bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiome Changes during Tuberculosis and Antituberculous Therapy
Authors: Hong Bo-Young , Maulén Nancy Paula , Adami Alexander J. , Granados Hector , Balcells María Elvira , Cervantes Jorge 
Published: September 2016

SUMMARY

The critical role of commensal microbiota in the human body has been increasingly recognized, and our understanding of its implications in human health and disease has expanded rapidly. The lower respiratory tract contains diverse communities of microbes known as lung microbiota, which are present in healthy individuals and in individuals with respiratory diseases. The dysbiosis of the airway microbiota in pulmonary tuberculosis (TB) may play a role in the pathophysiological processes associated with TB disease. Recent studies of the lung microbiome have pointed out changes in lung microbial communities associated with TB and other lung diseases and have also begun to elucidate the profound effects that antituberculous drug therapy can have on the human lung microbiome composition. In this review, the potential role of the human microbiome in TB pathogenesis and the changes in the human microbiome with
Mycobacterium tuberculosis
infection and TB therapy are presented and discussed.
Complete Genome Sequence of Kosakonia sacchari Strain BO-1, an Endophytic Diazotroph Isolated from a Sweet Potato
Authors: Shinjo Rina , Uesaka Kazuma , Ihara Kunio , Loshakova Kseniia , Mizuno Yuri , Yano Katsuya , Tanaka Aiko 
Published: September 2016

ABSTRACT

The complete genome sequence of the endophytic diazotroph
Kosakonia sacchari
, isolated from a sweet potato, was analyzed. The 4,902,106-bp genome with 53.7% G+C content comprises 4,638 open reading frames, including
nif
genes, 84 tRNAs, and seven complete rRNAs in a circular chromosome.
Draft Genome Sequences of 15 Isolates of Listeria monocytogenes Serotype 1/2a, Subgroup ST204
Authors: Allnutt Theodore R. , Bradbury Mark I. , Fanning Séamus , Chandry P. Scott , Fox Edward M. 
Published: September 2016

ABSTRACT

Listeria monocytogenes
sequence type 204 (ST204) strains have been isolated from a range of food, environmental, and clinical sources in Australia. This study describes the draft genome sequences of 15 isolates collected from meat and dairy associated sources.
Genome Sequence of
Marinobacter
sp. Strain MCTG268 Isolated from the Cosmopolitan Marine Diatom
Skeletonema costatum
Authors: Gutierrez Tony , Whitman William B. , Huntemann Marcel , Copeland Alex , Chen Amy , Kyrpides Nikos , Markowitz Victor , Pillay Manoj , Ivanova Natalia , Mikhailova Natalia , Ovchinnikova Galina , Andersen Evan , Pati Amrita , Stamatis Dimitrios , Reddy T. B. K. , Ngan Chew Yee , Chovatia Mansi , Daum Chris , Shapiro Nicole , Cantor Michael N. , Woyke Tanja 
Published: September 2016

ABSTRACT

Marinobacter
sp. strain MCTG268 was isolated from the cosmopolitan marine diatom
Skeletonema costatum
and can degrade oil hydrocarbons as sole sources of carbon and energy. Here, we present the genome sequence of this strain, which is 4,449,396 bp with 4,157 genes and an average G+C content of 57.0%.
Draft Genome Sequence of Tepidimonas taiwanensis Strain VT154-175
Authors: Valeriani Federica , Biagini Tommaso , Giampaoli Saverio , Crognale Silvia , Santoni Daniele , Romano Spica Vincenzo 
Published: September 2016

ABSTRACT

The slightly thermophilic bacterium
Tepidimonas taiwanensis
strain VT154-175 has been isolated from a hot spring in the area of Viterbo, Italy. The whole draft genome of 2.9 Mb obtained by paired-end next-generation sequencing and divided into 60 scaffolds is presented.
Draft Genome Sequence of Leptospira interrogans Serovar Bataviae Strain LepIMR 22 Isolated from a Rodent in Johor, Malaysia
Authors: Amran Fairuz , Mohd Khalid Mohd Khairul Nizam , Mohamad Saharuddin , Mat Ripen Adiratna , Ahmad Norazah , Goris Marga G. A. , Muhammad Ayu Haslin , Noor Halim Nurul Atiqah 
Published: September 2016

ABSTRACT

Leptospira interrogans
serovar Bataviae was recently identified as one of the persistent
Leptospira
serovars in Malaysia. Here, we report the draft genome sequence of the
L. interrogans
serovar Bataviae strain LepIMR 22 isolated from kidney of a rodent in Johor, Malaysia.
Complete Genome Sequence of a South Korean Isolate of
Habenaria mosaic virus
Authors: Igori Davaajargal , Lim Seungmo , Zhao Fumei , Baek Dasom , Moon Jae Sun 
Published: September 2016

ABSTRACT

Habenaria mosaic virus
(HaMV), a member of the genus
Potyvirus
in the family
Potyviridae
, was first discovered from
Habenaria radiata
in Japan
.
The complete genomic sequence of a South Korean isolate (PA1) of HaMV infecting
Plantago asiatica
L. was determined with high-throughput RNA sequencing.
Complete Genome Sequences of Neisseria gonorrhoeae with Coresistance to First-Line Antimicrobials
Authors: Bharat Amrita , Martin Irene , Demczuk Walter , Allen Vanessa , Haldane David , Hoang Linda , Mulvey Michael R. 
Published: September 2016

ABSTRACT

Neisseria gonorrhoeae
strains with coresistance to the first-line antimicrobial treatments azithromycin and ceftriaxone are an emerging public health threat. Here, we present the complete genome sequences of three strains of
N. gonorrhoeae
, including one susceptible strain and two strains with coresistance to ceftriaxone and azithromycin.
Draft Genome Sequence of Two Strains of Xanthomonas arboricola Isolated from
Prunus persica
Which Are Dissimilar to Strains That Cause Bacterial Spot Disease on
Prunus
spp
Authors: Garita-Cambronero Jerson , Palacio-Bielsa Ana , López María M. , Cubero Jaime 
Published: September 2016

ABSTRACT

The draft genome sequences of two strains of
Xanthomonas arboricola
, isolated from asymptomatic peach trees in Spain, are reported here. These strains are avirulent and do not belong to the same phylogroup as
X. arboricola
pv. pruni, a causal agent of bacterial spot disease of stone fruits and almonds.
Weight loss efficacy of a novel mobile Diabetes Prevention Program delivery platform with human coaching
Authors: Michaelides Andreas , Raby Christine , Wood Meghan , Farr Kit , Toro-Ramos Tatiana 
Published: September 2016

ObjectiveTo evaluate the weight loss efficacy of a novel mobile platform delivering the Diabetes Prevention Program.Research Design and Methods43 overweight or obese adult participants with a diagnosis of prediabetes signed-up to receive a 24-week virtual Diabetes Prevention Program with human coaching, through a mobile platform. Weight loss and engagement were the main outcomes, evaluated by repeated measures analysis of variance, backward regression, and mediation regression.ResultsWeight loss at 16 and 24 weeks was significant, with 56% of starters and 64% of completers losing over 5% body weight. Mean weight loss at 24 weeks was 6.58% in starters and 7.5% in completers. Participants were highly engaged, with 84% of the sample completing 9 lessons or more. In-app actions related to self-monitoring significantly predicted weight loss.ConclusionsOur findings support the effectiveness of a uniquely mobile prediabetes intervention, producing weight loss comparable to studies with high engagement, with potential for scalable population health management.
Fasting with diabetes: a prospective observational study
Authors: Noon Muhammad Jawad , Khawaja Haseeb Ahmad , Ishtiaq Osama , Khawaja Quratulain , Minhas Sana , Niazi Asfandyar Khan , Minhas Abdul Mannan Khan , Malhi Umar Rasool 
Published: September 2016

ObjectivesTo determine the proportion of diabetic patients who develop adverse glycaemic events when fasting regularly.DesignProspective observational study conducted at a tertiary care hospital in South Asia. Five hundred and twenty-three patients were assessed for eligibility, and 150 were included in the final analysis. Diabetic patients over 18 years of age who were willing to fast regularly and make a chart of their daily blood sugar levels were included in the study. The main outcome measures were hypoglycaemic and hyperglycaemic events. Frequencies and percentages were calculated for quantitative variables, while mean±SD were documented for qualitative variables. Relative risk was calculated as a measure of association.ResultsOf a total of 150 individuals, 10% experienced hypoglycaemia, while 3.3% reported hyperglycaemic episodes. Only 8.7% of the participants discontinued one or more fasts; however, none of them required hospitalisation. There is a negative association between a visit to a physician by diabetic patients before they begin to fast regularly and the risk of developing hypoglycaemia (relative risk 0.73).ConclusionsMany diabetic patients who fast regularly are at high risk of adverse glycaemic events. Most diabetics do not consult their physicians before fasting to adjust medications and lifestyle. Various strategies should be planned and implemented for the awareness and education of such patients to avoid adverse glycaemic events and subsequent complications.
Subclonal diversity arises early even in small colorectal tumours and contributes to differential growth fates
Authors: Sievers Chelsie K , Zou Luli S , Pickhardt Perry J , Matkowskyj Kristina A , Albrecht Dawn M , Clipson Linda , Bacher Jeffery W , Pooler B Dustin , Moawad Fouad J , Cash Brooks D , Reichelderfer Mark , Vo Tien N , Newton Michael A , Larget Bret R , Halberg Richard B 
Published: September 2016

Objective and designThe goal of the study was to determine whether the mutational profile of early colorectal polyps correlated with growth behaviour. The growth of small polyps (6–9 mm) that were first identified during routine screening of patients was monitored over time by interval imaging with CT colonography. Mutations in these lesions with known growth rates were identified by targeted next-generation sequencing. The timing of mutational events was estimated using computer modelling and statistical inference considering several parameters including allele frequency and fitness.ResultsThe mutational landscape of small polyps is varied both within individual polyps and among the group as a whole but no single alteration was correlated with growth behaviour. Polyps carried 0–3 pathogenic mutations with the most frequent being inAPC,KRAS/NRAS,BRAF,FBXW7andTP53. In polyps with two or more pathogenic mutations, allele frequencies were often variable, indicating the presence of multiple populations within a single tumour. Based on computer modelling, detectable mutations occurred at a mean polyp size of 30±35 crypts, well before the tumour is of a clinically detectable size.ConclusionsThese data indicate that small colon polyps can have multiple pathogenic mutations in crucial driver genes that arise early in the existence of a tumour. Understanding the molecular pathway of tumourigenesis and clonal evolution in polyps that are at risk for progressing to invasive cancers will allow us to begin to better predict which polyps are more likely to progress into adenocarcinomas and which patients are at greater risk of developing advanced disease.
On groups Gnk, braids and Brunnian braids
Authors: Kim S. , Manturov V. O. 
Published: September 2016

In [V. O. Manturov, arXiv:1501.05208v1 ], the second author defined the [Formula: see text]-free braid group with [Formula: see text] strands [Formula: see text]. These groups appear naturally as groups describing dynamical systems of [Formula: see text] particles in some “general position”. Moreover, in [V. O. Manturov and I. M. Nikonov, J. Knot Theory Ramification 24 (2015) 1541009] the second author and Nikonov showed that [Formula: see text] is closely related to classical braids. The authors showed that there are homomorphisms from the pure braids group on [Formula: see text] strands to [Formula: see text] and [Formula: see text] and they defined homomorphisms from [Formula: see text] to the free products of [Formula: see text]. That is, there are invariants for pure free braids by [Formula: see text] and [Formula: see text]. On the other hand in [D. A. Fedoseev and V. O. Manturov, J. Knot Theory Ramification 24(13) (2015) 1541005, 12 pages] Fedoseev and the second author studied classical braids with addition structures: parity and points on each strands. The authors showed that the parity, which is an abstract structure, has geometric meaning — points on strands. In [S. Kim, arXiv:submit/1548032], the first author studied [Formula: see text] with parity and points. the author constructed a homomorphism from [Formula: see text] to the group [Formula: see text] with parity. In the present paper, we investigate the groups [Formula: see text] and extract new powerful invariants of classical braids from [Formula: see text]. In particular, these invariants allow one to distinguish the non-triviality of Brunnian braids.
Facile synthesis of carbon sphere@Ni(OH)2and derivatives for high-performance supercapacitors
Authors: Le Qiujian , Wang Tian , Zhu Shijin , Zhang Junming , Zhang Yuxin 
Published: September 2016

Herein, Ni(OH)2on carbon sphere nanostructure together with its derivatives, including NiO on carbon sphere, yolk–shell structure of NiO on carbon sphere and hollow NiO, were prepared with precise control and then applied as supercapacitors. Among them, NiO on carbon sphere exhibits a high specific capacitance (270.4[Formula: see text]F g[Formula: see text] at 0.5[Formula: see text]A g[Formula: see text]), excellent rate performance (77.6% retention with 20-time current density increase) and good cycling stability (75.9% retention after 2000 cycles). The results indicate that carbon sphere plays a significant role in enhancing the electrical conductivity and electronic transportation process, ensuring the synergistic effects between carbon sphere and NiO shell.
HIV, Cocaine Use, and Hepatitis C Virus
Authors: Lucas Gregory M. , Atta Mohamed G. , Fine Derek M. , McFall Allison M. , Estrella Michelle M. , Zook Katie , Stein James H. 
Published: September 2016

Objective—
We assessed cross-sectional and longitudinal associations of 3 nontraditional cardiovascular disease risk factors—HIV, cocaine use, and chronic hepatitis C virus infection—with 3 validated markers of subclinical cardiovascular disease: carotid artery plaque, albuminuria, and aortic pulse wave velocity in a well-characterized cohort.

Approach and Results—

We measured carotid plaque at baseline and after 24 months, urine albumin/creatinine ratio every 6 months, and pulse wave velocity annually for up to 36 months in a predominantly black cohort of 292 participants (100 HIV negative and 192 HIV positive). Thirty-nine percent had chronic hepatitis C virus infection and 20%, 28%, and 52% were never, past, and current cocaine users, respectively. Sixteen percent, 47%, and 64% of those with none, 1 or 2, or all 3 nontraditional risk factors had ≥2 abnormal cardiovascular disease risk markers (
P
=0.001). In fully adjusted models that included all 3 nontraditional risk factors, HIV infection was independently associated with carotid plaque progression (increase in the number of anatomic segments with plaque), albuminuria (albumin–creatinine ratio >30 mg/g), albuminuria progression (doubling of albumin–creatinine ratio from baseline to a value >30 mg/g), and pulse wave velocity. Cocaine use was associated with an ≈3-fold higher odds of carotid plaque at baseline, and hepatitis C virus infection was significantly associated with a higher risk of carotid plaque progression.

Conclusions—
These results suggest that HIV infection, cocaine use, and hepatitis C virus infection are important nontraditional risk factors for cardiovascular disease and highlight the need to understand the distinct and overlapping mechanisms of the associations.
Cardiac and Carotid Markers Link With Accelerated Brain Atrophy
Authors: Sabayan Behnam , van Buchem Mark A. , Sigurdsson Sigurdur , Zhang Qian , Meirelles Osorio , Harris Tamara B. , Gudnason Vilmundur , Arai Andrew E. , Launer Lenore J. 
Published: September 2016

Objective—
Pathologies in the heart–brain axis might, independently or in combination, accelerate the process of brain parenchymal loss. We aimed to investigate the association of serum N-terminal brain natriuretic peptide (NT-proBNP), as a marker of cardiac dysfunction, and carotid intima media thickness (CIMT), as a marker of carotid atherosclerosis burden, with structural brain changes.

Approach and Results—
In the longitudinal population-based AGES–Reykjavik study (Age, Gene/Environment Susceptibility–Reykjavik), we included 2430 subjects (mean age, 74.6 years; 41.4% men) with baseline data on NT-proBNP and CITM (assessed by ultrasound imaging). Participants underwent a high-resolution brain magnetic resonance imaging at baseline and 5 years later to assess total brain (TBV), gray matter, and white matter volumes. Each unit higher log-transformed NT-proBNP was associated with 3.6 mL (95% confidence interval [CI], −6.0 to −1.1) decline in TBV and 3.5 mL (95% CI, −5.7 to −1.3) decline in gray matter volume. Likewise, each millimeter higher CIMT was associated with 10.8 mL (95% CI, −17.3 to −4.2) decline in TBV and 8.6 mL (95% CI, −14.4 to −2.8) decline in gray matter volume. There was no association between NT-proBNP and CIMT and changes in white matter volume. Compared with participants with low NT-proBNP and CIMT, participants with both high NT-proBNP and CIMT had 3.8 mL (95% CI, −6.0 to −1.6) greater decline in their TBV and 4 mL (95% CI, −6.0 to −2.0) greater decline in GMW. These associations were independent of sociodemographic and cardiovascular factors.

Conclusions—
Older subjects with both cardiac dysfunction and carotid atherosclerosis are at an increased risk for brain parenchymal loss. Accumulated pathologies in the heart–brain axis might accelerate brain atrophy.
Coronary Plaque Characteristics Associated With Reduced TIMI (Thrombolysis in Myocardial Infarction) Flow Grade in Patients With ST-Segment–Elevation Myocardial Infarction
Authors: Higuma Takumi , Soeda Tsunenari , Yamada Masahiro , Yokota Takashi , Yokoyama Hiroaki , Nishizaki Fumie , Xing Lei , Yamamoto Erika , Bryniarski Krzysztof , Dai Jiannan , Lee Hang , Okumura Ken , Jang Ik-Kyung 
Published: September 2016

Background—
Previous studies reported that reduced TIMI (Thrombolysis in Myocardial Infarction) flow grade before procedure was associated with worse clinical outcomes in patients with ST-segment–elevation myocardial infarction undergoing primary percutaneous coronary intervention. The aim of this study was to identify specific morphological characteristics of the culprit plaque associated with poor TIMI flow grade at baseline in patients with ST-segment–elevation myocardial infarction using both optical coherence tomography and intravascular ultrasound.

Methods and Results—

A total of 111 ST-segment–elevation myocardial infarction patients who underwent percutaneous coronary intervention within 24 hours of symptom onset were included. Both optical coherence tomography and intravascular ultrasound were performed after thrombectomy. Patients were divided into 2 groups according to preprocedural TIMI flow grade (TIMI 0–1 [n=82] and TIMI 2–3 [n=29]). Patients with preprocedural TIMI 0 to 1 had a greater lipid arc (
P
=0.037), a longer lipid length (
P
=0.021), and a greater lipid index (
P
=0.007) determined by optical coherence tomography and a larger external elastic membrane cross-sectional area (
P
=0.030) and plaque plus media cross-sectional area (
P
=0.030) determined by intravascular ultrasound, compared with patients with preprocedural TIMI 2 to 3.

Conclusions—
ST-segment–elevation myocardial infarction patients with reduced TIMI flow grade at baseline have greater lipid burden, larger vessel sizes, and larger plaque areas.
Ethnic Comparison of 30-Day Potentially Preventable Readmissions After Stroke in Hawaii
Authors: Nakagawa Kazuma , Ahn Hyeong Jun , Taira Deborah A. , Miyamura Jill , Sentell Tetine L. 
Published: September 2016

Background and Purpose—
Ethnic disparities in readmission after stroke have been inadequately studied. We sought to compare potentially preventable readmissions (PPR) among a multiethnic population in Hawaii.

Methods—
Hospitalization data in Hawaii from 2007 to 2012 were assessed to compare ethnic differences in 30-day PPR after stroke-related hospitalizations. Multivariable models using logistic regression were performed to assess the impact of ethnicity on 30-day PPR after controlling for age group (<65 and ≥65 years), sex, insurance, county of residence, substance use, history of mental illness, and Charlson Comorbidity Index.

Results—
Thirty-day PPR was seen in 840 (8.4%) of 10 050 any stroke-related hospitalizations, 712 (8.7%) of 8161 ischemic stroke hospitalizations, and 128 (6.8%) of 1889 hemorrhagic stroke hospitalizations. In the multivariable models, only the Chinese ethnicity, compared with whites, was associated with 30-day PPR after any stroke hospitalizations (odds ratio [OR] [95% confidence interval {CI}], 1.40 [1.05–1.88]) and ischemic stroke hospitalizations (OR, 1.42 [CI, 1.04–1.96]). When considering only one hospitalization per individual, the impact of Chinese ethnicity on PPR after any stroke hospitalization (OR, 1.22 [CI, 0.89–1.68]) and ischemic stroke hospitalization (OR, 1.21 [CI, 0.86–1.71]) was attenuated. Other factors associated with 30-day PPR after any stroke hospitalizations were Charlson Comorbidity Index (per unit increase) (OR, 1.21 [CI, 1.18–1.24]), Medicaid (OR, 1.42 [CI, 1.07–1.88]), Hawaii county (OR, 0.78 [CI, 0.62–0.97]), and mental illness (OR, 1.37 [CI, 1.10–1.70]).

Conclusions—
In Hawaii, Chinese may have a higher risk of 30-day PPR after stroke compared with whites. However, this seems to be driven by the high number of repeated PPR within the Chinese ethnic group.
Preventive Suboccipital Decompressive Craniectomy for Cerebellar Infarction
Authors: Kim Myeong Jin , Park Sang Kyu , Song Jihye , Oh Se-yang , Lim Yong Cheol , Sim Sook Yong , Shin Yong Sam , Chung Joonho 
Published: September 2016

Background and Purpose—
No evidence is available on the benefits of preventive suboccipital decompressive craniectomy (SDC) for patients with cerebellar infarction. The purpose of this matched case–control study was to investigate whether preventive SDC was associated with good clinical outcomes in patients with cerebellar infarction and to evaluate its predisposing factors.

Methods—
Between March 2007 and September 2015, 28 patients underwent preventive SDC. We performed propensity score matching to establish a proper control group among 721 patients with cerebellar infarction during the same period. Group A (n=28) consists of those who underwent preventive SDC, and group B (n=56) consists of those who did not undergo preventive SDC. We analyzed and compared clinical outcomes between groups.

Results—

Clinical outcomes were better in group A than in group B at discharge (
P
=0.048) and 12-month follow-up (
P
=0.030). Group B had more deaths within 12 months than group A (log-rank,
P
<0.05). Logistic regression analysis showed that preventive SDC (odds ratio, 4.815;
P
=0.009) and the absence of brain stem infarction (odds ratio, 2.862;
P
=0.033) were independently associated with favorable outcomes (modified Rankin Scale score of 0–2) at 12-month follow-up.

Conclusions—
Favorable clinical outcomes including overall survival can be expected after preventive SDC in patients with a volume ratio between 0.25 and 0.33 and the absence of brain stem infarction. Among these patients, preventive SDC might be better than the best medical treatment alone.