bluuebunny/crossref_metadata_2025_split huggingface dataset:
Durability and Decay of Treatment Benefit of Cognitive Behavioral Therapy for Irritable Bowel Syndrome: 12-Month Follow-Up
Authors: Lackner Jeffrey M. , Jaccard James , Radziwon Christopher D. , Firth Rebecca S. , Gudleski Gregory D. , Hamilton Frank , Katz Leonard A. , Keefer Laurie , Krasner Susan S. , Ma Chang-Xing , Sitrin Michael D. , Brenner Darren M. 
Published: November 2018

BACKGROUND:
There is a need for safe and effective IBS treatments that provide immediate and sustained improvement of IBS symptoms, particularly among more severe patients. The aim was to assess long-term clinical response of cognitive behavioral therapy (CBT) with reference to IBS education.

METHODS:
A total of 436 Rome III-diagnosed IBS patients (80% F, M age = 41 years) were randomized to: 4 session home-based CBT (minimal contact (MC-CBT)), 10 session clinic-based CBT (standard (S-CBT)), or 4 session IBS education (EDU). Follow-up occurred at 2 weeks and 3, 6, 9, and 12 months following treatment completion. Treatment response was based a priori on the Clinical Global Improvement Scale (global IBS symptom improvement) and IBS Symptom Severity Scale (IBS-SSS).

RESULTS:
Post-treatment CGI gains were generally maintained by MC-CBT patients at quarterly intervals through 12-month follow-up with negligible decay. For MC-CBT and S-CBT, 39 and 33% of respondents maintained treatment response at every follow-up assessment. The corresponding percent for EDU was 19%, which was significantly lower (p < 0.05) than for the CBT groups. On the IBS-SSS, therapeutic gains also showed a pattern of maintenance with trends towards increased efficacy over time in all conditions, with the mean unit reductions between baseline and follows-up being approximately −76 at immediate and approximately −94 at 12 months (−50 = clinically significant).

CONCLUSIONS:
For treatment-refractory IBS patients, home- and clinic-based CBT resulted in substantial and enduring relief of multiple IBS symptoms that generally extended to 12-month post treatment.
Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics
Authors: Shelton Amanda N , Seth Erica C , Mok Kenny C , Han Andrew W , Jackson Samantha N , Haft David R , Taga Michiko E 
Published: November 2018

Abstract
The vitamin B12 family of cofactors known as cobamides are essential for a variety of microbial metabolisms. We used comparative genomics of 11,000 bacterial species to analyze the extent and distribution of cobamide production and use across bacteria. We find that 86% of bacteria in this data set have at least one of 15 cobamide-dependent enzyme families, but only 37% are predicted to synthesize cobamides de novo. The distribution of cobamide biosynthesis and use vary at the phylum level. While 57% of Actinobacteria are predicted to biosynthesize cobamides, only 0.6% of Bacteroidetes have the complete pathway, yet 96% of species in this phylum have cobamide-dependent enzymes. The form of cobamide produced by the bacteria could be predicted for 58% of cobamide-producing species, based on the presence of signature lower ligand biosynthesis and attachment genes. Our predictions also revealed that 17% of bacteria have partial biosynthetic pathways, yet have the potential to salvage cobamide precursors. Bacteria with a partial cobamide biosynthesis pathway include those in a newly defined, experimentally verified category of bacteria lacking the first step in the biosynthesis pathway. These predictions highlight the importance of cobamide and cobamide precursor salvaging as examples of nutritional dependencies in bacteria.
Design of an inherently-stable water oxidation catalyst
Authors: Chakraborty Biswarup , Gan-Or Gal , Raula Manoj , Gadot Eyal , Weinstock Ira A. 
Published: November 2018

AbstractWhile molecular water-oxidation catalysts are remarkably rapid, oxidative and hydrolytic processes in water can convert their active transition metals to colloidal metal oxides or hydroxides that, while quite reactive, are insoluble or susceptible to precipitation. In response, we propose using oxidatively-inert ligands to harness the metal oxides themselves. This approach is demonstrated by covalently attaching entirely inorganic oxo-donor ligands (polyoxometalates) to 3-nm hematite cores, giving soluble anionic structures, highly resistant to aggregation, yet thermodynamically stable to oxidation and hydrolysis. Using orthoperiodate (at pH 8), and no added photosensitizers, the hematite-core complex catalyzes visible-light driven water oxidation for seven days (7600 turnovers) with no decrease in activity, far exceeding the documented lifetimes of molecular catalysts under turnover conditions in water. As such, a fundamental limitation of molecular complexes is entirely bypassed by using coordination chemistry to harness a transition-metal oxide as the reactive center of an inherently stable, homogeneous water-oxidation catalyst.
CMV and EBV targets recognized by tumor-infiltrating B lymphocytes in pancreatic cancer and brain tumors
Authors: Meng Qingda , Valentini Davide , Rao Martin , Dodoo Ernest , Maeurer Markus 
Published: November 2018

AbstractTargeted antiviral immune responses to the widespread human pathogens cytomegalovirus (CMV) and Epstein-Barr virus (EBV) play a pivotal role in determining immune fitness. We show here for the first time that tumor-infiltrating B cell (TIB)- derived immunoglobulin G (IgG) from patients with pancreatic cancer or glioblastoma have unique anti-CMV/EBV immune recognition patterns compared to serum IgG. There is also great heterogeneity between patients, as well as between serum and TIB-IgG, while some viral targets elicited strongly both T-cell and IgG reactivity in tumor infiltrating T- and B-cells. These observations suggest that the anti-CMV/EBV humoral immune response in situ is highly unique and can be instrumental in developing next-generation immuno-biomarkers in addition to supplementing cellular therapy strategies for personalized cancer therapy targeting CMV or EBV in the tumor microenvironment.
Stable pH Suppresses Defense Signaling and is the Key to Enhance Agrobacterium-Mediated Transient Expression in Arabidopsis Seedlings
Authors: Wang Yi-Chieh , Yu Manda , Shih Po-Yuan , Wu Hung-Yi , Lai Erh-Min 
Published: November 2018

AbstractAgrobacterium-mediated transient expression is a powerful analysis platform for diverse plant gene functional studies, but the mechanisms regulating the expression or transformation levels are poorly studied. Previously, we developed a highly efficient and robust Agrobacterium-mediated transient expression system, named AGROBEST, for Arabidopsis seedlings. In this study, we found that AGROBEST could promote the growth of agrobacteria as well as inhibit the host immunity response. When the factor of agrobacterial growth is minimized, maintaining pH at 5.5 with MES buffer was the key to achieving optimal transient expression efficiency. The expression of plant immunity marker genes, FRK1 and NHL10, was suppressed in the pH-buffered medium as compared with non-buffered conditions in Col-0 and an efr-1 mutant lacking the immunity receptor EFR recognizing EF-Tu, a potent pathogen- or microbe-associated molecular pattern (PAMP or MAMP) of A. tumefaciens. Notably, such immune suppression could also occur in Arabidopsis seedlings without Agrobacterium infection. Furthermore, the PAMP-triggered influx of calcium ions was compromised in the pH-buffered medium. We propose that the enhanced transient expression efficiency by stable pH was due to inhibiting calcium ion uptake and subsequently led to suppressing immunity against Agrobacterium.
The shift in ocular dominance from short-term monocular deprivation exhibits no dependence on duration of deprivation
Authors: Min Seung Hyun , Baldwin Alex S. , Reynaud Alexandre , Hess Robert F. 
Published: November 2018

AbstractDeprivation of visual information from one eye for a 120-minute period in normal adults results in a temporary strengthening of the patched eye’s contribution to binocular vision. This plasticity for ocular dominance in adults has been demonstrated by binocular rivalry as well as binocular fusion tasks. Here, we investigate how its dynamics depend on the duration of the monocular deprivation. Using a binocular combination task, we measure the magnitude and recovery of ocular dominance change after durations of monocular deprivation ranging from 15 to 300 minutes. Surprisingly, our results show that the dynamics are of an all-or-none form. There was virtually no significant dependence on the duration of the initial deprivation.
Piezoresistive temperature sensors fabricated by a surface micromachining CMOS MEMS process
Authors: Cai Chunhua , Tan Junyan , Hua Di , Qin Ming , Zhu Nianfang 
Published: November 2018

AbstractThis paper presents a micromachined monocrystalline silicon piezoresistive temperature sensor fabricated by a surface micromachining CMOS (Complementary Metal Oxide Semiconductor) MEMS (Micro-Electro-Mechanical System) process. The design of the temperature sensor is based on the structure of the multi-layer cantilever beam and the bimetallic effect. The temperature change of the cantilever beam is translated into the change of the piezoresistance’s value. The test results show that the sensitivities of the sensors are 27.9 mV/°C with 100 Ω/▯ piezoresistance between −40 °C to 60 °C and 7.4 mV/°C with 400 Ω/▯ piezoresistance between −90 °C to 60 °C. The temperature sensor proposed in this paper can be used in radiosondes for its low operating temperature (as low as −90 °C), small size (below 1 mm2) and low heat capacity.
Novel Insect Florivory Strategy Initiates Autogamy in Unopened Allogamous Flowers
Authors: Hillier N. K. , Evans E. , Evans R. C. 
Published: November 2018

AbstractInsects may influence plant development via pollination, galling, and a range of herbivorous interactions, including florivory. Here, we report a novel form of insect-plant interaction in the form of florivory-initiated autogamy. Mompha capella larvae, feeding on petal bases of Crocanthemum canadense before flowers open, while providing no benefit to the plant, cause autogamy and subsequent seed and fruit development. This interaction provides a clear benefit to the florivore because it enters the developing fruit and consumes most seeds; however, surviving seeds are viable. This novel interaction is discussed with respect to the dimorphic cleistogamous reproduction employed by this plant species. Moreover, this represents a previously undocumented insect-plant interaction in the form of a florivory-initiated pollination.
Establishment of an efficient in vitro propagation system for Iris sanguinea
Authors: Wang Ling , Du Yu , Rahman Md. Mahbubur , Tang Biao , Fan Li-Juan , Kilaru Aruna 
Published: November 2018

AbstractIris sanguinea is a perennial flowering plant that is typically cultivated through seeds or bulbs. However, due to limitations in conventional propagation, an alternate regeneration system using seeds was developed. The protocol included optimization of sterilization, stratification and scarification methods as iris seeds exhibit physiological dormancy. In addition to chlorine-based disinfection, alkaline or heat treatment was used to break seed dormancy and reduce contamination. When seeds were soaked in water at 80 °C overnight, and sterilized with 75% EtOH for 30 s and 4% NaOCl solution for 20 minutes, contamination was reduced to 10% and a 73.3% germination was achieved. The germinated seedlings with 2-3 leaves and radicle were used as explants to induce adventitious buds. The optimal MS medium with 0.5 mg L−1 6-benzylaminopurine, 0.2 mg L−1 NAA, and 1.0 mg L−1 kinetin resulted in 93.3% shoot induction and a proliferation coefficient of 5.30. Medium with 0.5 mg L−1 NAA achieved 96.4% rooting of the adventitious shoots. The survival rate was more than 90% after 30 days growth in the cultivated matrix. In conclusion, a successful regeneration system for propagation of I. sanguinea was developed using seeds, which could be utilized for large-scale propagation of irises of ecological and horticultural importance.
Downregulation of intratumoral expression of miR-205, miR-200c and miR-125b in primary human cutaneous melanomas predicts shorter survival
Authors: Sánchez-Sendra Beatriz , Martinez-Ciarpaglini Carolina , González-Muñoz José F. , Murgui Amelia , Terrádez Liria , Monteagudo Carlos 
Published: November 2018

AbstractWhile only 15–25 percent of melanoma patients develop distant metastasis and die, this disease is still responsible for the majority of skin cancer-related deaths. The availability of adjuvant therapies makes the selection of high-risk patients essential. We evaluated the intratumoral expression of ten miRNAs in primary melanomas in relation to its ability to predict melanoma survival. To this end, we correlated miRNA expression in 132 cryopreserved primary and metastatic tumors with clinicopathological factors and clinical outcome. We found sequential downregulation of intratumoral expression of miR-125b, miR-182, miR-200c and miR-205 over the full spectrum of melanoma progression. Moreover, downregulation of these miRNAs occurred in primary melanomas that further disseminated to distant sites. Furthermore, miR-125b, miR-200c and miR-205 correlated as independent factors with shorter survival. Our in vitro findings demonstrate that loss of miR-205 potentiates the invasive ability of melanoma cells. We conclude that the downregulation of miR-205 in primary melanomas is an intrinsic property that might contribute to distant metastasis. In particular, the interaction of melanoma cells with the extracellular matrix is one of the key mechanisms by which miR-205 influences melanoma metastasis. In conclusion, miR-125b, miR-200c and miR-205 are useful prognostic biomarkers at the time of diagnosis to select high-risk patients.
Helical organization of microtubules occurs in a minority of tunneling membrane nanotubes in normal and cancer urothelial cells
Authors: Resnik Nataša , Prezelj Tim , De Luca Giulia Maria Rita , Manders Erik , Polishchuk Roman , Veranič Peter , Kreft Mateja Erdani 
Published: November 2018

AbstractTunneling membrane nanotubes (TnTs) are membrane protrusions connecting nearby or distant cells in vitro and in vivo. Functions of TnTs in cellular processes are various and rely on TnT structure, which also depends on cytoskeletal composition. In the present study, we focused on the organization of microtubules (MTs) and intermediate filaments (IFs) in TnTs of urothelial cells. We analysed TnTs of normal porcine urothelial cells, which morphologically and physiologically closely resemble normal human urothelial cells, and of cancer cells derived from invasive human urothelial neoplasm. Wide-field fluorescence, confocal and super-resolution microscopy techniques, together with image analyses and 3D reconstructions enlightened specific MT-IF organization in TnTs, and for the first time revealed that MTs and IFs co-occur in the majority of normal and cancer urothelial cell TnTs. Our findings show that in the initiation segment of TnTs, MTs are cross-linked with each other into filamentous network, however in the middle and the attaching segment of TnT, MTs can helically enwrap IFs, the phenomenon that has not been shown before within the TnTs. In this study, we assess MT-IF co-occurrence in TnTs and present evidence that such helical organization of MTs enwrapping IFs is only occurring in a minority of the TnTs. We also discuss the possible cell-biological and physiological reasons for helical organization of MTs in TnTs.
Genome-wide identification and analysis of non-specific Lipid Transfer Proteins in hexaploid wheat
Authors: Kouidri Allan , Whitford Ryan , Suchecki Radoslaw , Kalashyan Elena , Baumann Ute 
Published: November 2018

AbstractNon-specific Lipid Transfer Proteins (nsLTPs) are involved in numerous biological processes. To date, only a fraction of wheat (Triticum aestivum L.) nsLTPs (TaLTPs) have been identified, and even fewer have been functionally analysed. In this study, the identification, classification, phylogenetic reconstruction, chromosome distribution, functional annotation and expression profiles of TaLTPs were analysed. 461 putative TaLTPs were identified from the wheat genome and classified into five types (1, 2, C, D and G). Phylogenetic analysis of the TaLTPs along with nsLTPs from Arabidopsis thaliana and rice, showed that all five types were shared across species, however, some type 2 TaLTPs formed wheat-specific clades. Gene duplication analysis indicated that tandem duplications contributed to the expansion of this gene family in wheat. Analysis of RNA sequencing data showed that TaLTPs were expressed in most tissues and stages of wheat development. Further, we refined the expression profile of anther-enriched expressed genes, and identified potential cis-elements regulating their expression specificity. This analysis provides a valuable resource towards elucidating the function of TaLTP family members during wheat development, aids our understanding of the evolution and expansion of the TaLTP gene family and, additionally, provides new information for developing wheat male-sterile lines with application to hybrid breeding.
All-optical generation and ultrafast tuning of non-linear spin Hall current
Authors: Wätzel Jonas , Berakdar Jamal 
Published: November 2018

AbstractSpin Hall effect, one of the cornerstones in spintronics refers to the emergence of an imbalance in the spin density transverse to a charge flow in a sample under voltage bias. This study points to a novel way for an ultrafast generation and tuning of a unidirectional nonlinear spin Hall current by means of subpicosecond laser pulses of optical vortices. When interacting with matter, the optical orbital angular momentum (OAM) carried by the vortex and quantified by its topological charge is transferred to the charge carriers. The residual spin-orbital coupling in the sample together with confinement effects allow exploiting the absorbed optical OAM for spatio-temporally controlling the spin channels. Both the non-linear spin Hall current and the dynamical spin Hall angle increase for a higher optical topological charge. The reason is the transfer of a higher amount of OAM and the enhancement of the effective spin-orbit interaction strength. No bias voltage is needed. We demonstrate that the spin Hall current can be all-optically generated in an open circuit geometry for ring-structured samples. These results follow from a full-fledged propagation of the spin-dependent quantum dynamics on a time-space grid coupled to the phononic environment. The findings point to a versatile and controllable tool for the ultrafast generation of spin accumulations with a variety of applications such as a source for ultrafast spin transfer torque and charge and spin current pulse emitter.
Evaluation of Dynamic Tumor-tracking Intensity-modulated Radiotherapy for Locally Advanced Pancreatic Cancer
Authors: Nakamura Akira , Hiraoka Masahiro , Itasaka Satoshi , Nakamura Mitsuhiro , Akimoto Mami , Ishihara Yoshitomo , Mukumoto Nobutaka , Goto Yoko , Kishi Takahiro , Yoshimura Michio , Matsuo Yukinori , Yano Shinsuke , Mizowaki Takashi 
Published: November 2018

AbstractIntensity-modulated radiotherapy (IMRT) is now regarded as an important treatment option for patients with locally advanced pancreatic cancer (LAPC). To reduce the underlying tumor motions and dosimetric errors during IMRT as well as the burden of respiratory management for patients, we started to apply a new treatment platform of the dynamic tumor dynamic tumor-tracking intensity-modulated radiotherapy (DTT-IMRT) using the gimbaled linac, which can swing IMRT toward the real-time tumor position under patients’ voluntary breathing. Between June 2013 and March 2015, ten patients were treated, and the tumor-tracking accuracy and the practical benefits were evaluated. The mean PTV size in DTT-IMRT was 18% smaller than a conventional ITV-based PTV. The root-mean-squared errors between the predicted and the detected tumor positions were 1.3, 1.2, and 1.5 mm in left-right, anterior-posterior, and cranio-caudal directions, respectively. The mean in-room time was 24.5 min. This high-accuracy of tumor-tracking with reasonable treatment time are promising and beneficial to patients with LAPC.
Diffracted X-ray Blinking Tracks Single Protein Motions
Authors: Sekiguchi Hiroshi , Kuramochi Masahiro , Ikezaki Keigo , Okamura Yu , Yoshimura Kazuki , Matsubara Ken , Chang Jae-Won , Ohta Noboru , Kubo Tai , Mio Kazuhiro , Suzuki Yoshio , Chavas Leonard M. G. , Sasaki Yuji C. 
Published: November 2018

AbstractSingle molecule dynamics studies have begun to use quantum probes. Single particle analysis using cryo-transmission electron microscopy has dramatically improved the resolution when studying protein structures and is shifting towards molecular motion observations. X-ray free-electron lasers are also being explored as routes for determining single molecule structures of biological entities. Here, we propose a new X-ray single molecule technology that allows observation of molecular internal motion over long time scales, ranging from milliseconds up to 103 seconds. Our method uses both low-dose monochromatic X-rays and nanocrystal labelling technology. During monochromatic X-ray diffraction experiments, the intensity of X-ray diffraction from moving single nanocrystals appears to blink because of Brownian motion in aqueous solutions. X-ray diffraction spots from moving nanocrystals were observed to cycle in and out of the Bragg condition. Consequently, the internal motions of a protein molecule labelled with nanocrystals could be extracted from the time trajectory using this diffracted X-ray blinking (DXB) approach. Finally, we succeeded in distinguishing the degree of fluctuation motions of an individual acetylcholine-binding protein (AChBP) interacting with acetylcholine (ACh) using a laboratory X-ray source.
Interannual and decadal variability of the North Equatorial Undercurrents in an eddy-resolving ocean model
Authors: Li Yiwen , Liu Hailong , Lin Pengfei 
Published: November 2018

AbstractIn the present study, the mean states of the North Equatorial Undercurrents (NEUCs) simulated in an eddy-resolving ocean model are evaluated, and the variability of the three NEUC jets is analyzed. This analysis provides a reference for future observations regarding how long the in-situ observations should be conducted to obtain a complete picture of NEUCs. We show that the primary features of the three eastward NEUC jets are fairly well reproduced by the high-resolution model of LICOM, such as the locations, tilting directions and widths of the three jets. However, the simulated NEUCs have slightly weaker magnitude and are located at shallower depths. In addition, two dominant time scales on interannual (2–7 years) and decadal (12–19 years) time scales for all three NEUC jets are found in a 39-year high-resolution LICOM simulation, although the latter is not statistically significant. The variation of these jets is related to the remarkable interannual and decadal variability in the Pacific Ocean. Our decomposition analysis indicates that both the small- and large-scale currents contribute to the total variation. Furthermore, the low-pass temporal filter of zonal velocity shows that the quasi-steady cross-basin NEUC jets can only emerge on time scales longer than the interannual periodicity.