bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chaotic time series prediction for prenatal exposure to polychlorinated biphenyls in umbilical cord blood using the least squares SEATR model
Authors: Xu Xijin , Tang Qian , Xia Haiyue , Zhang Yuling , Li Weiqiu , Huo Xia 
Published: April 2016

AbstractChaotic time series prediction based on nonlinear systems showed a superior performance in prediction field. We studied prenatal exposure to polychlorinated biphenyls (PCBs) by chaotic time series prediction using the least squares self-exciting threshold autoregressive (SEATR) model in umbilical cord blood in an electronic waste (e-waste) contaminated area. The specific prediction steps basing on the proposal methods for prenatal PCB exposure were put forward and the proposed scheme’s validity was further verified by numerical simulation experiments. Experiment results show: 1) seven kinds of PCB congeners negatively correlate with five different indices for birth status: newborn weight, height, gestational age, Apgar score and anogenital distance; 2) prenatal PCB exposed group at greater risks compared to the reference group; 3) PCBs increasingly accumulated with time in newborns; and 4) the possibility of newborns suffering from related diseases in the future was greater. The desirable numerical simulation experiments results demonstrated the feasibility of applying mathematical model in the environmental toxicology field.
A novel serine protease, Sep1, from Bacillus firmus DS-1 has nematicidal activity and degrades multiple intestinal-associated nematode proteins
Authors: Geng Ce , Nie Xiangtao , Tang Zhichao , Zhang Yuyang , Lin Jian , Sun Ming , Peng Donghai 
Published: April 2016

AbstractPlant-parasitic nematodes (PPNs) cause serious harm to agricultural production. Bacillus firmus shows excellent control of PPNs and has been produced as a commercial nematicide. However, its nematicidal factors and mechanisms are still unknown. In this study, we showed that B. firmus strain DS-1 has high toxicity against Meloidogyne incognita and soybean cyst nematode. We sequenced the whole genome of DS-1 and identified multiple potential virulence factors. We then focused on a peptidase S8 superfamily protein called Sep1 and demonstrated that it had toxicity against the nematodes Caenorhabditis elegans and M. incognita. The Sep1 protein exhibited serine protease activity and degraded the intestinal tissues of nematodes. Thus, the Sep1 protease of B. firmus is a novel biocontrol factor with activity against a root-knot nematode. We then used C. elegans as a model to elucidate the nematicidal mechanism of Sep1 and the results showed that Sep1 could degrade multiple intestinal and cuticle-associated proteins and destroyed host physical barriers. The knowledge gained in our study will lead to a better understanding of the mechanisms of B. firmus against PPNs and will aid in the development of novel bio-agents with increased efficacy for controlling PPNs.
Transcriptome signature for dampened Th2 dominance in acellular pertussis vaccine-induced CD4+ T cell responses through TLR4 ligation
Authors: Brummelman Jolanda , Raeven René H. M. , Helm Kina , Pennings Jeroen L. A. , Metz Bernard , van Eden Willem , van Els Cécile A. C. M. , Han Wanda G. H. 
Published: April 2016

AbstractCurrent acellular pertussis (aP) vaccines promote a T helper 2 (Th2)-dominated response, while Th1/Th17 cells are protective. As our previous study showed, after adding a non-toxic TLR4 ligand, LpxL1, to the aP vaccine in mice, the Bordetella pertussis-specific Th2 response is decreased and Th1/Th17 responses are increased as measured at the cytokine protein level. However, how this shift in Th response by LpxL1 addition is regulated at the gene expression level remains unclear. Transcriptomics analysis was performed on purified CD4+ T cells of control and vaccinated mice after in vitro restimulation with aP vaccine antigens. Multiple key factors in Th differentiation, including transcription factors, cytokines and receptors, were identified within the differentially expressed genes. Upregulation of Th2- and downregulation of follicular helper T cell-associated genes were found in the CD4+ T cells of both aP- and aP+LpxL1-vaccinated mice. Genes exclusively upregulated in CD4+ T cells of aP+LpxL1-vaccinated mice included Th1 and Th17 signature cytokine genes Ifng and Il17a respectively. Overall, our study indicates that after addition of LpxL1 to the aP vaccine the Th2 component is not downregulated at the gene expression level. Rather an increase in expression of Th1- and Th17-associated genes caused the shift in Th subset outcome.
A hybrid system with highly enhanced graphene SERS for rapid and tag-free tumor cells detection
Authors: Yi Ningbo , Zhang Chen , Song Qinghai , Xiao Shumin 
Published: April 2016

AbstractBy dint of unique physical/chemical properties and bio-compatibility, graphene can work as a building block for a SERS substrate and open up a unique platform for tumor cells detection with high sensitivity. Herein we demonstrate a facile system with highly enhanced surface enhanced Raman spectroscopy of graphene (G-SERS). The system consists of a reduced graphene oxide (rGO) sandwiched by silver and gold nanostructures. Due to the ultrasmall thickness of rGO, the inter-coupling between Ag and Au nanoparticles is precisely controlled and the local field enhancement has been improved to more than 70 times. Associated with the unique chemical mechanism of rGO, the hybrid system has been utilized to identify tumor cells without using any biomarkers. We believe this research will be important for the applications of rGO in cancer screening.
Rem2, a member of the RGK family of small GTPases, is enriched in nuclei of the basal ganglia
Authors: Liput Daniel J. , Lu Van B. , Davis Margaret I. , Puhl Henry L. , Ikeda Stephen R. 
Published: April 2016

AbstractRem2 is a member of the RGK subfamily of RAS small GTPases. Rem2 inhibits high voltage activated calcium channels, is involved in synaptogenesis and regulates dendritic morphology. Rem2 is the primary RGK protein expressed in the nervous system, but to date, the precise expression patterns of this protein are unknown. In this study, we characterized Rem2 expression in the mouse nervous system. In the CNS, Rem2 mRNA was detected in all regions examined, but was enriched in the striatum. An antibody specific for Rem2 was validated using a Rem2 knockout mouse model and used to show abundant expression in striatonigral and striatopallidal medium spiny neurons but not in several interneuron populations. In the PNS, Rem2 was abundant in a subpopulation of neurons in the trigeminal and dorsal root ganglia, but was absent in sympathetic neurons of superior cervical ganglia. Under basal conditions, Rem2 was subject to post-translational phosphorylation, likely at multiple residues. Further, Rem2 mRNA and protein expression peaked at postnatal week two, which corresponds to the period of robust neuronal maturation in rodents. This study will be useful for elucidating the functions of Rem2 in basal ganglia physiology.
A life course approach to explore the biological embedding of socioeconomic position and social mobility through circulating inflammatory markers
Authors: Castagné Raphaële , Delpierre Cyrille , Kelly-Irving Michelle , Campanella Gianluca , Guida Florence , Krogh Vittorio , Palli Domenico , Panico Salvatore , Sacerdote Carlotta , Tumino Rosario , Kyrtopoulos Soterios , Hosnijeh Fatemeh Saberi , Lang Thierry , Vermeulen Roel , Vineis Paolo , Stringhini Silvia , Chadeau-Hyam Marc 
Published: April 2016

AbstractLower socioeconomic position (SEP) has consistently been associated with poorer health. To explore potential biological embedding and the consequences of SEP experiences from early life to adulthood, we investigate how SEP indicators at different points across the life course may be related to a combination of 28 inflammation markers. Using blood-derived inflammation profiles measured by a multiplex array in 268 participants from the Italian component of the European Prospective Investigation into Cancer and Nutrition cohort, we evaluate the association between early life, young adulthood and later adulthood SEP with each inflammatory markers separately, or by combining them into an inflammatory score. We identified an increased inflammatory burden in participants whose father had a manual occupation, through increased plasma levels of CSF3 (G-CSF; β = 0.29; P = 0.002) and an increased inflammatory score (β = 1.96; P = 0.029). Social mobility was subsequently modelled by the interaction between father’s occupation and the highest household occupation, revealing a significant difference between “stable Non-manual” profiles over the life course versus “Manual to Non-manual” profiles (β = 2.38, P = 0.023). Low SEP in childhood is associated with modest increase in adult inflammatory burden; however, the analysis of social mobility suggests a stronger effect of an upward social mobility over the life course.
Body mass scaling of passive oxygen diffusion in endotherms and ectotherms
Authors: Gillooly James F. , Gomez Juan Pablo , Mavrodiev Evgeny V. , Rong Yue , McLamore Eric S. 
Published: April 2016

Significance
Biologists have long sought to understand how differences in the structure of vertebrate respiratory systems are related to differences in oxygen consumption rates associated with metabolism. In particular, they have sought to understand how structural constraints on passive oxygen diffusion through gills or lungs are related to the nonlinear body mass scaling of oxygen consumption rates. Here we show that the body mass dependence of oxygen diffusion capacity, which is governed by the area and thickness of respiratory surfaces, matches the body mass dependence of respiration in diverse endothermic (birds and mammals) and ectothermic (reptiles, amphibians, and fishes) vertebrates. These results provide a step toward a more complete understanding of the structural differences that underlie changes in oxygen consumption rates with body size.
Tobacco mosaic virus-directed reprogramming of auxin/indole acetic acid protein transcriptional responses enhances virus phloem loading
Authors: Collum Tamara D. , Padmanabhan Meenu S. , Hsieh Yi-Cheng , Culver James N. 
Published: April 2016

Significance
For plant viruses a successful infection correlates with the ability to access the vascular phloem and move systemically into distal tissues. However, how viruses gain access to and usurp vascular tissues is poorly understood. Here we show how tobacco mosaic virus (TMV) enhances its access to the phloem of mature plant tissues through the targeted disruption of auxin/indole acetic acid (Aux/IAA) transcriptional regulators that control expression of host genes involved in virus cell-to-cell movement, plasmodesmata gating, and defense. TMV’s ability to disrupt Aux/IAA function successfully confers a significant advantage in the systemic spread of this virus, allowing it to outcompete nondisrupting viruses. In summary, TMV interacts with Aux/IAA proteins to reprogram the vascular phloem, making it more conducive to systemic movement.
Big data visualization identifies the multidimensional molecular landscape of human gliomas
Authors: Bolouri Hamid , Zhao Lue Ping , Holland Eric C. 
Published: April 2016

SignificanceWe demonstrate that computational visualization of large-scale molecular and clinical datasets can delineate molecularly defined groups of highly similar patients that are well separated from other subgroups. We show that our approach is applicable to multiple data types (sequence, expression, DNA methylation), and that it provides the ability to discover clusters of tumors with targetable lesions. Our methods are generally applicable to all diseases and provide an intuitive means for physicians and bench scientists to work directly with “big” biomedical data.
Monitoring Demographic and Genetic Responses of a Threatened Inland Trout to Habitat Reconnection
Authors: Neville Helen , Dauwalter Dan , Peacock Mary 
Published: April 2016

AbstractFreshwater fishes living in streams and rivers can be affected strongly by isolation, which causes a disproportionate degree of fragmentation in such dendritic systems. Isolation disrupts important ecological and migratory processes as well as the ability to access refuge habitats during disturbances. The restoration of habitat connectivity, then, should be a productive strategy for improving the resiliency of freshwater fish populations, but the local and broader ecological benefits of barrier removal are still poorly understood. We report on a long‐term, spatially intensive effort to monitor the responses of inland trout to stream habitat reconnection at a watershed scale, using both demographic and genetic techniques. Individual‐based genetic assignment uncovered clear evidence of movement into the primary tributary of interest, which had been blocked by an assumedly complete barrier, but the source population generating this movement varied over time. A linear mixed‐effect model suggested trout densities in this target stream increased threefold and the population sustained more large migratory‐sized individuals after habitat reconnection. Densities overall did not respond to fire or variable spring flows which occurred during the course of the study, but a negative parameter estimate for “year” suggested a possible decline in densities over the study period (although 95% CIs barely overlapped with 0). Population genetic metrics showed no change in population differentiation or metrics of genetic diversity in most cases, except for a significant decline in allelic richness in the target population. The effective biological reconnection documented in our study should improve population resiliency in the future, but we discuss the benefits of spatially intensive monitoring at a watershed scale and combined inference from both demographic and genetic metrics to uncover unexpectedly complex fish responses to habitat reconnection.Received September 18, 2015; accepted December 10, 2015 Published online April 27, 2016
Carbon Dioxide as a Tool to Deter the Movement of Invasive Bigheaded Carps
Authors: Donaldson Michael R. , Amberg Jon , Adhikari Shivani , Cupp Aaron , Jensen Nathan , Romine Jason , Wright Adam , Gaikowski Mark , Suski Cory D. 
Published: April 2016

AbstractNonnative bigheaded carps are established in the Mississippi River and there is substantial concern about their potential entry into the interconnected Laurentian Great Lakes. While electrical barriers currently exist as a preventative measure, there is need for additional control mechanisms to promote barrier security through redundancy. We tested the effectiveness of infused carbon dioxide gas (CO2) as a tool to influence the movement and behavior invasive bigheaded carps, namely Bighead Carp Hypophthalmichthys nobilis and Silver Carp H. molitrix, as well as native Bigmouth Buffalo Ictiobus cyprinellus, Channel Catfish Ictalurus punctatus, Paddlefish Polyodon spathula, and Yellow Perch Perca flavescens in an experimental pond. Individuals were monitored with acoustic telemetry before, during, and after CO2 addition to the pond. We noted distinct changes in fish behavior following CO2 addition. Each species except Paddlefish maintained farther distances from the CO2 infusion manifold relative to controls. Both bigheaded carp species had slower persistence velocities (persistence of a movement in a given direction) following CO2 infusion and Bighead Carp used a smaller area of the pond immediately after CO2 addition. Pond pH progressively decreased up to 1.5 units following CO2 infusion. This work provides evidence that could inform future research to enhance existing control measures used to deter high‐risk invasive fishes, such as bigheaded carps.Received July 27, 2015; accepted January 11, 2016 Published online April 27, 2016
Distinguishing Three Unprofessional Behavior Profiles of Medical Students Using Latent Class Analysis
Authors: Mak-van der Vossen Marianne C. , van Mook Walther N.K.A. , Kors Joyce M. , van Wieringen Wessel N. , Peerdeman Saskia M. , Croiset Gerda , Kusurkar Rashmi A. 
Published: April 2016

Purpose
Because unprofessional behavior of physicians is associated with unprofessional behavior in medical school, identifying unprofessional behavior in medical school is critical. Research has noted the difficulty in assessing professional behavior. Instead of identifying isolated behaviors, it could be more helpful to recognize behavioral patterns to evaluate students’ professional behavior. The authors aimed to identify patterns in the unprofessional behaviors of medical students and to construct descriptions based on these patterns.

Method
Content analysis of research articles yielded a template of unprofessional behaviors for coding student evaluation forms indicating unsatisfactory professional behavior, collected from 2012 to 2014 at the VUmc School of Medical Sciences, Amsterdam, the Netherlands. Latent class analysis was used to identify classes of students with a high chance of displaying comparable unprofessional behaviors. Teachers’ feedback of prototype students was summarized to generate profile descriptions.

Results
A template of 109 behaviors was used to code 232 evaluation forms of 194 students (3.9% students/year). Latent class analysis identified three hypothetical classes of students: Class 1 (43%) was labeled as “Poor reliability,” class 2 (20%) was labeled as “Poor reliability and poor insight,” and class 3 (37%) was labeled as “Poor reliability, poor insight, and poor adaptability.”

Conclusions
These profiles of unprofessional behavior might help to improve the evaluation of unprofessional behavior in medical school. Further research should provide evidence for confidently accepting or rejecting the profiles as an instrument to identify which students are expected to benefit from remediation trajectories.
Risk of Recurrence After Surviving Severe Sepsis: A Matched Cohort Study
Authors: Shen Hsiu-Nien , Lu Chin-Li , Yang Hsi-Hsing 
Published: April 2016

Objectives:
To examine the risk of recurrence in adults who survived first-episode severe sepsis for at least 3 months.

Design:
A matched cohort study.

Setting:
Inpatient claims data from Taiwan’s National Health Insurance Research Database.

Subjects:
We analyzed 10,818 adults who survived first-episode severe sepsis without recurrence for at least 3 months in 2000 (SS group; mean age, 62.7 yr; men, 54.7%) and a group of age/sex-matched (1:1) population controls who had no prior history of severe sepsis. All subjects were followed from the study entry to the occurrence of end-point, death, or until December 31, 2008, whichever date came first.

Interventions:
None.

Measurements and Main Results:
Primary end-point was severe sepsis that occurred after January 1, 2001 (the study entry). Relative risk of the end-point was assessed using competing risk regression model. During the follow-up period, severe sepsis and death occurred in 35.0% and 26.5% of SS group and in 4.3% and 18.6% of controls, respectively, representing a covariate-adjusted sub–hazard ratio of 8.89 (95% CI, 8.04–9.83) for the risk of recurrence. In stratified analysis by patient characteristics, the sub–hazard ratios ranged from 7.74 in rural area residents to 23.17 in young adults. In subgroup analysis by first-episode infection sites in SS group, the sub–hazard ratios ranged from 4.82 in intra-abdominal infection to 9.99 in urinary tract infection.

Conclusions:
Risk of recurrence after surviving severe sepsis is substantial regardless of patient characteristics or infection sites. Further research is necessary to find underlying mechanisms for the high risk of recurrence in these patients.
Comparison of Three Assays to Quantify Infliximab, Adalimumab, and Etanercept Serum Concentrations
Authors: van Bezooijen Ji S. , Koch Birgit C. P. , van Doorn Martijn B. A. , Prens Errol P. , van Gelder Teun , Schreurs Marco W. J. 
Published: April 2016

Background:
To optimize treatment of inflammatory diseases, interest in the measurement of anti–tumor necrosis factor alpha (anti-TNFα) serum drug concentrations is increasing. Preferably, assays for the detection of these drugs should be compared using the same reference material. In this study, 2 commercially available enzyme-linked immunosorbent assays (ELISAs) and a commercially available bioassay for the determination of anti-TNFα drugs are compared.

Methods:
Serum samples from infliximab-, adalimumab-, and etanercept-treated patients, control samples from ustekinumab-treated patients, and healthy donors were obtained. ELISAs manufactured by Sanquin and Theradiag and the iLite reporter gene–based bioassay from Biomonitor were compared.

Results:
Sanquin, Theradiag, and iLite assays concordantly (100%) detected infliximab, adalimumab, and etanercept in the relevant patient groups. The Sanquin ELISAs specifically detected the anti-TNFα drug they were designed for, whereas the Theradiag and iLite showed cross-reactivity with other anti-TNFα drugs. Ustekinumab was not detected in any of the assays. Sanquin, Theradiag, and iLite exhibited linear quantitative correlation for all drug concentration assays. However, there were statistically significant quantitative differences in measured concentrations.

Conclusions:
All 3 commercially available assays seem suitable for therapeutic drug monitoring of anti-TNFα drugs, allowing sensitive and comparable detection of infliximab, adalimumab, and etanercept concentrations, however with differences in specificity and recovery.
Aesthetic Total Reconstruction of Lower Eyelid Using Scapha Cartilage Graft on a Vascularized Propeller Flap
Authors: Uemura Tetsuji , Watanabe Hidekata , Masumoto Kazuyuki , Kikuchi Mamoru , Satake Yoshiyasu , Yanai Tetsu , Harada Yoshimi , Ishihara Yasuhiro , Yasuta Masato 
Published: April 2016

Background:
The aim of this study was to review the results of a cohort of patients based on our experience with a new technique for total lower eyelid reconstruction after a large defect caused by malignant tumor and trauma. A scapha cartilage graft with small skin on a vascularized propeller flap was used for 16 cases requiring lower eyelid reconstruction.

Methods:
Patients were identified from a database, and a retrospective case note review was conducted. The scapha cartilage graft was sutured to the margin of the defect of the palpebral conjunctiva and tarsus. The propeller flap, rotated by a perforator-based lateral orbital flap or a subcutaneous-based nasolabial flap, was vascularized on the scapha cartilage graft as anterior lining of the lower eyelid. The follow-up, including results of slit-lamp examination, lasted for varying periods, but often it was for 12 months.

Results:
The scapha cartilage graft with small skin on a vascularized propeller flap was viable in all cases. Slit-lamp examination detected no irritation or injury of the conjunctiva and cornea, and visual acuity was maintained in all cases. A deformity in the donor helix by this technique was also improved by getting a smaller skin harvested from the scapha.

Conclusion:
Use of the scapha cartilage graft with small skin on a vascularized propeller flap allows for a good fit to the orbit, short operative time under local anesthesia, good graft viability, and a good esthetic result with minimal donor site morbidity.