bluuebunny/crossref_metadata_2025_split huggingface dataset:
B‐cell lymphoma with plasmacytoid differentiation, atypical cytoplasmic inclusions, and secondary leukemia in a dog
Authors: Kol A. , Christopher M.M. , Skorupski K.A. , Tokarz D. , Vernau W. 
Published: December 2012

AbstractA 7‐year‐old male castrated Jack Russell Terrier was presented to the oncology service at the University of California–Davis Veterinary Medical Teaching Hospital for evaluation of suspected lymphoma. The dog had several enlarged lymph nodes and moderate lymphocytosis. Aspirates of an enlarged inguinal lymph node contained a bimorphic population of large immature lymphocytes and smaller cells with plasmacytoid features. Both cell types often contained a single large cytoplasmic inclusion that varied from clear to pale pink to sky blue. Cytologic changes were interpreted as most consistent with lymphoid neoplasia. Based on the predominantly mature cell morphology and some morphologic heterogeneity, the peripheral lymphocytosis was interpreted as most likely reactive in nature. However, the immunophenotype of the cells (CD20+, CD21+, CD79a+, MUM‐1+, and MHCII+) and clonality assays showed that tissue and blood lymphocytes were neoplastic B cells with clonal identity despite their different morphologic appearances. The cytoplasmic inclusions were positive with periodic acid‐Schiff and were immunoreactive for IgM and IgG. By transmission electron microscopy, inclusions consisted of aberrant rough endoplasmic reticulum; a few small Russell bodies were also noted. A final diagnosis of high‐grade B‐cell lymphoma with plasmacytoid differentiation, atypical cytoplasmic inclusions, and secondary leukemia was made. Chemotherapy was initiated, but the dog was euthanized due to severe and uncontrolled seizures 9 months after the initial diagnosis. This case extends the morphologic repertoire of canine plasmacytoid neoplasms and emphasizes their continuum with multicentric lymphoma. This case also demonstrates the need for advanced diagnostic techniques in establishing blood involvement in lymphoma in some instances.
Assessment of wastewater treatment technologies: life cycle approach
Authors: Kalbar Pradip P. , Karmakar Subhankar , Asolekar Shyam R. 
Published: December 2012

AbstractFour municipal wastewater treatment plants (WWTPs) in India based on different technologies are compared by conducting Life Cycle Assessment (LCA) using field data. CML 2 baseline 2000 methodology is adopted in which eight impact categories are considered. SBRs ranked highest in energy consumption and global warming potential (GWP) but also produced the best effluent with respect to organics and nutrients. Constructed wetlands have negligible energy consumption and negative GWP because of carbon sequestration in the macrophytes. Emissions associated with electricity production required to operate the WWTPs, emissions to water from treated effluent and heavy metal emissions from waste sludge applied to land are identified as main contributors for overall environmental impacts of WWTPs. This comparison of technologies suggests that results from LCA can be used as indicators in a multicriteria decision‐making framework along with other sustainability indicators.
Inactivation of enveloped and non‐enveloped viruses in the process of chemical treatment and gamma irradiation of bovine‐derived grafting materials
Authors: Lee Kwang‐Il , Lee Jung‐Soo , Jung Hong‐Hee , Lee Hwa‐Yong , Moon Seong‐Hwan , Kang Kyoung‐Tak , Shim Young‐Bock , Jang Ju‐Woong 
Published: December 2012

Lee K‐I, Lee J‐S, Jung H‐H, Lee H‐Y, Moon S‐H, Kang K‐T, Shim Y‐B, Jang J‐W. Inactivation of enveloped and non‐enveloped viruses in the process of chemical treatment and gamma irradiation of bovine‐derived grafting materials. Xenotransplantation 2012; 19: 365–369. © 2012 John Wiley & Sons A/S.AbstractBackground: Xenografts, unlike other grafting products, cannot be commercialized unless they conform to stringent safety regulations. Particularly with bovine‐derived materials, it is essential to remove viruses and inactivate infectious factors because of the possibility that raw materials are imbrued with infectious viruses. The removal of the characteristics of infectious viruses from the bovine bone grafting materials need to be proved and inactivation process should satisfy the management provision of the Food and Drug Administration (FDA). To date, while most virus inactivation studies were performed in human allograft tissues, there have been almost no studies on bovine bone.Methods: To evaluate the efficacy of virus inactivation after treatment of bovine bone with 70% ethanol, 4% sodium hydroxide, and gamma irradiation, we selected a variety of experimental model viruses that are known to be associated with bone pathogenesis, including bovine parvovirus (BPV), bovine herpes virus (BHV), bovine viral diarrhea virus (BVDV), and bovine parainfluenza‐3 virus (BPIV‐3). The cumulative virus log clearance factor or cumulative virus log reduction factor for the manufacturing process was obtained by calculating the sum of the individual virus log clearance factors or log reduction factors determined for individual process steps with different physicochemical methods.Results: The cumulative log clearance factors achieved by three different virus inactivation processes were as follows: BPV ≥17.73, BHV ≥20.53, BVDV ≥19.00, and BPIV‐3 ≥16.27. On the other hand, the cumulative log reduction factors achieved were as follows: BPV ≥16.95, BHV ≥20.22, BVDV ≥19.27, and BPIV‐3 ≥15.58.Conclusions: Treatment with 70% ethanol, 4% sodium hydroxide, or gamma irradiation was found to be very effective in virus inactivation, since all viruses were at undetectable levels during each process. We have no doubt that application of this established process to bovine bone graft manufacture will be effective and essential.
Genome Sequence of Francisella tularensis subspecies holarctica Strain FSC200, Isolated from a Child with Tularemia
Authors: Svensson Kerstin , Sjödin Andreas , Byström Mona , Granberg Malin , Brittnacher Mitchell J. , Rohmer Laurence , Jacobs Michael A. , Sims-Day Elizabeth H. , Levy Ruth , Zhou Yang , Hayden Hillary S. , Lim Regina , Chang Jean , Guenthener Donald , Kang Allison , Haugen Eric , Gillett Will , Kaul Rajinder , Forsman Mats , Larsson Pär , Johansson Anders 
Published: December 2012

ABSTRACT

Here we report the complete, accurate 1.89-Mb genome sequence of
Francisella tularensis
subsp.
holarctica
strain FSC200, isolated in 1998 in the Swedish municipality Ljusdal, which is in an area where tularemia is highly endemic. This genome is important because strain FSC200 has been extensively used for functional and genetic studies of
Francisella
and is well-characterized.
Revised Sequence and Annotation of the Rhodobacter sphaeroides 2.4.1 Genome
Authors: Kontur Wayne S. , Schackwitz Wendy S. , Ivanova Natalia , Martin Joel , LaButti Kurt , Deshpande Shweta , Tice Hope N. , Pennacchio Christa , Sodergren Erica , Weinstock George M. , Noguera Daniel R. , Donohue Timothy J. 
Published: December 2012

ABSTRACT

The DNA sequences of chromosomes I and II of
Rhodobacter sphaeroides
strain 2.4.1 have been revised, and the annotation of the entire genomic sequence, including both chromosomes and the five plasmids, has been updated. Errors in the originally published sequence have been corrected, and ∼11% of the coding regions in the original sequence have been affected by the revised annotation.
Complete Genome Sequence of Brucella melitensis 133, an Isolate of Biovar 1 of Sequence Type 32
Authors: Ke Yuehua , Zhen Qing , Li Tiefeng , Wang Yufei , Yuan Xitong , Xu Jie , Huang Liuyu , Wang Dali , Song Hongbin , Chen Zeliang 
Published: December 2012

ABSTRACT

Brucellosis is highly epidemic in China. Of the six classical species,
Brucella melitensis
and biovar 1 are the most represented species and biovar that cause human brucellosis in China. Here, we report the genome sequence of
Brucella melitensis
strain 133, a strain of biovar 1 of sequence type 32.
Genome Sequence of Brucella melitensis Strain 128, an Isolate of Biovar 3 of Sequence Type 8
Authors: Li Tiefeng , Yuan Xitong , Ding Jiabo , Zhen Qing , Ke Yuehua , Wang Yufei , Huang Liuyu , Mao Kairong , Chen Zeliang , Wang Dali 
Published: December 2012

ABSTRACT

Brucella melitensis
is the most common
Brucella
species causing human brucellosis.
B. melitensis
is divided into 3 biovars. Here, we report the complete genome sequence of
B. melitensis
strain 128, a strain of biovar 3 of sequence type 8, which is prevalent in China.
Full Genome Sequences of All Nine Chlamydia psittaci Genotype Reference Strains
Authors: Van Lent Sarah , Piet Jurgen R. , Beeckman Delphine , van der Ende Arie , Van Nieuwerburgh Filip , Bavoil Patrik , Myers Garry , Vanrompay Daisy , Pannekoek Yvonne 
Published: December 2012

ABSTRACT

Chlamydia psittaci
primarily infects birds, but zoonotic transmission occurs in people in close contact with infected birds. The clinical outcome ranges from inapparent disease to pneumonia. Here we report the genome sequences of all 9
Chlamydia psittaci
genotype reference strains.
Draft Genome Sequence of Methanobacterium formicicum DSM 3637, an Archaebacterium Isolated from the Methane Producer Amoeba Pelomyxa palustris
Authors: Gutiérrez Gabriel 
Published: December 2012

ABSTRACT

Here is reported the draft genome sequence of
Methanobacterium formicicum
DSM 3637, which was isolated from the methane-producing amoeba
Pelomyxa palustris
. This bacterium was determined to be an endosymbiont living in the cytoplasm of
P. palustris
and the source of methane; however, the global characteristics of its genome suggest a free-living lifestyle rather than an endosymbiotic one.
Genome Sequence and Comparative Genomics Analysis of a Vibrio cholerae O1 Strain Isolated from a Cholera Patient in Malaysia
Authors: Osama Abdulrazak , Gan Han Ming , Teh Cindy Shuan Ju , Yap Kien-Pong , Thong Kwai-Lin 
Published: December 2012

ABSTRACT

The genome sequence analysis of a clinical
Vibrio cholerae
VC35 strain from an outbreak case in Malaysia indicates multiple genes involved in host adaptation and a novel Na
+
-driven multidrug efflux pump-coding gene in the genome of
Vibrio cholerae
with the highest similarity to VMA_001754 of
Vibrio mimicus
VMA223.
Genome Sequence of Moraxella catarrhalis RH4, an Isolate of Seroresistant Lineage
Authors: Zomer Aldert , de Vries Stefan P. W. , Riesbeck Kristian , Meinke Andreas L. , Hermans Peter W. M. , Bootsma Hester J. 
Published: December 2012

ABSTRACT

Here we report the annotated genome sequence of
Moraxella catarrhalis
strain RH4, a seroresistant-lineage strain isolated from the blood of an infected patient. This genome sequence will allow us to gain further insight into the genetic diversity of clinical
M. catarrhalis
isolates and will facilitate study of
M. catarrhalis
pathogenesis.
Draft Genome Sequence of the Biocontrol Bacterium Bacillus amyloliquefaciens Strain M27
Authors: Lee Sang-Yeob , Kim Byung-Yong , Ahn Jae-Hyung , Song Jaekyeong , Seol Young-Joo , Kim Wan-Gyu , Weon Hang-Yeon 
Published: December 2012

ABSTRACT

Bacillus amyloliquefaciens
strain M27 is a biocontrol agent with antagonistic activities against a wide range of fungal pathogens. Here we present the 3.86-Mb draft genome sequence of the bacterium with the aims of providing insights into the genomic basis of its antifungal mechanism and facilitating its application in the biocontrol of plant diseases.
Genome Sequence of an Alkane-Degrading Bacterium, Alcanivorax pacificus Type Strain W11-5, Isolated from Deep Sea Sediment
Authors: Lai Qiliang , Shao Zongze 
Published: December 2012

ABSTRACT

Alcanivorax pacificus
W11-5
T
was isolated from a pyrene-degrading consortium, enriched from the deep sea sediment of the Pacific Ocean. Strain W11-5
T
can degrade various
n
-alkanes. Here we report the draft genome of W11-5
T
and genes associated with alkane degradation.
Complete Genome Sequence of Acidovorax sp. Strain KKS102, a Polychlorinated-Biphenyl Degrader
Authors: Ohtsubo Yoshiyuki , Maruyama Fumito , Mitsui Hisayuki , Nagata Yuji , Tsuda Masataka 
Published: December 2012

ABSTRACT

We report the complete genome sequence of
Acidovorax
sp. strain KKS102, a polychlorinated-biphenyl-degrading strain isolated from a soil sample in Tokyo. The genome contains a single circular 5,196,935-bp chromosome and no plasmids.
Genome Sequence of Idiomarina xiamenensis Type Strain 10-D-4
Authors: Lai Qiliang , Wang Liping , Wang Wanpeng , Shao Zongze 
Published: December 2012

ABSTRACT

Idiomarina xiamenensis
strain 10-D-4
T
was isolated from an oil-degrading consortium enriched from surface seawater around the Xiamen island. Here, we present the draft genome of strain 10-D-4
T
, which contains 2,899,282 bp with a G+C content of 49.48% and contains 2,673 protein-coding genes and 43 tRNA genes.
Genome Sequence of Oceanibaculum indicum Type Strain P24
Authors: Lai Qiliang , Shao Zongze 
Published: December 2012

ABSTRACT

Oceanibaculum indicum
type strain P24 was isolated from a polycyclic-aromatic-hydrocarbon-degrading consortium enriched from a deep-seawater sample collected from the Indian Ocean. Here we present the draft genome of strain P24
T
, which contains 3,952,792 bp with a G+C content of 65.5% and contains 3,755 protein-coding genes and 45 tRNAs.
Complete Genome Sequence of Bacillus thuringiensis Serovar Sichuansis Strain MC28
Authors: Guan Peng , Ai Peng , Dai Xiaojuan , Zhang Jing , Xu Lizhi , Zhu Jun , Li Qiao , Deng Qiming , Li Shuangcheng , Wang Shiquan , Liu Huannian , Wang Lingxia , Li Ping , Zheng Aiping 
Published: December 2012

ABSTRACT

Bacillus thuringiensis
is an important microbial insecticide used in the control of agricultural pests. Here we report the finished, annotated genome sequence of
Bacillus thuringiensis
serovar Sichuansis strain MC28, which can form parasporal crystals consisting of Cry4Cc1, Cry30Fa1, Cry53Ab1, Cry54Aa1, Cry54Ab1, Cry68Aa1, Cry69Aa1, Cry69Aa2, Cry70Ba1, Cyt1Da1, and Cyt2Aa3. It is also highly toxic to lepidopterous and dipterous insects.
Genome Sequence of Borrelia afzelii Strain HLJ01, Isolated from a Patient in China
Authors: Jiang Bao-Gui , Zheng Yuan-Chun , Tong Yi-Gang , Jia Na , Huo Qiu-Bo , Fan Hang , Ni Xue-Bing , Ma Lan , Yang X. Frank , Jiang Jia-Fu , Cao Wu-Chun 
Published: December 2012

ABSTRACT

We report here the genome sequence of
Borrelia afzelii
strain HLJ01, isolated from a patient with Lyme disease in China. It is the first report of the whole genome of a
B. burgdorferi
sensu lato isolate from a human in China.
Genome Sequence of the Bacteriocin-Producing Strain Lactococcus garvieae DCC43
Authors: Gabrielsen Christina , Brede Dag A. , Hernández Pablo E. , Nes Ingolf F. , Diep Dzung B. 
Published: December 2012

ABSTRACT

This work describes the draft genome sequence of
Lactococcus garvieae
DCC43. The 2.2-Mb draft genome contains 2,227 predicted protein-coding genes, among which is a region encoding the bacteriocin garvicin ML. No antibiotic resistance genes or capsule-related virulence genes were identified. Two plasmid replication regions indicate that this strain likely contains plasmids. Comparative genomics suggests that this strain displays a high degree of sequence variation from the previously sequenced
L. garvieae
strains.
Genome Sequence of Clostridium tunisiense TJ, Isolated from Drain Sediment from a Pesticide Factory
Authors: Sun Lili , Wang Yu , Yu Chunyan , Zhao Yongqin , Gan Yinbo 
Published: December 2012

ABSTRACT

Clostridium tunisiense
is a Gram-positive, obligate anaerobe that was first isolated in an anaerobic evironment under eutrophication. Here we report the first genome sequence of the
Clostridium tunisiense
TJ isolated from drain sediment of a pesticide factory in Tianjin, China. The genome is of great importance for both basic and application research.
Draft Genome Sequence of the Bean-Nodulating Sinorhizobium fredii Strain GR64
Authors: Torres Tejerizo Gonzalo , Lozano Luis , González Víctor , Bustos Patricia , Romero David , Brom Susana 
Published: December 2012

ABSTRACT

Sinorhizobium fredii
GR64 is a peculiar strain that is able to effectively nodulate bean but not soybean, the common host of
S. fredii
. Here we present the draft genome of
S. fredii
GR64. This information will contribute to a better understanding of the symbiotic rhizobium-plant interaction and of rhizobial evolution.
Genome Sequence of Strain IMCC14465, Isolated from the East Sea, Belonging to the PS1 Clade of Alphaproteobacteria
Authors: Yang Seung-Jo , Kang Ilnam , Cho Jang-Cheon 
Published: December 2012

ABSTRACT

Strain IMCC14465 was isolated from surface seawater of the East Sea using dilution-to-extinction culturing. Phylogenetic analysis indicated that the strain belongs to the PS1 clade, which is closely related to the OCS116 clade in the
Alphaproteobacteria
. Here, we report the genome sequence of IMCC14465, the first isolate of the PS1 clade.
Genome Sequence of Thalassospira profundimaris Type Strain WP0211
Authors: Lai Qiliang , Shao Zongze 
Published: December 2012

ABSTRACT

Thalassospira profundimaris
WP0211
T
was isolated from a pyrene-degrading consortium, enriched from deep-sea sediment collected from the West Pacific Ocean. Here, we present the draft genome of strain WP0211
T
, which contains 4,380,232 bp with a G+C content of 55.19% and contains 4,040 protein-coding genes and 45 tRNAs.
Complete Genome Sequence of Clostridium sp. Strain BNL1100, a Cellulolytic Mesophile Isolated from Corn Stover
Authors: Li Luen-Luen , Taghavi Safiyh , Izquierdo Javier A. , van der Lelie Daniel 
Published: December 2012

ABSTRACT

We present the full genome sequence of
Clostridium
sp. strain BNL1100, a Gram-positive, endospore-forming, lignocellulolytic bacterium isolated from a corn stover enrichment culture. The 4,613,747-bp genome of strain BNL1100 contains 4,025 putative protein-coding genes, of which 103 are glycoside hydrolases, the highest detected number in cluster III clostridia.
Draft Genome Sequence of Streptomyces sp. Strain SS, Which Produces a Series of Uridyl Peptide Antibiotic Sansanmycins
Authors: Wang Lifei , Xie Yunying , Li Qinglian , He Ning , Yao Entai , Xu Hongzhang , Yu Ying , Chen Ruxian , Hong Bin 
Published: December 2012

ABSTRACT

Streptomyces
sp. SS produces a series of uridyl peptide antibiotic sansanmycins. Here, we present a draft genome sequence of
Streptomyces
sp. SS containing the biosynthetic gene cluster for the antibiotics. The identification of the biosynthetic gene cluster of sansanmycins may provide further insight into biosynthetic mechanisms for uridyl peptide antibiotics.
Genome Sequence of Nitratireductor indicus Type Strain C115
Authors: Lai Qiliang , Li Guizhen , Yu Zhiwei , Shao Zongze 
Published: December 2012

ABSTRACT

Nitratireductor indicus
strain C115
T
was isolated from a crude-oil-degrading consortium enriched from deep seawater of the Indian Ocean. Here, we present the draft genome of strain C115
T
, which contains 4,992,479 bp with a G+C content of 60.8% and contains 4,825 protein-coding genes and 45 tRNA genes.
Genome Sequence of the Protease-Producing Bacterium Rheinheimera nanhaiensis E407-8
T
, Isolated from Deep-Sea Sediment of the South China Sea
Authors: Zhang Xi-Ying , Zhang Yan-Jiao , Qin Qi-Long , Xie Bin-Bin , Chen Xiu-Lan , Zhou Bai-Cheng , Zhang Yu-Zhong 
Published: December 2012

ABSTRACT

The protease-producing bacterium E407-8
T
was isolated from deep-sea sediment of the South China Sea and has been identified recently as representing a new species,
Rheinheimera nanhaiensis
. The draft genome of
R. nanhaiensis
E407-8
T
consists of 3,987,205 bp and contains 3,730 predicated protein-coding genes, including 82 extracellular peptidase genes.
Genome Sequence of Bartonella rattaustraliani, a Bacterium Isolated from an Australian Rat
Authors: Merhej Vicky , Croce Olivier , Robert Catherine , Rolain Jean-Marc , Raoult Didier 
Published: December 2012

ABSTRACT

Bartonella rattaustraliani
is a facultative intracellular bacterium isolated from the blood of a
Rattus
sp. in Australia. The present study reports the draft genome of
B. rattaustraliani
strain AUST/NH4 (CSUR B609
T
).
Genome Sequence of Enterobacter sp. Strain SP1, an Endophytic Nitrogen-Fixing Bacterium Isolated from Sugarcane
Authors: Zhu Bo , Chen Mingyue , Lin Li , Yang Litao , Li Yangrui , An Qianli 
Published: December 2012

ABSTRACT

Enterobacter
sp. strain SP1 is an endophytic nitrogen-fixing bacterium isolated from a sugarcane stem and can promote plant growth. The draft genome sequence of strain SP1 presented here will promote comparative genomic studies to determine the genetic background of interactions between endophytic enterobacteria and plants.
Monophyly of some North American species ofRamalinaand inferred polyketide synthase gene function
Authors: Timsina Brinda A. , Stocker-Wörgötter E. , Piercey-Normore Michele D. 
Published: December 2012

Ramalina thrausta (Ach.) Nyl., Ramalina roesleri (Hochst. Ex Schaerer) Hue, and Ramalina dilacerata (Hoffm.) Hoffm. are three common North American species that have not been placed in a phylogeny and are sympatric in their distribution leading to uncertainty about monophyly. Species characters include secondary metabolites (polyketides) in Ramalina that may be both hereditary and influenced by environmental conditions, but little is known about the function of polyketide synthase (PKS) genes. The main goal of this study was to examine the monophyly among some of the more common species in northern North America and secondarily to compare potential PKS gene function with the phylogeny. Nucleotide sequences of two genes, the internal transcribed spacer 1 of ribosomal DNA and the mitochondrial small subunit, were used to infer a phylogeny. Gene function was inferred from three PKS genes by the ratio of nonsynonymous to synonymous substitutions (dN:dS) ratios. Although seven species of Ramalina are highly supported in monophyletic clades, two other species form clusters with low support: Ramalina americana Hale is paraphyletic, and Ramalina pollinaria (Westr.) Ach. is polyphyletic. Three PKS genes were inferred to be functional but were not present in all samples. Functional PKS genes could enable adaptation to new habitats and facilitate species diversification.
Reply to the discussion of the reply by R.L. Romer and U. Kroner on “Geochemical signature of Ordovician Mn-rich sedimentary rocks on the Avalonian shelf” 1Appears in the Canadian Journal of Earth Sciences, 49(11): 1372–1377 [doi:10.1139/e2012-049].
Authors: Romer Rolf L. , Kroner Uwe 
Published: December 2012

Romer and Kroner (2012) stated “the core of the Harlech Dome (i) in part is made up of Ordovician deposits and (ii) contains tectonic repetitions”. In their comment, Schofield et al. (this issue) distort this statement and state that (i) we claim the entire sedimentary sequence of the Harlech Dome is Ordovician and (ii) we misinterpreted their zircon data. We disagree. In our reply, we demonstrate that the argumentation of Schofield et al. (this issue) is driven by circular argumentation and that their use and interpretation of U–Pb zircon data is inadequate.