bluuebunny/crossref_metadata_2025_split huggingface dataset:
The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography
Authors: Edlund Petra , Takala Heikki , Claesson Elin , Henry Léocadie , Dods Robert , Lehtivuori Heli , Panman Matthijs , Pande Kanupriya , White Thomas , Nakane Takanori , Berntsson Oskar , Gustavsson Emil , Båth Petra , Modi Vaibhav , Roy-Chowdhury Shatabdi , Zook James , Berntsen Peter , Pandey Suraj , Poudyal Ishwor , Tenboer Jason , Kupitz Christopher , Barty Anton , Fromme Petra , Koralek Jake D. , Tanaka Tomoyuki , Spence John , Liang Mengning , Hunter Mark S. , Boutet Sebastien , Nango Eriko , Moffat Keith , Groenhof Gerrit , Ihalainen Janne , Stojković Emina A. , Schmidt Marius , Westenhoff Sebastian 
Published: October 2016

AbstractPhytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.
Genome-wide profiling of the human papillomavirus DNA integration in cervical intraepithelial neoplasia and normal cervical epithelium by HPV capture technology
Authors: Liu Ying , Zhang Chaoting , Gao Weijiao , Wang Limin , Pan Yaqi , Gao Yunong , Lu Zheming , Ke Yang 
Published: October 2016

AbstractHPV integration plays an important role in cervical carcinogenesis. HPV genotypes and the exact integration sites were investigated using HPV capture technology combined with next generation sequencing in 166 women. Three, one and six integration sites were verified in 7 HPV-positive ‘normal cervical epithelium’, 6 HPV-positive CIN2 and 15 HPV-positive CIN 3 samples, respectively. Of the 10 integrations, one and nine were involved with HPV33 and HPV16, respectively. Our study accurately evaluated HPV integration level in CINs and normal cervical tissues using high-throughput viral integration detection method providing basic evidence for HPV integration-driven cervical carcinogenesis.
Historical dimensions of population structure in a continuously distributed marine species: The case of the endemic Chilean dolphin
Authors: Pérez-Alvarez M. J. , Olavarría C. , Moraga R. , Baker C. S. , Hamner R. M. , Poulin E. 
Published: October 2016

AbstractThe complementarity of historical and contemporary processes contributes to understanding the genetic structure of continuously distributed marine species with high dispersal capabilities. Cephalorhynchus eutropia, has a continuous coastal distribution with strong genetic differentiation identified by nuclear DNA markers. We explored the historical dimension of this genetic differentiation between northern and southern populations to evaluate phylogeographic structure. Additionally, we conducted mtDNA and microsatellite analyses to detect past and recent demographic changes. The southern population was characterized by lower genetic diversity with a signal of population expansion, likely associated with ice retreat and habitat extension after the Last Glacial Maximum (LGM). In contrast, structure within the northern population was more consistent with stable historical population size. Approximate Bayesian Computation analyses suggested that during the LGM, C. eutropia persisted in the northern area; while the south was colonized by dispersal ~11,000 years ago followed by population expansion. This study shows that Chilean dolphin population structure is consistent with predictions from the Expansion-Contraction biogeographic model, with a poleward post-glacial shift revealed in current genetic structure. The results also confirm the validity of the population units previously identified, demonstrating their historical origin and highlighting the utility of integrating genetic markers with different temporal scale resolutions.
Nondestructive, real-time determination and visualization of cellulose, hemicellulose and lignin by luminescent oligothiophenes
Authors: Choong Ferdinand X. , Bäck Marcus , Steiner Svava E. , Melican Keira , Nilsson K. Peter R. , Edlund Ulrica , Richter-Dahlfors Agneta 
Published: October 2016

AbstractEnabling technologies for efficient use of the bio-based feedstock are crucial to the replacement of oil-based products. We investigated the feasibility of luminescent conjugated oligothiophenes (LCOs) for non-destructive, rapid detection and quality assessment of lignocellulosic components in complex biomass matrices. A cationic pentameric oligothiophene denoted p-HTEA (pentamer hydrogen thiophene ethyl amine) showed unique binding affinities to cellulose, lignin, hemicelluloses, and cellulose nanofibrils in crystal, liquid and paper form. We exploited this finding using spectrofluorometric methods and fluorescence confocal laser scanning microscopy, for sensitive, simultaneous determination of the structural and compositional complexities of native lignocellulosic biomass. With exceptional photostability, p-HTEA is also demonstrated as a dynamic sensor for real-time monitoring of enzymatic cellulose degradation in cellulolysis. These results demonstrate the use of p-HTEA as a non-destructive tool for the determination of cellulose, hemicellulose and lignin in complex biomass matrices, thereby aiding in the optimization of biomass-converting technologies.
Biologically responsive carrier-mediated anti-angiogenesis shRNA delivery for tumor treatment
Authors: Che Junyi , Tao Anqi , Chen Shun , Li Xiaoming , Zhao Yi , Yuan Weien 
Published: October 2016

AbstractSmall interfering RNA (siRNA) has increased the hope for highly-efficient treatment of gene-related diseases. However, the stable and efficient delivery of therapeutic nucleic acids is a prerequisite for the successful clinical translation of RNA interfering therapy. To achieve this, we condensed the low molecular weight polyethyleneimine (PEI, Mw < 2000) with 2,6-pyridinedicarboxaldehyde (PDA) to synthesize a biologically responsive and degradable cationic polymer (abbreviated to PDAPEI) which was utilized as a gene vector for the delivery of a VEGF-A shRNA expression plasmid DNA (pDNA). The resulting electrostatic interaction between PDAPEI and pDNA led to the self-assembly of nanoscale polyplexes with suitable particle size and stable zeta potential. The PDAPEI/pDNA polyplexes demonstrated an outstanding gene transfection and silencing efficiency at 30 w/w ratio, as well as negligible cytotoxicity. Also, the designed polymer showed no stimulation to the innate immune system. Moreover, compared with PEI 25 KDa, the polyplexes accomplished comparatively better anti-angiogenesis efficacy, which resulted in the inhibition of tumor growth in subcutaneous tumor mice models. In conclusion, PDAPEI has great potential to be a gene delivery vector for cancer therapy.
Impact of sialic acids on the molecular dynamic of bi-antennary and tri-antennary glycans
Authors: Guillot Alexandre , Dauchez Manuel , Belloy Nicolas , Jonquet Jessica , Duca Laurent , Romier Beatrice , Maurice Pascal , Debelle Laurent , Martiny Laurent , Durlach Vincent , Baud Stephanie , Blaise Sebastien 
Published: October 2016

AbstractSialic acids (SA) are monosaccharides that can be located at the terminal position of glycan chains on a wide range of proteins. The post-translational modifications, such as N-glycan chains, are fundamental to protein functions. Indeed, the hydrolysis of SA by specific enzymes such as neuraminidases can lead to drastic modifications of protein behavior. However, the relationship between desialylation of N-glycan chains and possible alterations of receptor function remains unexplored. Thus, the aim of the present study is to establish the impact of SA removal from N-glycan chains on their conformational behavior. We therefore undertook anin silicoinvestigation using molecular dynamics to predict the structure of an isolated glycan chain. We performed, for the first time, 3 independent 500 ns simulations on bi-antennary and tri-antennary glycan chains displaying or lacking SA. We show that desialylation alters both the preferential conformation and the flexibility of the glycan chain. This study suggests that the behavior of glycan chains induced by presence or absence of SA may explain the changes in the protein function.
Jak/Stat signaling regulates the proliferation and neurogenic potential of Müller glia-derived progenitor cells in the avian retina
Authors: Todd Levi , Squires Natalie , Suarez Lilianna , Fischer Andy J. 
Published: October 2016

AbstractMüller glia are capable of de-differentiating and proliferating to become Müller glia-derived progenitor cells (MGPCs) with the ability to regenerate retinal neurons. One of the cell-signaling pathways that drives the reprogramming of Müller glia into MGPCs in the zebrafish retina is the Jak/Stat-pathway. However, nothing is known about the influence of Jak/Stat-signaling during the formation of MGPCs in the retinas of warm-blooded vertebrates. Accordingly, we examined whether Jak/Stat-signaling influences the formation of MGPCs and differentiation of progeny in the avian retina. We found that Jak/Stat-signaling is activated in Müller glia in response to NMDA-induced retinal damage or by CNTF or FGF2 in the absence of retinal damage. Inhibition of gp130, Jak2, or Stat3 suppressed the formation of proliferating MGPCs in NMDA-damaged and FGF2-treated retinas. Additionally, CNTF combined with FGF2 enhanced the formation of proliferating MGPCs in the absence of retinal damage. In contrast to the zebrafish model, where activation of gp130/Jak/Stat is sufficient to drive neural regeneration from MGPCs, signaling through gp130 inhibits the neurogenic potential of MGPCs and promotes glial differentiation. We conclude that gp130/Jak/Stat-signaling plays an important role in the network of pathways that drives the formation of proliferating MGPCs; however, this pathway inhibits the neural differentiation of the progeny.
Directionally selective retinal ganglion cells suppress luminance responses during natural viewing
Authors: Im Maesoon , Fried Shelley I. 
Published: October 2016

AbstractThe ON-OFF directionally selective cells of the retina respond preferentially to movement in a preferred direction, but under laboratory conditions they are also sensitive to changes in the luminance of the stationary stimulus. If the response of these neurons contains information about both direction and luminance downstream neurons are faced with the challenge of extracting the motion component, a computation that may be difficult under certain viewing conditions. Here, we show that during natural viewing the response to luminance is suppressed, leaving a relatively pure motion signal that gets transmitted to the brain.
Charge Distribution Dependent Spectral Analysis of the Oxidized Diferrocenyl-Oligothienylene-Vinylene Molecular Wires
Authors: Xia Lixin , Wang Jing , Ma Caiqing , Wu Shiwei , Song Peng 
Published: October 2016

AbstractThe vibrational spectra have been investigated for revealing the comprehensive structure of diferrocenyl-oligothienylene-vinylene complex, stimulated by the excellent experimental reports [group of Casado J. Am. Chem. Soc. 2012, 134, 12, 5675]. The IR and Raman spectra were simulated. It is found that the change of charge distribution and bond length are associated with the variation in the frequencies of specific vibration in infrared spectra for the neutral and radical oxidation states. The theoretical simulation of charge difference density indicate that charge transfer mechanism for neutral and dication states are significant different. The results can offer hints for the rational design of novel and interesting oligomer semiconductor.
Reducing frequency domain spectroscopy measurement time for condition monitoring of transformer oil‐paper insulation using non‐sinusoidal excitations
Authors: Chatterjee Soumya , Pradhan Arpan Kumar , Dalai Sovan , Chatterjee Biswendu , Chakravorti Sivaji 
Published: October 2016

In conventional frequency domain spectroscopy (FDS) measurement, sinusoidal excitation is applied to a composite oil‐paper insulation under test, for a minimum of two cycles over a wide range of frequencies typically starting from 1 kHz to 1 mHz or even upto 0.1 mHz. The frequency sweep down to 1 mHz, is inevitably time consuming especially in lower frequency ranges. Considering the aforesaid fact, the main aim of the present study is to reduce overall FDS measurement time. The insulation under test is subjected to some fraction of one full cycle of excitation, and the corresponding dielectric response current is measured for each fraction. Using least square curve‐fitting technique, response current over two cycles is predicted from which dielectric dissipation factor (tanδ) is calculated. For this contribution, sinusoidal and non‐sinusoidal excitations in form of triangular waveform with five different initial slopes are used as excitation voltage. The technique is experimentally validated on three samples with different preset moisture contents prepared in the laboratory. The dielectric dissipation factor obtained by using the proposed technique is compared with the conventional method using two cycles, which show negligible differences. Most important of all is the overall test time, which can be brought down significantly when compared with conventional FDS measurement.
HGP-write : après la lecture, l’écriture ?
Authors: Jordan Bertrand 
Published: October 2016

The recently proposed « HGP-write » project aims to synthetize a full human genome and to introduce it into cells. This ambitious endeavour is fraught with financial and technical uncertainties and, if successful, would make « synthetic humans » a definite possibility even though this is not part of its announced goals. Accordingly, it has not been received with enthusiasm.
Caulobacter
PopZ forms an intrinsically disordered hub in organizing bacterial cell poles
Authors: Holmes Joshua A. , Follett Shelby E. , Wang Haibi , Meadows Christopher P. , Varga Krisztina , Bowman Grant R. 
Published: October 2016

Significance
Despite being the simplest organisms, bacteria have complex subcellular anatomies. How does such organization occur in openly diffusive cytoplasm? We find that the cell pole organizing protein PopZ facilitates network formation by binding directly to at least eight other proteins. The binding region in PopZ is intrinsically disordered, suggesting PopZ has a flexible structure that adopts a different interface for each partner protein. In this way, PopZ resembles eukaryotic hub proteins, such as p53 and BRCA1, which coordinate complex signaling networks. Rapid cycles of binding, unbinding, and rebinding within PopZ networks indicate that bacterial cell poles, similar to their eukaryotic counterparts, are highly dynamic structures.
Synthesis, oxygen radical absorbance capacity, and tyrosinase inhibitory activity of glycosides of resveratrol, pterostilbene, and pinostilbene
Authors: Uesugi Daisuke , Hamada Hiroki , Shimoda Kei , Kubota Naoji , Ozaki Shin-ichi , Nagatani Naoki 
Published: October 2016

Abstract
The stilbene compound resveratrol was glycosylated to give its 4′-O-β-D-glucoside as the major product in addition to its 3-O-β-D-glucoside by a plant glucosyltransferase from Phytolacca americana expressed in recombinant Escherichia coli. This enzyme transformed pterostilbene to its 4′-O-β-D-glucoside, and converted pinostilbene to its 4′-O-β-D-glucoside as a major product and its 3-O-β-D-glucoside as a minor product. An analysis of antioxidant capacity showed that the above stilbene glycosides had lower oxygen radical absorbance capacity (ORAC) values than those of the corresponding stilbene aglycones. The 3-O-β-D-glucoside of resveratrol showed the highest ORAC value among the stilbene glycosides tested, and pinostilbene had the highest value among the stilbene compounds. The tyrosinase inhibitory activities of the stilbene aglycones were improved by glycosylation; the stilbene glycosides had higher activities than the stilbene aglycones. Resveratrol 3-O-β-D-glucoside had the highest tyrosinase inhibitory activity among the stilbene compounds tested.
cAMP-dependent protein kinase involves calcium tolerance through the regulation of Prz1 inSchizosaccharomyces pombe
Authors: Matsuo Yasuhiro , Kawamukai Makoto 
Published: October 2016

AbstractThe cAMP-dependent protein kinase Pka1 is known as a regulator of glycogenesis, meiosis, and stress responses in Schizosaccharomyces pombe. We demonstrated that Pka1 is responsible for calcium tolerance. Loss of functional components of the PKA pathway such as Git3, Gpa2, Cyr1, and Pka1 yields a CaCl2-sensitive phenotype, while loss of Cgs1, a regulatory subunit of PKA, results in CaCl2 tolerance. Cytoplasmic distribution of Cgs1 and Pka1 is increased by the addition of CaCl2, suggesting that CaCl2 induces dissociation of Cgs1 and Pka1. The expression of Prz1, a transcriptional regulator in calcium homeostasis, is elevated in a pka1∆ strain and in a wild type strain under glucose-limited conditions. Accordingly, higher expression of Prz1 in the wild type strain results in a CaCl2-sensitive phenotype. These findings suggest that Pka1 is essential for tolerance to exogenous CaCl2, probably because the expression level of Prz1 needs to be properly regulated by Pka1.
Absorption of bovine angiogenin into peripheral blood of rats orally administered milk basic protein
Authors: Ishida Yuko , Yasueda Takehiko , Murakami Hiroki , Kato Ken 
Published: October 2016

Abstract
Bovine angiogenin is a major component of the bone resorption inhibitory activity of milk basic protein (MBP). The intestinal absorption of bovine angiogenin was investigated in a rat model, where it was detected in an intact form in the peripheral blood after the oral administration of MBP. This finding demonstrates that orally administered bovine angiogenin is absorbed without being degraded.
Corrections to: “On the equivariant K-theory of the nilpotent cone in the general linear group”
Authors: Achar Pramod 
Published: October 2016

In the paper [P. Achar, On the equivariant

K
K

-theory of the nilpotent cone in the general linear group, Represent. Theory 8 (2004), 180–211], the author gave a combinatorial algorithm for computing the Lusztig–Vogan bijection for

G
L
(
n
,

C

)

GL(n,\mathbb {C})

. However, that paper failed to mention one easy case that may sometimes arise, making the description of the algorithm incomplete. This note fills in that gap.
Diagnostic and Prognostic Significance of Brief Limited Intermittent Psychotic Symptoms (BLIPS) in Individuals at Ultra High Risk
Authors: Fusar-Poli Paolo , Cappucciati Marco , De Micheli Andrea , Rutigliano Grazia , Bonoldi Ilaria , Tognin Stefania , Ramella-Cravaro Valentina , Castagnini Augusto , McGuire Philip 
Published: October 2016

Abstract

Background
Brief Limited Intermittent Psychotic Symptoms (BLIPS) are key inclusion criteria to define individuals at ultra high risk for psychosis (UHR). Their diagnostic and prognostic significance is unclear.

Objectives
To address the baseline diagnostic relationship between BLIPS and the ICD-10 categories and examine the longitudinal prognostic impact of clinical and sociodemographic factors.

Methods
Prospective long-term study in UHR individuals meeting BLIPS criteria. Sociodemographic and clinical data, including ICD-10 diagnoses, were automatically drawn from electronic health records and analyzed using Kaplan–Meier failure function (1-survival), Cox regression models, bootstrapping methods, and Receiver Operating Characteristics (ROC) curve.

Results
Eighty BLIPS were included. At baseline, two-thirds (68%) of BLIPS met the diagnostic criteria for ICD-10 Acute and Transient Psychotic Disorder (ATPD), most featuring schizophrenic symptoms. The remaining individuals met ICD-10 diagnostic criteria for unspecified nonorganic psychosis (15%), mental and behavioral disorders due to use of cannabinoids (11%), and mania with psychotic symptoms (6%). The overall 5-year risk of psychosis was 0.54. Recurrent episodes of BLIPS were relatively rare (11%) but associated with a higher risk of psychosis (hazard ratio [HR] 3.98) than mono-episodic BLIPS at the univariate analysis. Multivariate analysis revealed that seriously disorganizing or dangerous features increased greatly (HR = 4.39) the risk of psychosis (0.89 at 5-year). Bootstrapping confirmed the robustness of this predictor (area under the ROC = 0.74).

Conclusions
BLIPS are most likely to fulfill the ATPD criteria, mainly acute schizophrenic subtypes. About half of BLIPS cases develops a psychotic disorder during follow-up. Recurrent BLIPS are relatively rare but tend to develop into psychosis. BLIPS with seriously disorganizing or dangerous features have an extreme high risk of psychosis.
An Index Case of Concomitant Tumoral and Ichthyosiform Mycosis Fungoides–Like Presentation of Chronic Adult T-cell Leukemia/Lymphoma Associated With Upregulation of TOX
Authors: Nguyen Giang Huong , Wang James Y. , Hymes Kenneth B. , Magro Cynthia M. 
Published: October 2016

Abstract:
Adult T-cell leukemia/lymphoma (ATLL) is a rare and often aggressive lymphoid malignancy known to be associated with human T-cell lymphotropic virus type 1. There are 2 broad categories: acute and chronic. In the acute category, there is a leukemic and a lymphomatous variant, whereas in the designated “chronic” form, there is mild peripheral blood lymphocytosis. The intermediate “smoldering” category is without peripheral blood lymphocytosis with only discernible skin involvement. We present a 68-year-old human T-cell lymphotropic virus type 1 seropositive female with a mild peripheral blood atypical lymphocytosis who had indurated nodules on her hands of 2 years duration and a new scaly ichthyosiform eruption on her lower extremities. Histopathologic examination of the hand biopsy revealed coalescing nodules of large atypical noncerebriform lymphocytes with focal areas of epidermotropism. Phenotypically, the infiltrate was positive for β-F1, CD2, CD4, CD5, CD7, Foxp3, and CD25. In both biopsies, there was striking upregulation of TOX (thymocyte selection–associated high mobility group box factor) in the nuclei of neoplastic cells. The second biopsy taken from the ichthyotic patch on the patient's left leg showed a subtle pattern of epidermal infiltration by atypical noncerebriform lymphocytes and a distinct compact scale consistent with the clinical picture of ichthyosis. The histopathologic appearance was that of a yet undescribed ichthyosiform mycosis fungoides–like presentation of chronic ATLL. In addition, the observed upregulation of nuclear TOX may play an oncogenic role in ATLL. The course to date in this patient has been relatively indolent, although the patients believe that large cell transformation could portend more aggressive disease.