bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating the population density of the Asian tapir (Tapirus indicus) in a selectively logged forest in Peninsular Malaysia
Authors: RAYAN D. Mark , MOHAMAD Shariff Wan , DORWARD Leejiah , AZIZ Sheema Abdul , CLEMENTS Gopalasamy Reuben , CHRISTOPHER Wong Chai Thiam , TRAEHOLT Carl , MAGINTAN David 
Published: August 2012

AbstractThe endangered Asian tapir (Tapirus indicus) is threatened by large‐scale habitat loss, forest fragmentation and increased hunting pressure. Conservation planning for this species, however, is hampered by a severe paucity of information on its ecology and population status. We present the first Asian tapir population density estimate from a camera trapping study targeting tigers in a selectively logged forest within Peninsular Malaysia using a spatially explicit capture–recapture maximum likelihood based framework. With a trap effort of 2496 nights, 17 individuals were identified corresponding to a density (standard error) estimate of 9.49 (2.55) adult tapirs/100 km2. Although our results include several caveats, we believe that our density estimate still serves as an important baseline to facilitate the monitoring of tapir population trends in Peninsular Malaysia. Our study also highlights the potential of extracting vital ecological and population information for other cryptic individually identifiable animals from tiger‐centric studies, especially with the use of a spatially explicit capture–recapture maximum likelihood based framework.
Identification of Predictors ofSalmonellaShedding in Adult Horses Presented for Acute Colic
Authors: Dallap Schaer B.L. , Aceto H. , Caruso M.A. , Brace M.A. 
Published: August 2012

BackgroundColic has been associated with shedding ofSalmonella. Horses with salmonellosis typically develop diarrhea, fever, and leukopenia. Overlooking additional predictors may result in failure to detect shedding horses and increase environmental contamination.ObjectivesEvaluate associations between signalment and clinicopathologic data during early hospitalization andSalmonellashedding in horses treated for acute colic.AnimalsHorses with acute colic admitted to a referral hospital. A total of 59 horses sheddingSalmonellacompared to 108Salmonella‐negative horses.MethodsRetrospective case‐control study evaluating patient andSalmonellaculture data. Associations between variables andSalmonellashedding were identified using logistic regression. Two multivariable models were developed pertaining to (1) information available within 24 hours of admission and (2) clinical findings that developed later during hospitalization.ResultsVariables retained for multivariable model 1 indicated that Warmbloods and Arabians had increased odds for sheddingSalmonella, as did horses requiring surgery (OR, 2.52; 95% CI, 1.10–5.75) or having more severe gastrointestinal disease (OR, 2.59; 95% CI, 1.08–6.20). Retained variables for model 2 demonstrated that horses that were treated surgically (OR, 1.60; 95% CI, 0.70–3.62), developed fever >103°F (OR, 2.70; 95% CI, 0.92–7.87), had abnormal leukocyte count (OR, 1.38; 95% CI, 0.61–3.09), or became inappetent and lethargic (OR, 16.69; 95% CI, 4.08–68.24) had increased odds for sheddingSalmonella.Conclusions and Clinical ImportanceIn horses with acute colic that present without signs of diarrhea, fever, or leukopenia, additional predictors associated with sheddingSalmonellacould be used to more promptly identify horses likely to shed organisms.
SGLT2 inhibitors: a promising new therapeutic option for treatment of type 2 diabetes mellitus
Authors: Misra Monika 
Published: August 2012

Abstract

Background
Hyperglycemia is an important pathogenic component in the development of microvascular and macrovascular complications in type 2 diabetes mellitus. Inhibition of renal tubular glucose reabsorption that leads to glycosuria has been proposed as a new mechanism to attain normoglycemia and thus prevent and diminish these complications. Sodium glucose cotransporter 2 (SGLT2) has a key role in reabsorption of glucose in kidney. Competitive inhibitors of SGLT2 have been discovered and a few of them have also been advanced in clinical trials for the treatment of diabetes.

Objective
To discuss the therapeutic potential of SGLT2 inhibitors currently in clinical development.

Key findings
A number of preclinical and clinical studies of SGLT2 inhibitors have demonstrated a good safety profile and beneficial effects in lowering plasma glucose levels, diminishing glucotoxicity, improving glycemic control and reducing weight in diabetes. Of all the SGLT2 inhibitors, dapagliflozin is a relatively advanced compound with regards to clinical development.

Summary
SGLT2 inhibitors are emerging as a promising therapeutic option for the treatment of diabetes. Their unique mechanism of action offers them the potential to be used in combination with other oral anti-diabetic drugs as well as with insulin.
Species Identification and Antifungal Susceptibility Testing of Candida Bloodstream Isolates from Population-Based Surveillance Studies in Two U.S. Cities from 2008 to 2011
Authors: Lockhart Shawn R. , Iqbal Naureen , Cleveland Angela A. , Farley Monica M. , Harrison Lee H. , Bolden Carol B. , Baughman Wendy , Stein Betsy , Hollick Rosemary , Park Benjamin J. , Chiller Tom 
Published: August 2012

ABSTRACT

Between 2008 and 2011, population-based candidemia surveillance was conducted in Atlanta, GA, and Baltimore, MD. Surveillance had been previously performed in Atlanta in 1992 to 1993 and in Baltimore in 1998 to 2000, making this the first population-based candidemia surveillance conducted over multiple time points in the United States. From 2,675 identified cases of candidemia in the current surveillance, 2,329
Candida
isolates were collected.
Candida albicans
no longer comprised the majority of isolates but remained the most frequently isolated species (38%), followed by
Candida glabrata
(29%),
Candida parapsilosis
(17%), and
Candida tropicalis
(10%). The species distribution has changed over time; in both Atlanta and Baltimore the proportion of
C. albicans
isolates decreased, and the proportion of
C. glabrata
isolates increased, while the proportion of
C. parapsilosis
isolates increased in Baltimore only. There were 98 multispecies episodes, with
C. albicans
and
C. glabrata
the most frequently encountered combination. The new species-specific CLSI
Candida
MIC breakpoints were applied to these data. With the exception of
C. glabrata
(11.9% resistant), resistance to fluconazole was very low (2.3% of isolates for
C. albicans
, 6.2% for
C. tropicalis
, and 4.1% for
C. parapsilosis
). There was no change in the proportion of fluconazole resistance between surveillance periods. Overall echinocandin resistance was low (1% of isolates) but was higher for
C. glabrata
isolates, ranging from 2.1% isolates resistant to caspofungin in Baltimore to 3.1% isolates resistant to anidulafungin in Atlanta. Given the increase at both sites and the higher echinocandin resistance,
C. glabrata
should be closely monitored in future surveillance.
Visual Detection ofrpoBMutations in Rifampin-Resistant Mycobacterium tuberculosis Strains by Use of an Asymmetrically Split Peroxidase DNAzyme
Authors: Deng Minggang , Feng Shuo , Luo Fengling , Wang Shaoru , Sun Xiaoming , Zhou Xiang , Zhang Xiao-Lian 
Published: August 2012

ABSTRACTMultidrug-resistantMycobacterium tuberculosisis resistant to two first-line antituberculosis drugs, isoniazid and rifampin, resulting in the relapse of tuberculosis.M. tuberculosisgrows very slowly, and thus traditional examination methods take time to test its drug resistance and cannot meet clinical needs. The use of a DNA probe makes it possible to test rifampin resistance. We developed an asymmetrical split-assembly DNA peroxidase assay to detect drug-resistant mutation of rifampin-resistantM. tuberculosisin therpoBgene rapidly and visibly. A new strategy was also designed to eliminate the adverse effects caused by the complicated secondary structure of the target DNA and to improve the efficiency of the probes. This detection system consists of five group detections, covers rifampin-resistant determination region of therpoBgene, and tests 40 kinds of mutations, including the most common mutations at codons 531 and 526. Every group detection or individual mutant allele detection can distinguish corresponding mutant DNA sequences from the wild-type DNA sequences.
Buruli Ulcer Disease in Travelers and Differentiation of Mycobacterium ulcerans Strains from Northern Australia
Authors: Lavender Caroline J. , Globan Maria , Johnson Paul D. R. , Charles Patrick G. P. , Jenkin Grant A. , Ghosh Niladri , Clark Benjamin M. , Martinello Marianne , Fyfe Janet A. M. 
Published: August 2012

ABSTRACT

Buruli ulcer (BU) is a necrotizing infection of skin and soft tissue caused by
Mycobacterium ulcerans
. In Australia, most cases of BU are linked to temperate, coastal Victoria and tropical, northern Queensland, and strains from these regions are distinguishable by variable-number tandem repeat (VNTR) typing. We present an epidemiological investigation of five patients found to have been infected during interstate travel and describe two nucleotide polymorphisms that differentiate
M. ulcerans
strains from northern Australia.
Development of Rapid Serotype-Specific PCR Assays for Eight Serotypes of Streptococcus suis
Authors: Wang Kaicheng , Sun Xueqiang , Lu Chengping 
Published: August 2012

ABSTRACT

Streptococcus suis
is an emerging zoonotic pathogen causing severe infections in pigs and humans. Thirty-three serotypes of
S. suis
have been identified using serum agglutination. The capsular polysaccharides synthesis (
cps
) locus is usually conserved among different strains of the same serotype. The
cps
loci of 15 serotypes have been sequenced, while the loci of the other serotypes remain unknown. In the present study, two to six serotype-specific genes of each of eight serotypes, i.e., serotypes 3, 4, 5, 8, 10, 19, 23, and 25, were identified using cross-hybridization with 93 nucleic acid probes specific to genes in the
cps
locus, and serotype-specific PCR assays for rapid and sensitive detection of the eight serotypes were then developed. The PCR typing results of the 148 serologically typeable isolates were completely consistent with agglutination results. Furthermore, some autoagglutinating, acapsular, and multiagglutinating strains which could not be differentiated by traditional serum agglutination assays were positive in the PCR assays. Use of the PCR assays with clinical tonsillar specimens showed that the assays are sensitive and able to identify samples with autoagglutinating isolates. To our knowledge, this is the first study to identify the serotype-specific genes of the eight
Streptococcus suis
serotypes and develop rapid and sensitive PCR assays for the eight serotypes which can be identified only by serum agglutination.
Type-Specific Identification of Anogenital Herpes Simplex Virus Infections by Use of a Commercially Available Nucleic Acid Amplification Test
Authors: Van Der Pol Barbara , Warren Terri , Taylor Stephanie N. , Martens Mark , Jerome Keith R. , Mena Leandro , Lebed Joel , Ginde Savita , Fine Paul , Hook Edward W. 
Published: August 2012

ABSTRACT

Herpes infections are among the most common sexually transmitted infections (STI), but diagnostic methods for genital herpes have not kept pace with the movement toward molecular testing. Here, we describe an FDA-approved molecular assay that identifies and types herpes simplex virus (HSV) infections for use in routine clinical settings. Paired samples from anogenital lesions were tested using the BD ProbeTec HSV Q
x
(HSVQ
x
) system, HSV culture and, a laboratory-developed PCR assay. Family planning, obstetrics/gynecology (OB/GYN), or sexually transmitted disease (STD) clinics in the United States served as recruitment sites. Sensitivity and specificity estimates, head-to-head comparisons, measures of agreement, and latent-class analyses were performed to provide robust estimates of performance. A total of 508 participants (174 men and 334 women) with anogenital lesions were included; 260 HSV-2 and 73 HSV-1 infections were identified. No differences in test performance based on gender, clinic type, location of the lesion, or type of lesion were observed. The sensitivity of HSV-2 detection ranged from 98.4 to 100% depending on the analytical approach, while the specificity ranged from 80.6%, compared to the less sensitive culture method, to 97.0%, compared to PCR. For HSV-1, the sensitivity and specificity ranges were 96.7 to 100% and 95.1 to 99.4%, respectively. This assay may improve our ability to accurately diagnose anogenital lesions due to herpes infection.
Microbiological Applications of High-Resolution Melting Analysis
Authors: Tong Steven Y. C. , Giffard Philip M. 
Published: August 2012

ABSTRACT
High-resolution melting (HRM) analysis uses real-time PCR instrumentation to interrogate DNA sequence variation and is a low-cost, single-step, closed-tube method. Here we describe HRM technology and provide examples of varied clinical microbiological applications to highlight the strengths and limitations of HRM analysis.
Defective HIV-1 Particle Assembly in AP-3-Deficient Cells Derived from Patients with Hermansky-Pudlak Syndrome Type 2
Authors: Liu Ling , Sutton Jessica , Woodruff Elvin , Villalta Fernando , Spearman Paul , Dong Xinhong 
Published: August 2012

ABSTRACT

Adaptor protein complex 3 (AP-3) is a heterotetramer that is involved in signal-mediated protein sorting to endosomal-lysosomal organelles. AP-3 deficiency in humans, induced by mutations in the
AP3B1
gene, which encodes the β3A subunit of the AP-3 complex, results in Hermansky-Pudlak syndrome 2 (HPS2), which is a rare genetic disorder with defective lysosome-related organelles. In a previous study, we identified the AP-3 complex as an important contributor to HIV-1 assembly and release. We hypothesized that cells from patients affected by HPS2 should demonstrate abnormalities of HIV-1 assembly. Here we report that HIV-1 particle assembly and release are indeed diminished in HPS2 fibroblast cultures. Transient or stable expression of the full-length wild-type β3A subunit in HPS2 fibroblasts restored the impaired virus assembly and release. In contrast, virus-like particle release mediated by MA-deficient Gag mutants lacking the AP-3 binding site was not altered in HPS2 cells, indicating that the MA domain serves as the major viral determinant required for the recruitment of the AP-3 complex. AP-3 deficiency decreased HIV-1 Gag localization at the plasma membrane and late endosomes and increased the accumulation of HIV-1 Gag at an intermediate step between early and late endosomes. Blockage of the clathrin-mediated endocytic pathway in HPS2 cells did not reverse the inhibited virus assembly and release imposed by the AP-3 deficiency. These results demonstrate that the intact and stable AP-3 complex is required for HIV-1 assembly and release, and the involvement of the AP-3 complex in late stages of the HIV-1 replication cycle is independent of clathrin-mediated endocytosis.
Role of Interferon Regulatory Factor 7 in T Cell Responses during Acute Lymphocytic Choriomeningitis Virus Infection
Authors: Zhou Shenghua , Cerny Anna M. , Fitzgerald Katherine A. , Kurt-Jones Evelyn A. , Finberg Robert W. 
Published: August 2012

ABSTRACT

Type I interferons (IFNs), predominantly IFN-α and -β, play critical roles in both innate and adaptive immune responses against viral infections. Interferon regulatory factor 7 (IRF7), a key innate immune molecule in the type I IFN signaling pathway, is essential for the type I IFN response to many viruses, including lymphocytic choriomeningitis virus (LCMV). Here, we show that although IRF7 knockout (KO) mice failed to control the replication of LCMV in the early stages of infection, they were capable of clearing LCMV infection. Despite the lack of type I IFN production, IRF7 KO mice generated normal CD4
+
T cell responses, and the expansion of naïve CD8
+
T cells into primary CD8
+
T cells specific for LCMV GP
33–41
was relatively normal. In contrast, the expansion of the LCMV NP
396
-specific CD8
+
T cells was severely impaired in IRF7 KO mice. We demonstrated that this defective CD8
+
T cell response is due neither to an impaired antigen-presenting system nor to any intrinsic role of IRF7 in CD8
+
T cells. The lack of a type I IFN response in IRF7 KO mice did not affect the formation of memory CD8
+
T cells. Thus, the present study provides new insight into the impact of the innate immune system on viral pathogenesis and demonstrates the critical contribution of innate immunity in controlling virus replication in the early stages of infection, which may shape the quality of CD8
+
T cell responses.
Acute Cytomegalovirus Infection Is Associated with Increased Frequencies of Activated and Apoptosis-Vulnerable T Cells in HIV-1-Infected Infants
Authors: Slyker Jennifer A. , Rowland-Jones Sarah L. , Dong Tao , Reilly Marie , Richardson Barbra , Emery Vincent C. , Atzberger Ann , Mbori-Ngacha Dorothy , Lohman-Payne Barbara L. , John-Stewart Grace C. 
Published: August 2012

ABSTRACTCytomegalovirus (CMV) coinfection is associated with infant HIV-1 disease progression and mortality. In a cohort of Kenyan HIV-infected infants, the frequencies of activated (CD38+HLA-DR+) and apoptosis-vulnerable (CD95+Bcl-2−) CD4+and CD8+T cells increased substantially during acute CMV infection. The frequency of activated CD4+T cells was strongly associated with both concurrent CMV coinfection (P= 0.001) and HIV-1 viral load (P= 0.05). The frequency of apoptosis-vulnerable cells was also associated with CMV coinfection in the CD4 (P= 0.02) and CD8 (P< 0.001) T cell subsets. Similar observations were made in HIV-exposed uninfected infants. CMV-induced increases in T cell activation and apoptosis may contribute to the rapid disease progression in coinfected infants.
Second-Site Mutations Selected in Transcriptional Regulatory Sequences Compensate for Engineered Mutations in the Vesicular Stomatitis Virus Nucleocapsid Protein
Authors: Harouaka Djamila , Wertz Gail W. 
Published: August 2012

ABSTRACT

The active template for RNA synthesis for vesicular stomatitis virus (VSV) and other negative-strand viruses is the RNA genome in association with the nucleocapsid (N) protein. The N protein molecules sequester the genomic RNA and are linked together by a network of noncovalent interactions. We previously demonstrated that mutations predicted to weaken interactions between adjacent N protein molecules altered the levels of RNA synthesis directed from subgenomic ribonucleoprotein (RNP) templates. To determine if these mutations affect virus replication, recombinant viruses containing single-amino-acid substitutions in the N protein were recovered. Four mutations altered transcription and genome replication levels, perturbed viral protein synthesis, and inhibited virus replication. Selective pressure for improved virus replication was applied by eight sequential passages. After five passages, virus replication improved and RNA synthesis recovered concomitantly with the restoration of the protein molar ratios to near-wild-type levels. Genome sequences were compared before and after passage to determine whether compensatory mutations were selected and to potentially identify interactions between N protein molecules or between the RNP template and the viral polymerase. Improved virus replication correlated with the selection of additional mutations located in
cis
-acting transcriptional regulatory sequences at the gene junctions of the genome rather than in coding sequences, with one exception. The engineered N gene mutations perturbed mRNA and protein expression levels, but the selection of modified transcriptional regulatory sequences with passage facilitated the restoration of wild-type protein expression by modulating transcription levels, reflecting the adaptability and versatility of gene regulation by transcriptional control.
The Genome of Pieris rapae Granulovirus
Authors: Zhang Bao-Qin , Cheng Ruo-Lin , Wang Xiao-Feng , Zhang Chuan-Xi 
Published: August 2012

ABSTRACT

Pieris rapae
granulovirus (PrGV) can infect and kill larvae of
Pieris rapae
, a worldwide and important pest of mustard family crops. The PrGV genome consists of 108,592 bp, is AT rich (66.8%), and is most structurally and organizationally similar to the
Choristoneura occidentalis
granulovirus genome. Of the predicted 120 open reading frames (ORFs), 32 genes specifically occurred in GVs, including four genes unique to PrGV (
Pr9
,
Pr32
,
Pr53
, and
Pr117
).
Complete Genome Sequence of a Highly Prevalent Isolate of Porcine Epidemic Diarrhea Virus in South China
Authors: Luo Yongwen , Zhang Jie , Deng Xianbo , Ye Yu , Liao Ming , Fan Huiying 
Published: August 2012

ABSTRACT
A widespread porcine epidemic diarrhea virus (PEDV) occurred in southern China during 2010 to 2012. A virulent field PEDV strain, GD-B, was isolated from a sucking piglet suffering from severe diarrhea in Guangdong, China. We sequenced and analyzed the complete genome of strain GD-B, which will promote a better understanding of the molecular epidemiology and genetic diversity of PEDV field isolates in southern China.
Complete Genome Sequence of an Avian-Like H4N8 Swine Influenza Virus Discovered in Southern China
Authors: Su Shuo , Qi Wen-bao , Chen Ji-dang , Cao Nan , Zhu Wan-jun , Yuan Li-guo , Wang Heng , Zhang Gui-hong 
Published: August 2012

ABSTRACT
We report here the complete genomic sequence of an avian-like H4N8 swine influenza virus containing an H5N1 avian influenza virus segment from swine in southern China. Phylogenetic analyses of the sequences of all eight viral RNA segments demonstrated that these are wholly avian influenza viruses of the Asia lineage. To our knowledge, this is the first report of interspecies transmission of an avian H4N8 influenza virus to domestic pigs under natural conditions.
Complete Genome Sequence of an Avian-Origin H3N2 Canine Influenza Virus Isolated from Dogs in South Korea
Authors: Park Seong-Jun , Moon Hyoung-Joon , Kang Bo-Kyu , Hong Minki , Na Woonseong , Kim Jeong-Ki , Poo Haryoung , Park Bong-Kyun , Song Dae-Sub 
Published: August 2012

ABSTRACT
An avian-origin Korean H3N2 canine influenza virus (CIV) strain, designated A/canine/Korea/01/2007 (H3N2), was isolated from nasal swabs of pet dogs exhibiting severe respiratory syndrome in 2007. In the present study, we report the first complete genome sequence containing 3′ and 5′ noncoding regions (NCRs) of H3N2 CIV, which will provide important insights into the molecular basis of pathogenesis, transmission, and evolution of CIV.
Necrotising fasciitis of the thumb
Authors: Dias Laura , Markeson Daniel , Evgeniou Evgenios , Misra Alok 
Published: August 2012

Necrotising fasciitis is a rare condition that should be diagnosed early and managed aggressively in order to avoid death. We present a case of necrotising fasciitis of the thumb and discuss the assessment and management of this serious condition. A 44-year-old woman presented with a painful and erythematous right thumb and progressive swelling of her hand following a minor injury to the tip of her thumb 3 days previously. A diagnosis of necrotising fasciitis was made and the patient underwent urgent debridement of non-viable tissue. She required 1 week of supportive therapy in intensive treatment unit and was discharged from hospital after 3 weeks. Necrotising fasciitis is a rapidly progressing life-threatening infection, usually caused by streptococcal organisms. Immediate resuscitation, broad-spectrum intravenous antibiotics and early surgical debridement are necessary in order to avoid significant morbidity and mortality.