bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development, implementation and benefits of a rheumatology‐specific electronic medical record application with automated display of outcome measures
Authors: MALAVIYA Anand N. , GOGIA Shashi B. 
Published: July 2010

AbstractObjectives:  To make a rheumatology‐specific electronic medical record (EMR) application for easy clinical data entry, automated display of outcome measures in real‐time that generates well laid‐out print‐outs; and provides an easily retrievable database for clinical analysis and research.Methods:  Highly labour‐intensive ‘MS‐WORD®’ template used earlier provided the basic framework for developing rheumatology‐EMR applications. The authors, a rheumatologist and a soft tissue surgeon with expertise in developing medical software, successfully created a rheumatology‐EMR application over a period of 2½ years using the same basic flow of work as used in the old ‘MS‐WORD®’ template.Results:  The resulting EMR application form has a standard medical record documenting demographic data, complete diagnosis, appropriate dates, visit number, disease status, history, physical examination, investigations, follow‐up and prescription page (with automatic updates wherever applicable). Mathematical calculations required for outcome measures (DAS, DAS28, CDAI, SDAI, AS‐DAS, BASDAI, BASFI, BASMI, SLE‐DAI and others) are embedded in the software, with automated updating as the examination of the musculoskeletal system proceeds in real time. Following implementation of this EMR application, more patients are being seen, patient waiting lists have been reduced; more time is available for academic and teaching work, without compromising the quality of notes, and print‐outs for patients. Data retrieval has simplified clinical research with increased numbers of abstracts being presented and research papers being published.Conclusion:  Healthcare workers with understanding of the basic principles of computers and softwares should interact with software engineers who are either themselves medical doctors or are familiar with the workflow and clinical evaluation processes to create an efficient speciality‐specific EMR application.
Blockage of Notch1 signaling modulates the T‐helper (Th)1/Th2 cell balance in chronic hepatitis B patients
Authors: Pei Jinxian , Tang Zhenghao , Zang Guoqing , Yu Yongsheng 
Published: July 2010

Aim:  Chronic hepatitis B virus (HBV) infection is thought to involve the imbalance of T‐helper (Th)1/Th2 cells. Many procedures found Notch signaling involved the proliferation and differentiation of T lymphocytes during development and peripheral functions. The aim of this study was to discover the effect of blockage of Notch1 signaling to Th cells and the mechanisms involved in chronic hepatitis B patients.Methods:  CD4+ T cells from hepatitis B patients and healthy volunteers were isolated, and Notch1 expression of CD4+ T cells was determined by reverse transcription polymerase chain reaction (RT–PCR). Blockage of Notch1 signaling of peripheral blood mononuclear cells (PBMC) from chronic hepatitis B patients, Th1‐ and Th2‐type cytokines were assayed by enzyme‐linked immunosorbent assay and levels of T‐bet, GATA‐3 mRNA were measured by RT–PCR.Results:  Notch1 expression of CD4+ T cells from chronic hepatitis B patients was upregulated, on the contrary to that from acute hepatitis B patients and healthy volunteers. Blockage of Notch1 signaling can strongly inhibit the production of Th2‐type cytokines and the expression of GATA‐3; the production of Th1‐type cytokines and the expression of T‐bet, however, were enhanced.Conclusion:  Blockage of Notch1 signaling could regulate the immune balance of Th1/Th2 in chronic hepatitis B patients, which may be mediated partly by regulating transcription factors T‐bet and GATA‐3.
Uterine torsion diagnosed in a mare at 515 days' gestation
Authors: López C. , Carmona J. U. 
Published: July 2010

SummaryA pregnant mare with a history of prolonged gestation (∼515 days) and suspected diagnosis of fetal mummification was examined. Rectal palpation revealed that the left broad ligament of the uterus was dorsal and medial to the right uterine ligament and it was not possible to observe the cervix during vaginal examination. Transabdominal ultrasound revealed fluid in the uterus, fetal membranes and the uterine walls defined and thickened. Free fluid was not seen in the peritoneal cavity. Laboratory tests (blood cell count and clinical chemistry) were normal. Based on clinical history, physical examination and ultrasound findings, a chronic uterine torsion with fetal death was diagnosed and the mare was subjected to exploratory celiotomy. The uterus was strongly adhered to the peritoneum of the ventral abdominal wall and there were multiple adhesions to the colon. Hysterotomy was performed to remove the fetus and to permit repositioning of the uterus. When the fetus was removed, a large devitalised grey tissue area of the right ventral uterine horn was observed. Multiple adhesions prevented a rescue hysterectomy and euthanasia of the patient was performed. During the necropsy, a 180° cranial cervix clockwise uterine torsion was observed. This rare case of uterine torsion appears to be the most chronic case reported in the equine literature.
Treatment of appendicular osteosarcoma in a horse
Authors: Gutierrez‐Nibeyro S. D. , Sullins K. E. , Powers B. E. 
Published: July 2010

SummaryA 14‐year‐old Arabian gelding was examined for a mass on the lateral aspect of the left tarsus and proximal lateral metatarsus. Radiography revealed a predominately osteolytic lesion involving the fourth tarsal bone and the proximal third and fourth metatarsal bone. Results of histopathological examination of the mass prior to surgery were consistent with an undifferentiated sarcoma. The mass was surgically excised and the remaining bone defect treated with absorbable beads containing cisplatin. Histology and immunohistochemistry of the mass removed at surgery revealed a telangiectatic osteosarcoma. The surgical site healed uneventfully and the horse was performing as a low level jumper 8.5 years after surgery.
Use of an Anti-Hepatitis C Virus (HCV) IgG Avidity Assay To Identify Recent HCV Infection
Authors: Gaudy-Graffin Catherine , Lesage Gérard , Kousignian Isabelle , Laperche Syria , Girault Annie , Dubois Frédéric , Goudeau Alain , Barin Francis 
Published: July 2010

ABSTRACT

There is no reliable and simple diagnostic marker available to diagnose recent hepatitis C virus (HCV) infection. It has been shown that the avidity of specific IgG antibody is low in primary viral infection and increases with time. We report the development of an anti-HCV avidity assay derived from a commercially available test. A panel of 117 sera was first examined for IgG avidity. It was composed of samples from patients with recent (group 1,
n
= 14), chronic (group 2,
n
= 70), and resolved (group 3,
n
= 33) HCV infections. Avidity index (AI) values observed in recently infected patients were significantly lower (12.0% ± 9.2% [mean ± standard deviation]) than those found in chronic carriers (83.1% ± 15.2%). Using a threshold of 43.0%, this assay distinguished between groups 1 and 2 with very high sensitivity (98%) and specificity (100%). For group 3, a broader distribution of the AI values was observed (54.8% ± 27.3%), suggesting that this index would not be useful in HCV RNA-negative patients. Blind validation of the test was carried out with a panel of 36 serum samples from 17 HCV seroconverters. The assay described here is a useful tool to distinguish recent from chronic infection in HCV-viremic patients.
Limited Utility of Culture for
Mycoplasma pneumoniae
and
Chlamydophila pneumoniae
for Diagnosis of Respiratory Tract Infections
Authors: She Rosemary C. , Thurber Andy , Hymas Weston C. , Stevenson Jeffery , Langer Janine , Litwin Christine M. , Petti Cathy A. 
Published: July 2010

ABSTRACT

We assessed the utility of culture for
Mycoplasma pneumoniae
and
Chlamydophila pneumoniae
to diagnose respiratory tract infections. Compared to PCR and IgM serology, culture was less sensitive and had extremely low yield. Culture is not recommended for these pathogens, and this method should be eliminated from routine practice.
Simultaneous Sequence Analysis of the 16S rRNA and
rpoB
Genes by Use of RipSeq Software To Identify
Mycobacterium
Species
Authors: Simmon Keith E. , Kommedal Øyvind , Saebo Øystein , Karlsen Bjarte , Petti Cathy A. 
Published: July 2010

ABSTRACT

The 16S rRNA gene is commonly used to identify
Mycobacterium
spp., but alternative DNA targets can provide better resolution to the species level. We evaluated a novel system that enables simultaneous amplification, sequencing, and analysis of two different DNA targets in a single tube to identify clinical isolates of
Mycobacterium
spp. For 139 clinical isolates, we found that the 16S rRNA gene alone identified 67 (48%) isolates as single species, 68 (49%) isolates to the complex or group level, and 4 (3%) isolates to the genus level only. The
rpoB
gene alone identified 117 (84%) isolates as single species, 10 (7%) isolates to the complex or group level, and 12 (8%) isolates to the genus level only. Combining the separate analyses for sequencing of two gene targets, 119 (86%) isolates were identified as single species and 10 (7%) isolates were identified to the complex or group level. Seven (5%) isolates were identified as novel species within established groups, and 3 (2%) were identified to the genus level only. Dual-locus identification identified 110 (79%) isolates as single species and 22 (16%) isolates to the complex or group level. Six (4%) were identified as novel species within established groups, and 1 (1%) was identified to the genus level only. Identifications were more accurate when both the 16S rRNA and
rpoB
genes were screened, and reliance on a single gene target was suboptimal. RipSeq dual-locus software provides an accurate alternative method for laboratories using two different gene targets for microorganism identification.
Identification of Newly Described
Streptococcus pneumoniae
Serotype 6D by Use of the Quellung Reaction and PCR
Authors: Oftadeh Shahin , Satzke Catherine , Gilbert Gwendolyn L. 
Published: July 2010

ABSTRACT
We tested 121 pneumococcal serogroup 6 isolates (including 30 serotype 6C and 24 serotype 6D isolates) by serotype-specific PCR and the Quellung reaction, using “old” and “new” pool B, factor 6b, and new factor 6d antisera. In combination with group B and other factor antisera, factor 6d antiserum can reliably identify the newly described serotype 6D.
Does a Feline Leukemia Virus Infection Pave the Way forBartonella henselaeInfection in Cats?
Authors: Buchmann Alexandra U. , Kershaw Olivia , Kempf Volkhard A. J. , Gruber Achim D. 
Published: July 2010

ABSTRACTDomestic cats serve as the reservoir hosts ofBartonella henselaeand may develop mild clinical symptoms or none after experimental infection. In humans,B. henselaeinfection can result in self-limiting cat scratch disease. However, immunocompromised patients may suffer from more-severe courses of infection or may even develop the potentially lethal disease bacillary angiomatosis. It was reasoned that cats with immunocompromising viral infections may react similarly toB. henselaeinfection. The aim of our study was to investigate the influence of the most important viruses known to cause immunosuppression in cats—Feline leukemia virus(FeLV),Feline immunodeficiency virus(FIV), andFeline panleukopenia virus(FPV)—on naturalB. henselaeinfection in cats. Accordingly, 142 cats from animal shelters were necropsied and tested forB. henselaeand concurrent infections with FeLV, FIV, or FPV by PCR and immunohistochemistry. A significant association was found betweenB. henselaeand FeLV infections (P= 0.00028), but not betweenB. henselaeand FIV (P= 1.0) or FPV (P= 0.756) infection, age (P= 0.392), or gender (P= 0.126). The results suggest that susceptibility toB. henselaeinfection is higher in cats with concurrent FeLV infections, regardless of whether the infection is latent or progressive. Histopathology and immunohistochemistry forB. henselaefailed to identify lesions that could be attributed specifically toB. henselaeinfection. We conclude that the course of naturalB. henselaeinfection in cats does not seem to be influenced by immunosuppressive viral infections in general but that latent FeLV infection may predispose cats toB. henselaeinfection or persistence.
Prevalence, Genetic Characteristics, and Zoonotic Potential of
Cryptosporidium
Species Causing Infections in Farm Rabbits in China
Authors: Shi Ke , Jian Fuchuan , Lv Chaochao , Ning Changshen , Zhang Longxian , Ren Xupeng , Dearen Theresa K. , Li Na , Qi Meng , Xiao Lihua 
Published: July 2010

ABSTRACT

To assess the prevalence and public health significance of rabbit cryptosporidiosis, a total of 1,081 fecal specimens were collected between October 2007 and April 2008 from rabbits on eight farms in five different areas in Henan Province, China, and were examined by microscopy after Sheather's sucrose flotation and modified acid-fast staining. The average infection rate of
Cryptosporidium
was 3.4% (37/1,081 samples). There was a significant association between the prevalence of
Cryptosporidium
and the age of animals (χ
2
= 57.13;
P
< 0.01); the prevalence of cryptosporidiosis in 1- to 3-month-old rabbits was the highest (10.9%). The
Cryptosporidium
species in microscopy-positive specimens were genotyped by sequence analyses of the 18S rRNA, 70-kDa heat shock protein (HSP70), oocyst wall protein (COWP), and actin genes and were subtyped by sequence analysis of the 60-kDa glycoprotein (gp60) gene. Only the
Cryptosporidium
rabbit genotype was identified, with 100% sequence identity to published sequences of the 18S rRNA, HSP70, COWP, and actin genes, and the strains belonged to three gp60 subtypes (VbA36, VbA35, and VbA29). In view of the recent finding of the
Cryptosporidium
rabbit genotype in human outbreak and sporadic cases, the role of rabbits in the transmission of human cryptosporidiosis should be reassessed.
Corynebacterium falsenii
Bacteremia Occurring in an Infant on Vancomycin Therapy
Authors: Tam Pui-Ying Iroh , Fisher Mark A. , Miller Nancy S. 
Published: July 2010

ABSTRACT

Corynebacterium falsenii
was described in 1998 as a new
Corynebacterium
species. We give the first detailed description of a clinically significant
Corynebacterium falsenii
bacteremia occurring in an infant while on vancomycin therapy.
Barriers to Intravenous Penicillin Use for Treatment of Nonmeningitis Pneumococcal Disease
Authors: Rosen Jennifer , Beekmann Susan , Polgreen Philip , Moore Matthew 
Published: July 2010

ABSTRACT
Infectious disease physicians were surveyed to determine whether the new penicillin breakpoint change will translate into increased penicillin use and to identify barriers to intravenous (i.v.) penicillin use for pneumococcal infections. The inconvenience of i.v. penicillin may limit its use despite a reduction in numbers of infections considered resistant.
Laboratory Surveillance for Prospective Plasmid-Mediated AmpC β-Lactamases in the Kinki Region of Japan
Authors: Yamasaki Katsutoshi , Komatsu Masaru , Abe Noriyuki , Fukuda Saori , Miyamoto Yugo , Higuchi Takeshi , Ono Tamotsu , Nishio Hisaaki , Sueyoshi Noriyuki , Kida Kaneyuki , Satoh Kaori , Toyokawa Masahiro , Nishi Isao , Sakamoto Masako , Akagi Masahiro , Nakai Isako , Kofuku Tomomi , Orita Tamaki , Wada Yasunao , Jikimoto Takumi , Kinoshita Shohiro , Miyamoto Kazuaki , Hirai Itaru , Yamamoto Yoshimasa 
Published: July 2010

ABSTRACT

Extended-spectrum β-lactamases, plasmid-mediated AmpC β-lactamases (PABLs), and plasmid-mediated metallo-β-lactamases confer resistance to many β-lactams. In Japan, although several reports exist on the prevalence of extended-spectrum β-lactamases and metallo-β-lactamases, the prevalence and characteristics of PABLs remain unknown. To investigate the production of PABLs, a total of 22,869 strains of 4 enterobacterial species,
Escherichia coli
,
Klebsiella pneumoniae
,
Klebsiella oxytoca
, and
Proteus mirabilis
, were collected during six 6-month periods from 17 clinical laboratories in the Kinki region of Japan. PABLs were detected in 29 (0.13%) of 22,869 isolates by the 3-dimensional test, PCR analysis, and DNA sequencing analysis. PABL-positive isolates were detected among isolates from 13 laboratories. Seventeen of 13,995 (0.12%)
E. coli
isolates, 8 of 5,970 (0.13%)
K. pneumoniae
isolates, 3 of 1,722 (0.17%)
K. oxytoca
isolates, and 1 of 1,182 (0.08%)
P. mirabilis
isolates were positive for PABLs. Of these 29 PABL-positive strains, 20 (69.0%), 6 (20.7%), 2 (6.9%), and 1 (3.4%) carried the genes for CMY-2, DHA-1, CMY-8, and MOX-1 PABLs, respectively. Pattern analysis of randomly amplified polymorphic DNA and pulsed-field gel electrophoretic analysis revealed that the prevalence of CMY-2-producing
E. coli
strains was not due to epidemic strains and that 3 DHA-1-producing
K. pneumoniae
strains were identical, suggesting their clonal relatedness. In conclusion, the DHA-1 PABLs were predominantly present in
K. pneumoniae
strains, but CMY-2 PABLs were predominantly present in
E. coli
strains. The present findings will provide significant information to assist in preventing the emergence and further spread of PABL-producing bacteria.
Equus caballus
Major Histocompatibility Complex Class I Is an Entry Receptor for Equine Herpesvirus Type 1
Authors: Kurtz Brian M. , Singletary Lauren B. , Kelly Sean D. , Frampton Arthur R. 
Published: July 2010

ABSTRACT

In this study,
Equus caballus
major histocompatibility complex class I (MHC-I) was identified as a cellular entry receptor for the alphaherpesvirus equine herpesvirus type 1 (EHV-1). This novel EHV-1 receptor was discovered using a cDNA library from equine macrophages. cDNAs from this EHV-1-susceptible cell type were inserted into EHV-1-resistant B78H1 murine melanoma cells, these cells were infected with an EHV-1
lacZ
reporter virus, and cells that supported virus infection were identified by X-Gal (5-bromo-4-chloro-3-indolyl-β-
d
-galactopyranoside) staining. Positive cells were subjected to several rounds of purification to obtain homogeneous cell populations that were shown to be uniformly infected with EHV-1. cDNAs from these cell populations were amplified by PCR and then sequenced. The sequence data revealed that the EHV-1-susceptible cells had acquired an
E. caballus
MHC-I cDNA. Cell surface expression of this receptor was verified by confocal immunofluorescence microscopy. The MHC-I cDNA was cloned into a mammalian expression vector, and stable B78H1 cell lines were generated that express this receptor. These cell lines were susceptible to EHV-1 infection while the parental B78H1 cells remained resistant to infection. In addition, EHV-1 infection of the B78H1 MHC-I-expressing cell lines was inhibited in a dose-dependent manner by an anti-MHC-I antibody.
Release of Genotype 1 Hepatitis E Virus from Cultured Hepatoma and Polarized Intestinal Cells Depends on Open Reading Frame 3 Protein and Requires an Intact PXXP Motif
Authors: Emerson Suzanne U. , Nguyen Hanh T. , Torian Udana , Burke Danielle , Engle Ronald , Purcell Robert H. 
Published: July 2010

ABSTRACT

Hepatitis E virus genotype 1 strain Sar55 replicated in subcloned Caco-2 intestinal cells and Huh7 hepatoma cells that had been transfected with
in vitro
transcribed viral genomes, and hepatitis E virions were released into the culture medium of both cell lines. Virus egress from cells depended on open reading frame 3 (ORF3) protein, and a proline-rich sequence in ORF3 was important for egress from cultured cells and for infection of macaques. Both intracellular ORF3 protein accumulation and virus release occurred at the apical membrane of polarized Caco-2 cells. ORF3 protein and lipids were intimately associated with virus particles produced in either cell line; ORF2 epitopes were masked in these particles and could not be immunoprecipitated with anti-ORF2.
JC Virus Latency in the Brain and Extraneural Organs of Patients with and without Progressive Multifocal Leukoencephalopathy
Authors: Tan Chen S. , Ellis Laura C. , Wüthrich Christian , Ngo Long , Broge Thomas A. , Saint-Aubyn Jenny , Miller Janice S. , Koralnik Igor J. 
Published: July 2010

ABSTRACT

JC virus (JCV) is latent in the kidneys and lymphoid organs of healthy individuals, and its reactivation in the context of immunosuppression may lead to progressive multifocal leukoencephalopathy (PML). Whether JCV is present in the brains or other organs of healthy people and in immunosuppressed patients without PML has been a matter of debate. We detected JCV large T DNA by quantitative PCR of archival brain samples of 9/24 (38%) HIV-positive PML patients, 5/18 (28%) HIV-positive individuals, and 5/19 (26%) HIV-negative individuals. In the same samples, we detected JCV regulatory region DNA by nested PCR in 6/19 (32%) HIV-positive PML patients, 2/11 (18%) HIV-positive individuals, and 3/17 (18%) HIV-negative individuals. In addition, JCV DNA was detected in some spleen, lymph node, bone, and kidney samples from the same groups.
In situ
hybridization data confirmed the presence of JCV DNA in the brains of patients without PML. However, JCV proteins (VP1 or T antigen) were detected mainly in the brains of 23/24 HIV-positive PML patients, in only a few kidney samples of HIV-positive patients, with or without PML, and rarely in the bones of HIV-positive patients with PML. JCV proteins were not detected in the spleen or lymph nodes in any study group. Furthermore, analysis of the JCV regulatory region sequences showed both rearranged and archetype forms in brain and extraneural organs in all three study groups. Regulatory regions contained increased variations of rearrangements correlating with immunosuppression. These results provide evidence of JCV latency in the brain prior to severe immunosuppression and suggest new paradigms in JCV latency, compartmentalization, and reactivation.
7SL RNA Is Retained in HIV-1 Minimal Virus-Like Particles as an S-Domain Fragment
Authors: Keene Sarra E. , King Steven R. , Telesnitsky Alice 
Published: July 2010

ABSTRACT
HIV-1 is known to package several small cellular RNAs in addition to its genome. Previous work consistently demonstrated that the host structural RNA 7SL is abundant in HIV-1 virions but has yielded conflicting results regarding whether 7SL is present in minimal, assembly-competent virus-like particles (VLPs). Here, we demonstrate that minimal HIV-1 VLPs retain 7SL RNA primarily as an endoribonucleolytic fragment, referred to as 7SL remnant (7SLrem). Nuclease mapping showed that 7SLrem is a 111-nucleotide internal portion of 7SL, with 5′ and 3′ ends corresponding to unpaired loops in the 7SL two-dimensional structure. Analysis of VLPs comprised of different subsets of Gag domains revealed that all NC-positive VLPs contained intact 7SL while the presence of 7SLrem correlated with the absence of the NC domain. Because 7SLrem, which maps to the 7SL S domain, was not detectable in infected cells, we propose a model whereby the species recruited to assembling VLPs is intact 7SL RNA, with 7SLrem produced by an endoribonuclease in the absence of NC. Since recruitment of 7SL RNA was a conserved feature of all tested minimal VLPs, our model further suggests that 7SL's recruitment is mediated, either directly or indirectly, through interactions with conserved features of all tested VLPs, such as the C-terminal domain of CA.