bluuebunny/crossref_metadata_2025 huggingface dataset:
The genome—seeing it clearly now
Authors: Larson Daniel R. , Misteli Tom
Published: July 2017

Genome architecture is revealed with electron tomography
Robot-driven downward pelvic pull to improve crouch gait in children with cerebral palsy
Authors: Kang J. , Martelli D. , Vashista V. , Martinez-Hernandez I. , Kim H. , Agrawal S. K.
Published: July 2017

Robotic training of children with crouch gait improved posture and walking by enhancing muscle strength and coordination.
Investigation of Respiratory Syncytial Virus Outbreak on an Adult Stem Cell Transplant Unit by Use of Whole-Genome Sequencing
Authors: Zhu Yijun , Zembower Teresa R. , Metzger Kristen E. , Lei Zhengdeng , Green Stefan J. , Qi Chao
Published: July 2017

A viral whole-genome sequencing (WGS) strategy, based on PCR amplification followed by next-generation sequencing, was used to investigate a nosocomial respiratory syncytial virus-B (RSV-B) outbreak in a hematology-oncology and stem cell transplant unit. RSV-B genomes from 16 patients and health care workers (HCWs) suspected to be involved in the outbreak were compared to RSV-B genomes that were acquired from outpatients during the same time period but epidemiologically unrelated to the outbreak. Phylogenetic analysis of the whole genome identified a cluster of 11 patients and HCWs who had an identical RSV-B strain which was clearly distinct from strains recovered from individuals unrelated to the outbreak. Sequence variation of the glycoprotein (G) gene alone was insufficient to distinguish the outbreak strains from the outbreak-unrelated strains, thereby demonstrating that WGS is valuable for local outbreak investigation.
Rapid Detection of Bacillus anthracis Bloodstream Infections by Use of a Novel Assay in the GeneXpert System
Authors: Banada Padmapriya P. , Deshpande Srinidhi , Russo Riccardo , Singleton Eric , Shah Darshini , Patel Bhavana , Burday Michele , Koshy Ranie , Wang Qing , Jones Martin , Gall Alexander , Lokhov Sergey , Kwiatkowski Robert , Persing David , Connell Nancy , Alland David
Published: July 2017

Bacillus anthracis
is a tier 1 select agent with the potential to quickly cause severe disease. Rapid identification of this pathogen may accelerate treatment and reduce mortality in the event of a bioterrorism attack. We developed a rapid and sensitive assay to detect
B. anthracis
bacteremia using a system that is suitable for point-of-care testing. A filter-based cartridge that included both sample processing and PCR amplification functions was loaded with all reagents needed for sample processing and multiplex nested PCR. The assay limit of detection (LOD) and dynamic range were determined by spiking
B. anthracis
DNA into individual PCR mixtures and
B. anthracis
CFU into human blood. One-milliliter blood samples were added to the filter-based detection cartridge and tested for
B. anthracis
on a GeneXpert instrument. Assay specificity was determined by testing blood spiked with non-anthrax bacterial isolates or by testing blood samples drawn from patients with concurrent non-
B. anthracis
bacteremia or nonbacteremic controls. The assay LODs were 5 genome equivalents per reaction and 10 CFU/ml blood for both the
B. anthracis
Sterne and V1B strains. There was a 6-log
10
dynamic range. Assay specificity was 100% for tests of non-
B. anthracis
bacterial isolates and patient blood samples. Assay time was less than 90 min. This automated system suitable for point-of-care detection rapidly identifies
B. anthracis
directly from blood with high sensitivity. This assay might lead to early detection and more rapid therapy in the event of a bioterrorism attack.
Genetic Stability of Parainfluenza Virus 5-Vectored Human Respiratory Syncytial Virus Vaccine Candidates after
In Vitro
and
In Vivo
Passage
Authors: Phan Shannon I. , Adam Carolyn M. , Chen Zhenhai , Citron Michael , Liang Xiaoping , Espeseth Amy S. , Wang Dai , He Biao
Published: July 2017

Human respiratory syncytial virus (RSV) is the leading etiologic agent of lower respiratory tract infections in children, but no licensed vaccine exists. Previously, we developed two parainfluenza virus 5 (PIV5)-based RSV vaccine candidates that protect mice against RSV challenge. PIV5 was engineered to express either the RSV fusion protein (F) or the RSV major attachment glycoprotein (G) between the hemagglutinin-neuraminidase (HN) and RNA-dependent RNA polymerase (L) genes of the PIV5 genome [PIV5-RSV-F (HN-L) and PIV5-RSV-G (HN-L), respectively]. To investigate the stability of the vaccine candidates
in vitro
, they were passaged in Vero cells at high and low multiplicities of infection (MOIs) for 11 generations and the genome sequences, growth kinetics, and protein expression of the resulting viruses were compared with those of the parent viruses. Sporadic mutations were detected in the consensus sequences of the viruses after high-MOI passages, and mutation rates increased under low-MOI-passage conditions. None of the mutations abolished antigen expression. Increased numbers of mutations correlated with increased growth rates
in vitro
, indicating that the viruses evolved through the course of serial passages. We also examined the
in vivo
stability of the vaccine candidates after a single passage in African green monkeys. No mutations were detected in the consensus sequences of viruses collected from the bronchoalveolar lavage (BAL) fluid of the animals.
In vivo
, mutations in RSV G and PIV5 L were found in individual isolates of PIV5-RSV-G (HN-L), but plaque isolates of PIV5-RSV-F (HN-L) had no mutations. To improve upon the PIV5-RSV-F (HN-L) candidate, additional vaccine candidates were generated in which the gene for RSV F was inserted into earlier positions in the PIV5 genome. These insertions did not negatively impact the sequence stability of the vaccine candidates. The results suggest that the RSV F and G gene insertions are stable in the PIV5 genome. However, the function of the foreign gene insertion may need to be considered when designing PIV5-based vaccines.

IMPORTANCE
The genetic stability of live viral vaccines is important for safety and efficacy. PIV5 is a promising live viral vector and has been used to develop vaccines. In this work, we examined the genetic stability of a PIV5-based RSV vaccine
in vitro
and
in vivo
. We found that insertions of foreign genes, such as the RSV F and G genes, were stably maintained in the PIV5 genome and there was no mutation that abolished the expression of RSV F or G. Interestingly, the function of the inserted gene may have an impact on PIV5 genome stability.
A Domain of Herpes Simplex Virus pU
L
33 Required To Release Monomeric Viral Genomes from Cleaved Concatemeric DNA
Authors: Yang Kui , Dang Xiaoqun , Baines Joel D.
Published: July 2017

Monomeric herpesvirus DNA is cleaved from concatemers and inserted into preformed capsids through the actions of the viral terminase. The terminase of herpes simplex virus (HSV) is composed of three subunits encoded by U
L
15, U
L
28, and U
L
33. The U
L
33-encoded protein (pU
L
33) interacts with pU
L
28, but its precise role in the DNA cleavage and packaging reaction is unclear. To investigate the function of pU
L
33, we generated a panel of recombinant viruses with either deletions or substitutions in the most conserved regions of U
L
33 using a bacterial artificial chromosome system. Deletion of 11 amino acids (residues 50 to 60 or residues 110 to 120) precluded viral replication, whereas the truncation of the last 10 amino acids from the pU
L
33 C terminus did not affect viral replication or the interaction of pU
L
33 with pU
L
28. Mutations that replaced the lysine at codon 110 and the arginine at codon 111 with alanine codons failed to replicate, and the pU
L
33 mutant interacted with pU
L
28 less efficiently. Interestingly, genomic termini of the large (L) and small (S) components were detected readily in cells infected with these mutants, indicating that concatemeric DNA was cleaved efficiently. However, the release of monomeric genomes as assessed by pulsed-field gel electrophoresis was greatly diminished, and DNA-containing capsids were not observed. These results suggest that pU
L
33 is necessary for one of the two viral DNA cleavage events required to release individual genomes from concatemeric viral DNA.

IMPORTANCE
This paper shows a role for pU
L
33 in one of the two DNA cleavage events required to release monomeric genomes from concatemeric viral DNA. This is the first time that such a phenotype has been observed and is the first identification of a function of this protein relevant to DNA packaging other than its interaction with other terminase components.
Roles of Cellular NSF Protein in Entry and Nuclear Egress of Budded Virions of Autographa californica Multiple Nucleopolyhedrovirus
Authors: Guo Ya , Yue Qi , Gao Jinli , Wang Zhe , Chen Yun-Ru , Blissard Gary W. , Liu Tong-Xian , Li Zhaofei
Published: July 2017

In eukaryotic cells, the
s
oluble
N
-ethylmaleimide-
s
ensitive
f
actor (NSF)
a
ttachment protein
re
ceptor (SNARE) proteins comprise the minimal machinery that triggers fusion of transport vesicles with their target membranes. Comparative studies revealed that genes encoding the components of the SNARE system are highly conserved in yeast, insect, and human genomes. Upon infection of insect cells by the virus Autographa californica multiple nucleopolyhedrovirus (AcMNPV), the transcript levels of most SNARE genes initially were upregulated. We found that overexpression of dominant-negative (DN) forms of NSF or knockdown of the expression of NSF, the key regulator of the SNARE system, significantly affected infectious AcMNPV production. In cells expressing DN NSF, entering virions were trapped in the cytoplasm or transported to the nucleus with low efficiency. The presence of DN NSF also moderately reduced trafficking of the viral envelope glycoprotein GP64 to the plasma membrane but dramatically inhibited production of infectious budded virions (BV). Transmission electron microscopy analysis of infections in cells expressing DN NSF revealed that progeny nucleocapsids were retained in a perinuclear space surrounded by inner and outer nuclear membranes. Several baculovirus conserved (core) proteins (Ac76, Ac78, GP41, Ac93, and Ac103) that are important for infectious budded virion production were found to associate with NSF, and NSF was detected within the assembled BV. Together, these data indicate that the cellular SNARE system is involved in AcMNPV infection and that NSF is required for efficient entry and nuclear egress of budded virions of AcMNPV.

IMPORTANCE
Little is known regarding the complex interplay between cellular factors and baculoviruses during viral entry and egress. Here, we examined the cellular SNARE system, which mediates the fusion of vesicles in healthy cells, and its relation to baculovirus infection. Using a DN approach and RNA interference knockdown, we demonstrated that a general disruption of the SNARE machinery significantly inhibited the production of infectious BV of AcMNPV. The presence of a DN NSF protein resulted in low-efficiency entry of BV and the retention of progeny nucleocapsids in the perinuclear space during egress. Combined with these effects, we also found that several conserved (core) baculovirus proteins closely associate with NSF, and these results suggest their involvement in the egress of BV. Our findings are the first to demonstrate that the SNARE system is required for efficient entry of BV and nuclear egress of progeny nucleocapsids of baculoviruses.
Targeted Genome Sequencing Reveals Varicella-Zoster Virus Open Reading Frame 12 Deletion
Authors: Cohrs Randall J. , Lee Katherine S. , Beach Addilynn , Sanford Bridget , Baird Nicholas L. , Como Christina , Graybill Chiharu , Jones Dallas , Tekeste Eden , Ballard Mitchell , Chen Xiaomi , Yalacki David , Frietze Seth , Jones Kenneth , Lenac Rovis Tihana , Jonjić Stipan , Haas Jürgen , Gilden Don
Published: July 2017

The neurotropic herpesvirus varicella-zoster virus (VZV) establishes a lifelong latent infection in humans following primary infection. The low abundance of VZV nucleic acids in human neurons has hindered an understanding of the mechanisms that regulate viral gene transcription during latency. To overcome this critical barrier, we optimized a targeted capture protocol to enrich VZV DNA and cDNA prior to whole-genome/transcriptome sequence analysis. Since the VZV genome is remarkably stable, it was surprising to detect that VZV32, a VZV laboratory strain with no discernible growth defect in tissue culture, contained a 2,158-bp deletion in open reading frame (ORF) 12. Consequently, ORF 12 and 13 protein expression was abolished and Akt phosphorylation was inhibited. The discovery of the ORF 12 deletion, revealed through targeted genome sequencing analysis, points to the need to authenticate the VZV genome when the virus is propagated in tissue culture.

IMPORTANCEViruses isolated from clinical samples often undergo genetic modifications when cultured in the laboratory. Historically, VZV is among the most genetically stable herpesviruses, a notion supported by more than 60 complete genome sequences from multiple isolates and following multiplein vitropassages. However, application of enrichment protocols to targeted genome sequencing revealed the unexpected deletion of a significant portion of VZV ORF 12 following propagation in cultured human fibroblast cells. While the enrichment protocol did not introduce bias in either the virus genome or transcriptome, the findings indicate the need for authentication of VZV by sequencing when the virus is propagated in tissue culture.
Human Immunodeficiency Virus and Simian Immunodeficiency Virus Maintain High Levels of Infectivity in the Complete Absence of Mucin-Type O-Glycosylation
Authors: Termini James M. , Church Elizabeth S. , Silver Zachary A. , Haslam Stuart M. , Dell Anne , Desrosiers Ronald C.
Published: July 2017

A highly conserved threonine near the C terminus of gp120 of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) was investigated for its contributions to envelope protein function and virion infectivity. When this highly conserved Thr residue was substituted with anything other than serine (the other amino acid that can accept O-glycosylation), the resulting virus was noninfectious. We found that this Thr was critical for the association of gp120 with the virion and that amino acid substitution increased the amount of dissociated gp120 in the cell culture supernatant. When HIV virions were generated in cells overexpressing polypeptide
N
-acetylgalactosaminyltransferase 1 (GalNAcT1), viral infectivity was increased 2.5-fold compared to that of virus produced in wild-type HEK293T cells; infectivity was increased 8-fold when the Thr499Ser mutant was used. These infectivity enhancements were not observed when GalNAcT3 was used. Using HEK293T knockout cell lines totally devoid of the ability to perform O-linked glycosylation, we demonstrated production of normal levels of virions and normal levels of infectivity in the complete absence of O-linked carbohydrate. Our data indicate that O-glycosylation is not necessary for the natural replication cycle of HIV and SIV. Nonetheless, it remains theoretically possible that the repertoire of GalNAc transferase isoforms in natural target cells for HIV and SIV
in vivo
could result in O-glycosylation of the threonine residue in question and that this could boost the infectivity of virions beyond the levels seen in the absence of such O-glycosylation.

IMPORTANCE
Approximately 50% of the mass of the gp120 envelope glycoprotein of both HIV and SIV is N-linked carbohydrate. One of the contributions of this N-linked carbohydrate is to shield conserved peptide sequences from recognition by humoral immunity. This N-linked glycosylation is one of the reasons that primary isolates of HIV and SIV are so heavily resistant to antibody-mediated neutralization. Much less studied is any potential contribution from O-linked glycosylation. The literature on this topic to date is somewhat confusing and ambiguous. Our studies described in this report demonstrate unambiguously that O-linked glycosylation is not necessary for the natural replication cycle of HIV and SIV. However, the door is not totally closed because of the diversity of numerous GalNAc transferase enzymes that initiate O-linked carbohydrate attachment and the theoretical possibility that natural target cells for HIV and SIV
in vivo
could potentially complete such O-linked carbohydrate attachment to further increase infectivity.
Unremitting watery diarrhoea in early childhood period
Authors: Sintusek Palittiya , Thammarakcharoen Thanita , Shuangshoti Shanop , Vivatvakin Boosba
Published: July 2017

Chronic watery diarrhoea can be a presentation of gastrointestinal disease itself or a less-evident systemic disease. A 17-month-old boy presented with intractable diarrhoea, failure to gain weight, refractory tachycardia and severe hypertension. The ability to recognise and make a quick diagnosis of secretory type of diarrhoea dictated the outcome of patients with this ailment. Catecholamine hypersecretion was considered with the additional clues of refractory tachycardia and hypertension, a well-recognised phenomenon of neuroblastic tumours. A neuroblastic tumour can lead to vasoactive intestinal peptide (VIP) overexpression, which may result in secretory diarrhoea. In this situation, measurements of plasma VIP enabled crucial diagnosis. Imaging studies were used to identify and localise a neuroblastic tumour. Subsequent removal of the tumour was curative and led to the resolution of the symptoms.
Persistent air leak after pulmonary transplantation
Authors: Pearmain Laurence , Krysiak Piotr , Blaikley John , Alaloul Mohamed
Published: July 2017

A 59-year-old man with bilateral apical emphysema underwent a double lung transplant for end-stagechronic obstructive pulmonary disease leaving remnant right apical native tissue due to pleural adhesions. Initial postoperative course was uneventful until the chest drains were removed. This revealed a small pneumomediastinum, which progressively increased in size causing gross surgical emphysema. Re-insertion of the chest drain stabilised the patient so that the cause could be identified and corrected. Two bronchoscopies excluded anastomotic dehiscence as a cause. Therefore the subcostal wound was refashioned under video-assisted thoracoscopic surgery in case there was a defect. Unfortunately this also failed to halt the air leak; therefore another cause was sought. A multidisciplinary team meeting review of the radiology revealed that the patient's native bullous tissue was still inflated. Subsequent bronchoscopy revealed a native bronchial communication, due to variant anatomy, proximal to the surgical anastomosis. This was subsequently occluded using a bronchial valve allowing the patient to make a swift recovery.
Giant oesophageal gastrointestinal stromal tumour presenting with dyspnoea and clubbed fingers
Authors: Yamamoto Yurie , Sasaki Yosuke , Kougame Michio , Tochigi Naobumi
Published: July 2017

Gastrointestinal stromal tumours (GISTs) are mesenchymal neoplasms of the gastrointestinal tract originating from the interstitial cells of Cajal. Giant oesophageal GISTs are rare since the oesophagus is rarely the primary site of GISTs, and they are usually diagnosed early due to complaints such as dysphagia. We present the case of a giant oesophageal GIST presenting with prominent clubbing. The case underlined the diagnostic importance of clubbing and the careful consideration of chemotherapy. Although clubbed fingers associated with GISTs are rare, our experience demonstrates the importance of physicians’ recognition of clubbing as a paraneoplastic phenomenon for early diagnosis of malignancies since patients seldom notice their own clubbing by themselves. Chemotherapy using imatinib, an Bcr-Abl kinase inhibitor, is the standard option for unresectable giant GISTs. However, careful consideration must be made of the risk of complications associated with rapid mass reduction due to imatinib such as bleeding, oesophageal perforation and mediastinitis.
Optimising the surgical outcome in a case of post-traumatic cataract using ultrasound biomicroscopy
Authors: Chaniyara Manthan Hasmukhbhai , Pujari Amar , Aron Neelima , Sharma Namrata
Published: July 2017

A 12-year-old boy was brought with the chief complaint of diminution of vision in his left eye for the past 1 month. History revealed a blunt trauma to his left eye with a wooden stick 6â€‰weeks ago.Visual acuity was 20/20 and hand movement close to face in right and left eye, respectively, without any relative afferent pupillarydefect. Slit-lamp examination showed a total cataractous lens with signs suggestive of suspected posterior capsular (PC) defect. The PC defect was screened initially using B-scan ultrasound of the posterior segment, followed by confirmation of the same using ultrasound biomicroscopy. Left eye lens aspiration along with limited anterior vitrectomy followed by placement of multipiece intraocular lens in the sulcus was performed. Best-corrected visual acuity at 6 months of follow-up was 20/20.
Severe hypokalaemia as a cause of acute transient quadriparesis
Authors: Lybecker Martin Bell , Madsen Henrik Bjørnsgaard , Bruun Jens Meldgaard
Published: July 2017

Hypokalaemic paralysis covers a heterogeneous group of disorders caused either by an enhanced shift of potassium into the cells or following a significant renal or gastrointestinal loss of potassium. We present the case of a 48-year-old Caucasian man with paralysis of both upper and lower extremities. ECG showed sinus rhythm and characteristic changes of hypokalaemia with depression of the ST segment, prolonged QTc interval of 581ms and U waves seen as a small positive deflection at the T wave in the middle precordial leads. We suspected the cause of hypokalaemia leading to paralysis to be due to administration of high doses of furosemide without oral potassium supplementation coupled with regular use of insulin. Initial therapy included both oral and intravenous potassium replacement and close monitoring of cardiac rhythm and serum potassium levels. Twenty-four hours after admission, the potassium level had normalised and the patient slowly recovered and gained strength. The patient was discharged after 1 week of careful follow-up and did not experience any serious degree of rebound hyperkalaemia. At the time of discharge, all laboratory tests were normal and ECG revealed a normal sinus rhythm and normal QTc intervals.
Ecthyma gangrenosum caused byCitrobacter freundii
Authors: Hawkley Tyson , Chang David , Pollard Whitney , Ferraro David
Published: July 2017

A 55-year-old man undergoing chemotherapy for recurrent multiple myeloma presented with a 2-day history of bilateral lower leg rash with pain and oedema. On examination, there were numerous non-palpable retiform pruritic patches over both lower legs. Skin pnch biopsy demonstrated a diffuse interstitial neutrophilic infiltrate with necrosis. Peripheral blood and skin tissue cultures both isolatedCitrobacterfreundii, consistent with a rare form of ecthyma gangrenosum. The patient responded with appropriate antibiotic therapy and removal of medical port. He made a full recovery from this infectious complication of his underlying immunosuppression.
Responsiveness to cigarette prices by different racial/ethnic groups of US adults
Authors: Yao Tingting , Ong Michael K , Max Wendy , Keeler Courtney , Wang Yingning , Yerger Valerie B , Sung Hai-Yen
Published: July 2017

Objective

To evaluate the impact of cigarette prices on adult smoking for four US racial/ethnic groups: whites, African–Americans, Asians and Hispanics.

Methods

We analysed pooled cross-sectional data from the 2006/2007 and 2010/2011 Tobacco Use Supplement to the Current Population Survey (n=339 921 adults aged 18+) and cigarette price data from the Tax Burden on Tobacco. Using a two-part econometric model of cigarette demand that controlled for sociodemographic characteristics, state-level antismoking sentiment, local-level smoke-free air laws and monthly indicator, we estimated for each racial/ethnic group the price elasticities of smoking participation, smoking intensity and total demand for cigarettes.

Results

Smoking prevalence for whites, African–Americans, Asians and Hispanics during the study period was 18.3%, 16.1%, 8.2% and 11.3%, respectively. The price elasticity of smoking participation was statistically significant for whites, African–Americans, Asians and Hispanics at −0.26, –0.10, −0.42 and −0.11, respectively. The price elasticity of smoking intensity was statistically significant among whites (−0.22) and African–Americans (−0.17). Overall, the total price elasticity of cigarette demand was statistically significant for all racial/ethnic groups: 0.48 for whites, −0.27 for African–Americans, −0.22 for Asians and −0.15 for Hispanics.

Conclusions

Our results suggest that raising cigarette prices, such as via tobacco tax increases, would result in reduced cigarette consumption for all racial/ethnic groups. The magnitude of the effect and the impact on cessation and reduced smoking intensity differ across these groups.
Association between inspiratory muscle weakness and slowed oxygen uptake kinetics in patients with chronic obstructive pulmonary disease
Authors: Wolpat Andiara , Lima Francisco V. , Silva Fabiola M. , Tochetto Micheli , de Freitas Andressa , Grandi Tatiane , Rodrigues Leonardo , Paiva Verônica , Cipriano Gerson , Chiappa Adriana M. , Zago Julio , Chiappa Gaspar R.
Published: July 2017

Patients with chronic obstructive pulmonary disease (COPD) may have poor inspiratory muscle function, which reduces minute and alveolar ventilation, leading to increased hypoxemia and slow pulmonary oxygen uptake kinetics. However, little is known about the effect of inspiratory muscle weakness (IMW) on oxygen uptake kinetics in patients with COPD. Thus, we tested the hypothesis that COPD patients with IMW have slowed oxygen uptake kinetics. An observational study was conducted that included COPD patients with moderate to severe airflow limitation and a history of intolerance to exercise. Participants were divided into 2 groups: (IMW+; n = 22) (IMW–; n = 23) of muscle weakness. The maximal inspiratory, expiratory, and sustained inspiratory strength as well as the maximal endurance of the inspiratory muscles were lower in IMW+ patients (36 ± 9.5 cm H2O; 52 ± 14 cm H2O; 20 ± 6.5 cm H2O; 94 ± 84 s, respectively) than in IMW– patients (88 ± 12 cm H2O; 97 ± 28 cm H2O; 82.5 ± 54 cm H2O; 559 ± 92 s, respectively; p < 0.05). Moreover, the 6-min walk test and peak oxygen uptake were reduced in the IMW+ patients. During the constant work test, oxygen uptake kinetics were slowed in the IMW+ compared with IMW– patients (88 ± 29 vs 61 ± 18 s, p < 0.05). Our findings demonstrate that inspiratory muscle weakness in COPD is associated with slowed oxygen uptake kinetics, and thus, reduced functional capacity.
Back to America: tracking the origin of European introduced populations ofQuercus rubraL.
Authors: Merceron Nastasia R. , Leroy Thibault , Chancerel Emilie , Romero-Severson Jeanne , Borkowski Daniel S. , Ducousso Alexis , Monty Arnaud , Porté Annabel J. , Kremer Antoine
Published: July 2017

Quercus rubra has been introduced in Europe since the end of the 17th century. It is widely distributed today across this continent and considered invasive in some countries. Here, we investigated the distribution of genetic diversity of both native and introduced populations with the aim of tracing the origin of introduced populations. A large sampling of 883 individuals from 73 native and 38 European locations were genotyped at 69 SNPs. In the natural range, we found a continuous geographic gradient of variation with a predominant latitudinal component. We explored the existence of ancestral populations by performing Bayesian clustering analysis and found support for two or three ancestral genetic clusters. Approximate Bayesian Computations analyses based on these two or three clusters support recent extensive secondary contacts between them, suggesting that present-day continuous genetic variation resulted from recent admixture. In the introduced range, one main genetic cluster was not recovered in Europe, suggesting that source populations were preferentially located in the northern part of the natural distribution. However, our results cannot refute the introduction of populations from the southern states that did not survive in Europe.
Method to acquire regions of fruit, branch and leaf from image of red apple in orchard
Authors: Lv Jidong , Xu Liming
Published: July 2017

This work proposed a method to acquire regions of fruit, branch and leaf from red apple image in orchard. To acquire fruit image, R-G image was extracted from the RGB image for corrosive working, hole filling, subregion removal, expansive working and opening operation in order. Finally, fruit image was acquired by threshold segmentation. To acquire leaf image, fruit image was subtracted from RGB image before extracting 2G-R-B image. Then, leaf image was acquired by subregion removal and threshold segmentation. To acquire branch image, dynamic threshold segmentation was conducted in the R-G image. Then, the segmented image was added to fruit image to acquire adding fruit image which was subtracted from RGB image with leaf image. Finally, branch image was acquired by opening operation, subregion removal and threshold segmentation after extracting the R-G image from the subtracting image. Compared with previous methods, more complete image of fruit, leaf and branch can be acquired from red apple image with this method.
Archaeologies of the Contemporary World
Authors: Harrison Rodney , Breithoff Esther
Published: July 2017

Archaeologists have long been interested in contemporary material culture, but only recently has a dedicated subfield of archaeology of the contemporary world begun to emerge. Although it is concerned mainly with the archaeology of the early to mid-twentieth and twenty-first centuries, in its explicit acknowledgment of the contemporary archaeological record as multi-temporal, the subfield is not defined by a focus on a specific time period so much as a particular disposition toward time, material things, the archaeological process, and its politics. This article considers how the subfield might be characterized by its approaches to particular sources and its current and emerging thematic foci. A significant point of debate concerns the role of archaeology as a discipline through which to explore ongoing, contemporary sociomaterial practices—is archaeology purely concerned with the abandoned and the ruined, or can it also provide a means by which to engage with and illuminate ongoing, contemporary, and future sociomaterial practices?
Humans and Animals in Northern Regions
Authors: Anderson David G.
Published: July 2017

This review weighs the importance of human–animal sociality in Northern ethnographies through an examination of key concepts such as totemism, ideas of the entitlement, and domestication. It shows how classic narratives of cultural evolution are linked to conservation discourse, whereas current theoretical conversations such as the “ontological turn” are rooted in older idioms of liberal egalitarianism. Using a broad comparative approach with literature from all parts of the circumpolar North, this review weighs the effect of older metaphors on the discipline and suggests that a focus on landscape sociality—or sentient ecology—would best represent Northern situations and stories.
The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs
Authors: Borges Adair L. , Davidson Alan R. , Bondy-Denomy Joseph
Published: July 2017

Bacteria and archaea use CRISPR-Cas adaptive immune systems to defend themselves from infection by bacteriophages (phages). These RNA-guided nucleases are powerful weapons in the fight against foreign DNA, such as phages and plasmids, as well as a revolutionary gene editing tool. Phages are not passive bystanders in their interactions with CRISPR-Cas systems, however; recent discoveries have described phage genes that inhibit CRISPR-Cas function. More than 20 protein families, previously of unknown function, have been ascribed anti-CRISPR function. Here, we discuss how these CRISPR-Cas inhibitors were discovered and their modes of action were elucidated. We also consider the potential impact of anti-CRISPRs on bacterial and phage evolution. Finally, we speculate about the future of this field.
Cross talk between increased intracellular zinc (Zn2+) and accumulation of reactive oxygen species in chemical ischemia
Authors: Slepchenko Kira G. , Lu Qiping , Li Yang V.
Published: July 2017

Both zinc (Zn2+) and reactive oxygen species (ROS) have been shown to accumulate during hypoxic-ischemic stress and play important roles in pathological processes. To understand the cross talk between the two of them, here we studied Zn2+ and ROS accumulation by employing fluorescent probes in HeLa cells to further the understanding of the cause and effect relationship of these two important cellular signaling systems during chemical-ischemia, stimulated by oxygen and glucose deprivation (OGD). We observed two Zn2+ rises that were divided into four phases in the course of 30 min of OGD. The first Zn2+ rise was a transient, which was followed by a latent phase during which Zn2+ levels recovered; however, levels remained above a basal level in most cells. The final phase was the second Zn2+ rise, which reached a sustained plateau called Zn2+ overload. Zn2+ rises were not observed when Zn2+ was removed by TPEN (a Zn2+ chelator) or thapsigargin (depleting Zn2+ from intracellular stores) treatment, indicating that Zn2+ was from intracellular storage. Damaging mitochondria with FCCP significantly reduced the second Zn2+ rise, indicating that the mitochondrial Zn2+ accumulation contributes to Zn2+ overload. We also detected two OGD-induced ROS rises. Two Zn2+ rises preceded two ROS rises. Removal of Zn2+ reduced or delayed OGD- and FCCP-induced ROS generation, indicating that Zn2+ contributes to mitochondrial ROS generation. There was a Zn2+-induced increase in the functional component of NADPH oxidase, p47phox, thus suggesting that NADPH oxidase may mediate Zn2+-induced ROS accumulation. We suggest a new mechanism of cross talk between Zn2+ and mitochondrial ROS through positive feedback processes that eventually causes excessive free Zn2+ and ROS accumulations during the course of ischemic stress.
Effects of different input pressure waveforms on the carotid sinus baroreflex-mediated sympathetic arterial pressure response in rats
Authors: Kawada Toru , Shimizu Shuji , Yamamoto Hiromi , Miyamoto Tadayoshi , Kamiya Atsunori , Shishido Toshiaki , Sugimachi Masaru
Published: July 2017

Although the pulsatility of an input pressure is an important factor that determines the arterial baroreflex responses, whether the difference in the input waveforms can meaningfully affect the baroreflex function remains unknown. This study aimed to compare baroreflex responses between two distinct pressure waveforms: a forward saw wave (FSW) and a backward saw wave (BSW). In seven anesthetized rats, carotid sinus pressure was exposed to the FSW or the BSW with a mean of 120 mmHg, pulse pressure of 40 mmHg, and pulse frequency of 1 Hz. Changes in efferent sympathetic nerve activity (SNA) and arterial pressure (AP) during six consecutive saw wave trials (FSW1, BSW1, FSW2, BSW2, FSW3, and BSW3) were examined. The steady-state SNA value during FSW1 was 91.1 ± 1.9%, which was unchanged during FSW2 and FSW3 but significantly increased during BSW1 (106.6 ± 3.4%, P < 0.01), BSW2 (110.6 ± 2.5%, P < 0.01), and BSW3 (111.6 ± 2.3%, P < 0.01). The steady-state AP value during FSW1 was 98.2 ± 8.1 mmHg, which was unchanged during FSW2 and FSW3 but significantly increased during BSW1 (106.7 ± 7.4 mmHg, P < 0.01), BSW2 (105.6 ± 7.8 mmHg, P < 0.01), and BSW3 (103.8 ± 7.2 mmHg, P < 0.05). In conclusion, the FSW was more effective than the BSW in reducing mean SNA and AP. The finding could be applied to designing an artificial pulsatile pressure such as that generated by left ventricular assist devices.

NEW & NOTEWORTHY This study examined whether the waveforms of an input pressure alone can affect the baroreflex function by using a forward saw wave and a backward saw wave with the same mean pressure, pulse pressure, and pulse frequency. The forward saw wave was more effective than the backward saw wave in reducing sympathetic nerve activity and arterial pressure. The finding could be applied to designing an artificial pulsatile pressure such as that generated by left ventricular assist devices.
Energy cost of running instability evaluated with wearable trunk accelerometry
Authors: Schütte Kurt H. , Sackey Saint , Venter Rachel , Vanwanseele Benedicte
Published: July 2017

Maintaining stability under dynamic conditions is an inherent challenge to bipedal running. This challenge may impose an energetic cost (Ec) thus hampering endurance running performance, yet the underlying mechanisms are not clear. Wireless triaxial trunk accelerometry is a simple tool that could be used to unobtrusively evaluate these mechanisms. Here, we test a cost of instability hypothesis by examining the contribution of trunk accelerometry-based measures (triaxial root mean square, step and stride regularity, and sample entropy) to interindividual variance in Ec (J/m) during treadmill running. Accelerometry and indirect calorimetry data were collected concurrently from 30 recreational runners (16 men; 14 women) running at their highest steady-state running speed (80.65 ± 5.99% V̇o2max). After reducing dimensionality with factor analysis, the effect of dynamic stability features on Ec was evaluated using hierarchical multiple regression analysis. Three accelerometry-based measures could explain an additional 10.4% of interindividual variance in Ec after controlling for body mass, attributed to anteroposterior stride regularity (5.2%), anteroposterior root mean square ratio (3.2%), and mediolateral sample entropy (2.0%). Our results lend support to a cost of instability hypothesis, with trunk acceleration waveform signals that are 1) more consistent between strides anteroposterioly, 2) larger in amplitude variability anteroposterioly, and 3) more complex mediolaterally and are energetically advantageous to endurance running performance. This study shows that wearable trunk accelerometry is a useful tool for understanding the Ec of running and that running stability is important for economy in recreational runners.

NEW & NOTEWORTHY This study evaluates and more directly lends support to a cost of instability hypothesis between runners. Moreover, this hypothesis was tested using a minimalist setup including a single triaxial trunk mounted accelerometer, with potential transferability to biomechanical and performance analyses in typical outdoor settings.
A Study of Time Series Model for Predicting Jute Yarn Demand: Case Study
Authors: Karmaker C. L. , Halder P. K. , Sarker E.
Published: July 2017

In today’s competitive environment, predicting sales for upcoming periods at right quantity is very crucial for ensuring product availability as well as improving customer satisfaction. This paper develops a model to identify the most appropriate method for prediction based on the least values of forecasting errors. Necessary sales data of jute yarn were collected from a jute product manufacturer industry in Bangladesh, namely, Akij Jute Mills, Akij Group Ltd., in Noapara, Jessore. Time series plot of demand data indicates that demand fluctuates over the period of time. In this paper, eight different forecasting techniques including simple moving average, single exponential smoothing, trend analysis, Winters method, and Holt’s method were performed by statistical technique using Minitab 17 software. Performance of all methods was evaluated on the basis of forecasting accuracy and the analysis shows that Winters additive model gives the best performance in terms of lowest error determinants. This work can be a guide for Bangladeshi manufacturers as well as other researchers to identify the most suitable forecasting technique for their industry.
CVD-Graphene-Based Flexible, Thermoelectrochromic Sensor
Authors: Januszko Adam , Iwan Agnieszka , Maleczek Stanislaw , Przybyl Wojciech , Pasternak Iwona , Krajewska Aleksandra , Strupinski Wlodzimierz
Published: July 2017

The main idea behind this work was demonstrated in a form of a new thermoelectrochromic sensor on a flexible substrate using graphene as an electrically reconfigurable thermal medium (TEChrom™). Our approach relies on electromodulation of thermal properties of graphene on poly(ethylene terephthalate) (PET) via mechanical destruction of a graphene layer. Graphene applied in this work was obtained by chemical vapor deposition (CVD) technique on copper substrate and characterized by Raman and scanning tunneling spectroscopy. Electrical parameters of graphene were evaluated by the van der Pauw method on the transferred graphene layers onto SiO2 substrates by electrochemical delamination method. Two configurations of architecture of sensors, without and with the thermochromic layer, were investigated, taking into account the increase of voltage from 0 to 50 V and were observed by thermographic camera to define heat energy. Current-voltage characteristics obtained for the sensor with damaged graphene layer are linear, and the resistivity is independent from the current applied. The device investigated under 1000 W/m2 exhibited rise of resistivity along with increased temperature. Flexible thermoelectrochromic device with graphene presented here can be widely used as a sensor for both the military and civil monitoring.
On Heat and Mass Transfer within Thermally Shocked Region of Enhanced Geothermal System
Authors: Jahan Bakhsh Kamran , Nakagawa Masami , Arshad Mahmood , Dunnington Lucila
Published: July 2017

An Enhanced Geothermal System (EGS) is an artificially created geothermal reservoir formed by hydrofracturing hot dry rock. Thermal shock occurs when the cold water contacts the hot rock near the injection borehole, creating a network of small, disorganized, closely spaced micro cracks. As the cold-water injection continues, the hot rock cools down and the micro cracks coalesce, becoming a better-defined network of thermal fractures. Thermal fractures in an EGS reservoir are believed to improve reservoir performance by increasing the surface area for heat exchange and lowering flow impedance; however, it is difficult to precisely predict how they grow and affect the permeability of the reservoir. The goal of this paper is to provide an insight into the transport mechanisms within the thin, permeable, thermally shocked region of an EGS reservoir. COMSOL Multiphysics® is used to set up an indealized porous region with identical geometrical features at different domain scales to show the scale dependence of heat and mass transport in the initial microscale crack network and in the later coalesced thermal fractures. This research shows the importance of EGS maturity in determining how heat and mass are transferred and how to select appropriate analytical tools for different stages of development.
Diosmin Attenuates Methotrexate‐Induced Hepatic, Renal, and Cardiac Injury: A Biochemical and Histopathological Study in Mice
Authors: Abdel-Daim Mohamed M. , Khalifa Hesham A. , Abushouk Abdelrahman Ibrahim , Dkhil Mohamed A. , Al-Quraishy Saleh A.
Published: July 2017

The current study was designed to investigate the beneficial role of diosmin, a biologically active flavonoid, against methotrexate‐ (MTX‐) induced hepatic, renal, and cardiac injuries in mice. Male Swiss albino mice received a single intraperitoneal injection of MTX (at 20 mg/kg, body weight) either alone or in combination with oral diosmin (at 50 or 100 mg/kg body weight, for 10 days). Serum was used to evaluate tissue injury markers, while hepatic, renal, and cardiac tissue samples were obtained for determination of antioxidant activity as well as histopathological examination. Diosmin treatment ameliorated the MTX‐induced elevation of serum alkaline phosphatase, aminotransferases, urea, creatinine, lactate dehydrogenase, and creatine kinases as well as plasma proinflammatory cytokines (interleukin‐1‐beta, interleukin‐6, and tumor necrosis factor‐alpha). Additionally, both diosmin doses significantly reduced tissue levels of malondialdehyde and nitric oxide and increased those of glutathione, glutathione peroxidase, glutathione reductase, glutathione S‐transferase, superoxide dismutase, and catalase, compared to the MTX‐intoxicated group. Histopathological examination showed that diosmin significantly minimized the MTX‐induced histological alterations and nearly restored the normal architecture of hepatic, renal, and cardiac tissues. Based on these findings, diosmin may be a promising agent for protection against MTX‐induced cytotoxicity in patients with cancer and autoimmune diseases.
Coal-Rock Recognition in Top Coal Caving Using Bimodal Deep Learning and Hilbert-Huang Transform
Authors: Zhang Guoxin , Wang Zengcai , Zhao Lei , Qi Yazhou , Wang Jinshan
Published: July 2017

This study employs the mechanical vibration and acoustic waves of a hydraulic support tail beam for an accurate and fast coal-rock recognition. The study proposes a diagnosis method based on bimodal deep learning and Hilbert-Huang transform. The bimodal deep neural networks (DNN) adopt bimodal learning and transfer learning. The bimodal learning method attempts to learn joint representation by considering acceleration and sound pressure modalities, which both contribute to coal-rock recognition. The transfer learning method solves the problem regarding DNN, in which a large number of labeled training samples are necessary to optimize the parameters while the labeled training sample is limited. A suitable installation location for sensors is determined in recognizing coal-rock. The extraction features of acceleration and sound pressure signals are combined and effective combination features are selected. Bimodal DNN consists of two deep belief networks (DBN), each DBN model is trained with related samples, and the parameters of the pretrained DBNs are transferred to the final recognition model. Then the parameters of the proposed model are continuously optimized by pretraining and fine-tuning. Finally, the comparison of experimental results demonstrates the superiority of the proposed method in terms of recognition accuracy.
Detection of Islet Cell Immune Reactivity with Low Glycemic Index Foods: Is This a Concern for Type 1 Diabetes?
Authors: Kharrazian Datis , Herbert Martha , Vojdani Aristo
Published: July 2017

Dietary management of autoimmune diabetes includes low glycemic foods classified from the glycemic index, but it does not consider the role that immunoreactive foods may play with the immunological etiology of the disease. We measured the reactivity of either monoclonal or polyclonal affinity-purified antibodies to insulin, insulin receptor alpha, insulin receptor beta, zinc transporter 8 (ZnT8), tyrosine phosphatase-based islet antigen 2 (IA2), and glutamic acid decarboxylase (GAD) 65 and 67 against 204 dietary proteins that are commonly consumed. Dietary protein determinants included unmodified (raw) and modified (cooked and roasted) foods, herbs, spices, food gums, brewed beverages, and additives. There was no immune reactivity between insulin or insulin receptor beta and dietary proteins. However, we identified strong to moderate immunological reactivity with antibodies against insulin receptor alpha, ZnT8, IA2, GAD-65, and GAD-67 with several dietary proteins. We also identified 49 dietary proteins found in foods classified as low glycemic foods with immune reactivity to autoimmune target sites. Laboratory analysis of immunological cross-reactivity between pancreas target sites and dietary proteins is the initial step necessary in determining whether dietary proteins may play a potential immunoreactive role in autoimmune diabetes.