the traditional nonflipped course. The FCPI was developed, and factor analysis revealed an intuitive two-factor structure: preclass activity and in-class application. Residents were surveyed before and after the monthlong curriculum to measure changes in perception, and the QI Knowledge Assessment Tool was employed to measure knowledge improvement.

Results
Postcourse FCPI scores significantly increased for three of the eight items. QI knowledge increased significantly among residents who experienced the FC compared with residents who completed the non-FC curriculum. Those without prior FC exposure demonstrated a significant increase in QI knowledge compared with those with previous FC experience. The FCPI had compelling validity evidence with improved scores after curriculum exposure and associations with greater engagement in online modules.

Conclusions
Residents who participated in the FC demonstrated improved QI knowledge compared with the control group. Residents valued the in-class application sessions more than the online component. These findings have important implications for graduate medical education as residency training programs increasingly use FC models.
A Clinical Prediction Algorithm to Stratify Pediatric Musculoskeletal Infection by Severity
Authors: Benvenuti Michael A. , An Thomas J. , Mignemi Megan E. , Martus Jeffrey E. , Mencio Gregory A. , Lovejoy Stephen A. , Schoenecker Jonathan G. , Williams Derek J. 
Published: September 2016

Objective:
There are currently no algorithms for early stratification of pediatric musculoskeletal infection (MSKI) severity that are applicable to all types of tissue involvement. In this study, the authors sought to develop a clinical prediction algorithm that accurately stratifies infection severity based on clinical and laboratory data at presentation to the emergency department.

Methods:
An IRB-approved retrospective review was conducted to identify patients aged 0 to 18 who presented to the pediatric emergency department at a tertiary care children’s hospital with concern for acute MSKI over a 5-year period (2008 to 2013). Qualifying records were reviewed to obtain clinical and laboratory data and to classify in-hospital outcomes using a 3-tiered severity stratification system. Ordinal regression was used to estimate risk for each outcome. Candidate predictors included age, temperature, respiratory rate, heart rate, C-reactive protein (CRP), and peripheral white blood cell count. We fit fully specified (all predictors) and reduced models (retaining predictors with a P-value ≤0.2). Discriminatory power of the models was assessed using the concordance (c)-index.

Results:
Of the 273 identified children, 191 (70%) met inclusion criteria. Median age was 5.8 years. Outcomes included 47 (25%) children with inflammation only, 41 (21%) with local infection, and 103 (54%) with disseminated infection. Both the full and reduced models accurately demonstrated excellent performance (full model c-index 0.83; 95% confidence interval, 0.79-0.88; reduced model 0.83; 95% confidence interval, 0.78-0.87). Model fit was also similar, indicating preference for the reduced model. Variables in this model included CRP, pulse, temperature, and an interaction term for pulse and temperature. The odds of a more severe outcome increased by 30% for every 10 U increase in CRP.

Conclusions:
Clinical and laboratory data obtained in the emergency department may be used to accurately differentiate pediatric MSKI severity. The predictive algorithm in this study stratifies pediatric MSKI severity at presentation irrespective of tissue involvement and anatomic diagnosis. Prospective studies are needed to validate model performance and clinical utility.

Level of Evidence:
Level II—prognostic study.