bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutational patterns and correlated amino acid substitutions in the HIV‐1 protease after virological failure to nelfinavir‐ and lopinavir/ritonavir‐based treatments
Authors: Garriga César , Pérez‐Elías María Jesús , Delgado Rafael , Ruiz Lidia , Nájera Rafael , Pumarola Tomàs , Alonso‐Socas María del Mar , García‐Bujalance Silvia , Menéndez‐Arias Luis 
Published: September 2007

AbstractHuman immunodeficiency virus type 1 (HIV‐1) antiviral drug resistance is a major consequence of therapy failure and compromises future therapeutic options. Nelfinavir and lopinavir/ritonavir‐based therapies have been widely used in the treatment of HIV‐infected patients, in combination with reverse transcriptase inhibitors. The aim of this observational study was the identification and characterization of mutations or combinations of mutations associated with resistance to nelfinavir and lopinavir/ritonavir in treated patients. Nucleotide sequences of 1,515 subtype B HIV‐1 isolates from 1,313 persons with different treatment histories (including naïve and treated patients) were collected in 31 Spanish hospitals over the years 2002–2005. Chi‐square contingency tests were performed to detect mutations associated with failure to protease inhibitor‐based therapies, and correlated mutations were identified using statistical methods. Virological failure to nelfinavir was associated with two different mutational pathways. D30N and N88D appeared mostly in patients without previous exposure to protease inhibitors, while K20T was identified as a secondary resistance mutation in those patients. On the other hand, L90M together with L10I, I54V, A71V, G73S, and V82A were selected in protease inhibitor‐experienced patients. A series of correlated mutations including L10I, M46I, I54V, A71V, G73S, and L90M appeared as a common cluster of amino acid substitutions, associated with failure to lopinavir/ritonavir‐based treatments. Despite the relatively high genetic barrier of some protease inhibitors, a relatively small cluster of mutations, previously selected under drug pressure, can seriously compromise the efficiency of nelfinavir‐ and lopinavir/ritonavir‐based therapies. J. Med. Virol. 79:1617–1628, 2007. © 2007 Wiley‐Liss, Inc.
Native early antigen of Epstein–Barr virus, a promising antigen for diagnosis of nasopharyngeal carcinoma
Authors: Paramita Dewi K. , Fachiroh Jajah , Artama Wayan T. , van Benthem Eric , Haryana Sofia M. , Middeldorp Jaap M. 
Published: September 2007

AbstractThe Epstein–Barr virus (EBV) early antigen (EA) complex consists of multiple proteins with relevance for diagnosis of acute, chronic and malignant EBV related diseases, including nasopharyngeal carcinoma (NPC). In a recent study, it was found that the molecular diversity of EBV‐specific IgG and IgA antibody responses in NPC patients and demonstrated that these reflect independent B‐cell triggering leading to distinct EBV antigen‐recognition profiles. The fine‐specificity of NPC‐related IgG and IgA responses was explored further against defined recombinant and synthetic EBV‐EA antigens using immunofluorescence, immunoblot and ELISA techniques and determined their diagnostic value in a large panel of sera from NPC (n = 154), non‐NPC tumor patients (n = 133), acute mononucleosis patients (n = 70) and healthy EBV carriers (n = 259). Individual recombinant EBV‐EA markers yielded sensitivity/specificity values not exceeding 86%, whereas selected EA‐specific peptide epitopes were rather poorly recognized by IgG and IgA antibodies in NPC sera. Surprisingly, we found that a “low salt” native EA‐protein extract reproducibly prepared from purified nuclei of EA‐induced HH514 cells, and containing characteristic EA(D)‐polypeptides, such as p47‐54 (BMRF1), p138 (BALF2), p55‐DNAse (BGLF5), and p65‐TK (BXLF1), but without viral capsid (VCA) or nuclear antigen (EBNA) reactivity, gave highest sensitivity (90.4%) and specificity (95.5%) values for NPC diagnosis in both IgG and IgA ELISA. The data support further the notion that EBV‐EA reactive IgG and IgA antibodies in NPC patients are directed against distinct conformational and—in part—linear epitopes on EBV‐specific proteins, barely recognized in other EBV‐related syndromes. The use of a defined native EBV EA‐specific antigen opens the way to further improve serological diagnosis of NPC. J. Med. Virol. 79:1710–1721, 2007. © 2007 Wiley‐Liss, Inc.
Molecular characterization of G11P[25] and G3P[3] human rotavirus strains associated with asymptomatic infection in South India
Authors: Banerjee Indrani , Iturriza‐Gomara Miren , Rajendran Priya , Primrose Beryl , Ramani Sasirekha , Gray James J. , Brown David W. , Kang Gagandeep 
Published: September 2007

AbstractRotaviruses are the major etiological agents of diarrhea in children less than 5 years of age. Two unusual rotavirus strains not previously reported in India, G11P[25] (CRI 10795) and G3P[3] (CRI 33594) were isolated from faecal samples of asymptomatic children in India. The strains were characterized by sequence analysis of the genes encoding the VP7, VP4, VP6, and NSP4. The G11P[25] strain was closely related to the human G11P[25] strains from Bangladesh (with 98% identity at the nucleotide [nt] level and the amino acid [aa] level for the VP7 gene and 96% identity at the nt and 98% at the aa level for the VP4 gene). The G3P[3] strain was found to be related to a G3P[3] strain isolated in Thailand (CMH222; 88% identity at the nt level and 97% at aa level for the VP7 gene and 84% identity at the nt level and 90% at the aa level for the VP4 gene). Phylogenetic analysis of the VP6 and the NSP4 genes revealed that the Vellore G11P[25] strain was of VP6 subgroup II and NSP4 genotype B. The G3P[3] strain was identified as NSP4 genotype C and the VP6 gene showed 97% identity at the deduced amino acid level with strain CMH222 (Thailand) strain but did not cluster with sequences of SGI, SGII, SGI+II or SG‐nonI/nonII. Both strains had gene segments of animal rotavirus origin suggesting inter‐species transmission of rotavirus, and in the case of G11P[25] possibly underwent reassortment subsequently with human strains resulting in an animal–human hybrid strain. J. Med. Virol. 79:1768–1774, 2007. © 2007 Wiley‐Liss, Inc.
Molecular characterization of calicivirus strains detected in outbreaks of gastroenteritis in Argentina
Authors: Gomes Karina A. , Stupka Juan A. , Gómez Jorge , Parra Gabriel I. 
Published: September 2007

AbstractEight outbreaks of acute gastroenteritis occurred in Argentina in 2004 were tested for the presence of Calicivirus, Rotavirus and Astrovirus as possible causative agents. Caliciviruses were found in 39 out of the 100 tested samples, followed by six Astrovirus‐positive samples and two Rotavirus‐positive samples. Thirty‐seven out of the 39 Calicivirus‐positive samples were typed as Norovirus while the remaining two were typed as Sapovirus. Sequence and phylogenetic analyses of 13 Norovirus‐positive samples revealed the presence of strains from the genogroups GI, GII, and GIV. Six Norovirus strains were grouped with the GIV‐1 strains, three with the GIIb strains, two with the Farmington Hill‐cluster (GII‐4) strains, and the remaining two with the GI strains. To our knowledge, this study constitutes the first report of molecular epidemiology of human Caliciviruses associated to gastroenteritis outbreaks in Argentina and the circulation of GIIb and GIV‐1 strains in South‐America. J. Med. Virol. 79:1703–1709, 2007. © 2007 Wiley‐Liss, Inc.
Genital herpes due to acyclovir‐sensitive herpes simplex virus caused secondary and recurrent herpetic whitlows due to thymidine kinase‐deficient/temperature‐sensitive virus
Authors: Shimada Yuka , Suzuki Mikiko , Shirasaki Fumiaki , Saito Eriko , Sogo Kana , Hasegawa Minoru , Takehara Kazuhiko , Phromjai Jurairatana , Chuhjo Tatsuya , Shiraki Kimiyasu 
Published: September 2007

AbstractHerpes simplex virus (HSV)‐2 caused a genital ulcer in a 40‐year‐old allogenic stem cell recipient, and a secondary herpetic whitlow appeared during 2 months of acyclovir (ACV) therapy. Both genital ulcer, and whitlow were cured 3 months later, but 6 months after recovery the whitlow alone recurred. DNA of the genital, first, and recurrent whitlow isolates showed similar endonuclease digestion fragment profiles. The genital virus was ACV‐sensitive, and the two whitlow isolates were ACV‐resistant/thymidine kinase (TK)‐deficient. The TK gene of the whitlow isolates had the same frame shift from the 274th amino acid and termination at the 347th amino acid due to the deletion of a cytosine at the 819th nucleotide. Because the temperature of the thumb is 33/34°C or lower, the temperature sensitivity of the isolates were compared, and both whitlow isolates were significantly more temperature‐sensitive (ts) at 39°C than the genital isolate. The two whitlow isolates showed cutaneous pathogenicity in mouse ear pinna but not midflank, while the genital isolate was pathogenic at both sites, suggesting that temperature adaptation was an important element of pathogenicity in the whitlow. The virus populations of isolates of the genital, and first whitlow were examined by 31, and 82 clones, respectively, and the clones from genital, and whitlow isolates were ACV‐sensitive, and ‐resistant, respectively, showing their homogeneity. The acyclovir‐sensitive genital lesion had spread as a TK‐deficient/ts herpetic whitlow during ACV treatment, and an apparently TK‐deficient virus adapted to the local temperature might have caused the whitlow recurrence. J. Med. Virol. 79:1731–1740, 2007. © 2007 Wiley‐Liss, Inc.
Characterization of hepatitis E virus from outbreak and sporadic cases in Turkmenistan
Authors: Albetkova Adilya , Drobeniuc Jan , Yashina Tatiana , Musabaev Erkin , Robertson Betty , Nainan Omana , Favorov Michael 
Published: September 2007

AbstractLarge outbreaks and sporadic cases of hepatitis E have been reported in Central Asia. We assessed the genetic relatedness of hepatitis E virus (HEV) strains from outbreak and sporadic cases in Turkmenistan. Specimens from outbreak and sporadic cases of acute hepatitis non‐A, non‐B were tested by reverse transcription (RT)‐polymerase chain reaction (PCR) to identify the presence of HEV RNA; nucleotide sequences were analyzed. HEV RNA was detected from 23/156 (15%) outbreak cases and 2/23 (9%) sporadic cases. The HEV outbreak isolates represented 14 unique sequences with genetic distances varying between 0.3% and 8.6%, 12 of which were closely related, with distances between 0.3% and 5.6%. Two unique sequences from outbreak cases 32 and 42 were closely related (99.7%) and shared 91.8–93.4% of sequence with the other 12 strains. The two strains were closely related to the previously published isolates from Burma (99.7–100%) and India‐Madras (95.7–96.1%). The two 1994 sporadic HEV strains were 97.4% distinct, wile revealing 91.4–94.1% homology to 1985 strains, and 94.4–94.7% to HEV from the neighboring China and Pakistan. Genetic diversity of HEV that caused the hepatitis E outbreak in Turkmenistan in 1985 suggests heterogeneity of viral sources. Sporadic hepatitis E that occurred in 1994 was caused by viral strains genetically distinct from those causing the outbreak in 1985, yet closely related to HEV from neighboring countries. The study suggests that circulation of a broad variety of strains of HEV may occur in Central Asia, regardless of international borders, presenting a significant public health threat to the population of the region. J. Med. Virol. 79:1696–1702, 2007. © 2007 Wiley‐Liss, Inc.
Virological and clinical aspects of HBV‐HCV coinfection in HIV positive patients
Authors: Filippini Pietro , Coppola Nicola , Pisapia Raffaella , Martini Salvatore , Marrocco Cecilia , Di Martino Filomena , Sagnelli Caterina , Filippini Alberico , Sagnelli Evangelista 
Published: September 2007

AbstractIn a long‐term follow‐up study the clinical and virological presentation of HBV/HCV coinfection in anti‐HIV positive patients was evaluated. Plasma HBV‐DNA, HCV‐RNA, and HIV‐RNA were determined by PCR in 5 HBsAg/anti‐HCV/anti‐HIV positive patients, in 4 HBsAg/anti‐HIV positive patients and in 82 anti‐HCV/anti‐HIV positive patients first observed at a Unit of Infectious Diseases in Naples (Italy) from 1990 to 2000 (follow up 6–16 years). All five hepatitis B and C coinfected patients showed reciprocal inhibition of viral replication on admission and during the follow up. At the end of the follow up a clearance of HBsAg from serum was observed in four patients and a clearance of anti‐HCV in one of them. In two patients after clearance of HBsAg, evidence of occult HBV infection was observed, at times associated with a hepatic flare. None of the four patients with HIV/HBV coinfection lost HBsAg and none of the 82 with HIV/HCV coinfection lost anti‐HCV during the follow up. In anti‐HIV positive patients HBV/HCV coinfection is characterized by reciprocal inhibition of viral replication, more evident in HBV expression in plasma and at times by progression to occult HBV infection. J. Med. Virol. 79:1679–1685, 2007. © 2007 Wiley‐Liss, Inc.
Linking climate change modelling to impacts studies: recent advances in downscaling techniques for hydrological modelling
Authors: Fowler H. J. , Blenkinsop S. , Tebaldi C. 
Published: September 2007

AbstractThere is now a large published literature on the strengths and weaknesses of downscaling methods for different climatic variables, in different regions and seasons. However, little attention is given to the choice of downscaling method when examining the impacts of climate change on hydrological systems. This review paper assesses the current downscaling literature, examining new developments in the downscaling field specifically for hydrological impacts. Sections focus on the downscaling concept; new methods; comparative methodological studies; the modelling of extremes; and the application to hydrological impacts.Consideration is then given to new developments in climate scenario construction which may offer the most potential for advancement within the ‘downscaling for hydrological impacts’ community, such as probabilistic modelling, pattern scaling and downscaling of multiple variables and suggests ways that they can be merged with downscaling techniques in a probabilistic climate change scenario framework to assess the uncertainties associated with future projections. Within hydrological impact studies there is still little consideration given to applied research; how the results can be best used to enable stakeholders and managers to make informed, robust decisions on adaptation and mitigation strategies in the face of many uncertainties about the future. It is suggested that there is a need for a move away from comparison studies into the provision of decision‐making tools for planning and management that are robust to future uncertainties; with examination and understanding of uncertainties within the modelling system. Copyright © 2007 Royal Meteorological Society
Human autologous plasma‐derived clot as a biological scaffold for mesenchymal stem cells in treatment of orthopedic healing
Authors: Trombi Luisa , Mattii Letizia , Pacini Simone , D'Alessandro Delfo , Battolla Barbara , Orciuolo Enrico , Buda Gabriele , Fazzi Rita , Galimberti Sara , Petrini Mario 
Published: September 2007

AbstractRecent advances in the isolation, expansion, and characterization of human mesenchymal stem cells (hMSCs) have raised the possibility of using them in cell therapies and tissue engineering for bone reconstruction. hMSCs, isolated from the bone marrow of eight normal adult patients, were minimally expanded ex vivo and pulsed twice toward osteogenic lineage. The cells were then included into autologous plasma‐derived clots. Cytofluorimetric analysis, immunocytochemistry (osteopontin), histochemistry (alkaline phosphatase, Alcian blue, Von Kossa, and alizarin red staining), and viable/proliferation tests were performed to study both stem and differentiating cells. Although two short inductions increased osteogenic markers in hMSCs, inside the clot the cells were able to terminally differentiate into osteoblasts. Moreover, we show that the clot is able to sustain cell proliferation under appropriate cell culture conditions. Our results suggested that clot could be useful for hMSC delivery into the site of the lesion to promote bone formation. Moreover, the plasticity of this material allowed good in vitro hMSC spreading and proliferation. The advantages of using this autologous biological material are its biocompatibility and reabsorption; furthermore, using a gel as scaffold, it is possible to mold it to the shape of a bone cavity. © 2007 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:176–183, 2008
Knee angle and force vector‐dependent variations in open and closed kinetic chain for M. popliteus activation
Authors: Stensdotter Ann‐Katrin , Dalén Tore , Holmgren Christer , Häger‐Ross Charlotte 
Published: September 2007

AbstractThe popliteus muscle is short and deeply situated in the posterior aspect of the knee, and contributes to control knee joint position. Little is known how activation of the popliteus is controlled. We hypothesized that for the purpose of securing knee joint position, the popliteus would be activated prior to the prime movers of the knee, and that activation would occur earlier and be amplified with increased structural laxity due to joint loading direction and position. Surface and fine wire electromyography (EMG) was used to measure onset and amplitude of muscle activity in the popliteus and three parts of the quadriceps in 10 healthy women (age 25 ± 4 years). Subjects performed seated isometric knee extensions in 30° and 90° knee flexion in open (OKC) and closed kinetic chain (CKC) in a reaction time task. The popliteus was activated after the quadriceps in all tasks, but with shorter latency relative to the quadriceps in CKC, independent of knee flexion angle. EMG amplitude was greatest for all muscles in OKC in the 30° knee flexion. Biomechanical variables alone do not explain popliteus activation. In addition to biomechanics, behavioral, and habitual aspects need to be considered in further studies. © 2007 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:217–224, 2008
Late Quaternary vegetation, climate and fire dynamics inferred from the El Tiro record in the southeastern Ecuadorian Andes
Authors: Niemann Holger , Behling Hermann 
Published: September 2007

AbstractIn order to study the stability and dynamics of mountain rainforest and paramo ecosystems, including the biodiversity of these ecosystems, the Holocene and late Pleistocene climate and fire variability, and human impact in the southeastern Ecuadorian Andes, we present a high‐resolution pollen record from El Tiro Pass (2810 m elevation), Podocarpus National Park. Palaeoenvironmental changes, investigated by pollen, spores and charcoal analysis, inferred from a 127 cm long core spanning the last ca. 21 000 cal. yr BP, indicate that grass‐paramo was the main vegetation type at the El Tiro Pass during the late Pleistocene period. The grass‐paramo was rich in Poaceae, Plantago rigida and Plantago australis, reflecting cold and moist climatic conditions. During the early Holocene, from 11 200 to 8900 cal. yr BP, subparamo and upper mountain rainforest vegetation expanded slightly, indicating a slow warming of climatic conditions during this period. From 8900 to 3300 cal. yr BP an upper mountain rainforest developed at the study site, indicated by an increase in Hedyosmun, Podocarpaceae, Myrsine and Ilex. This suggests a warmer climate than the present day at this elevation. The modern subparamo vegetation became established since 3300 cal. yr BP at El Tiro Pass. Fires, probably anthropogenic origin, were very rare during the late Pleistocene but became frequent after 8000 cal. yr BP. Copyright © 2007 John Wiley & Sons, Ltd.
Peniophora lycii phytase is stabile and degrades phytate and solubilises minerals in vitro during simulation of gastrointestinal digestion in the pig
Authors: Pontoppidan Katrine , Pettersson Dan , Sandberg Ann‐Sofie 
Published: September 2007

AbstractBACKGROUND: Microbial phytases (EC 3.1.3) are widely used in diets for monogastric animals to hydrolyse phytate present in the feed and thereby increase phosphorus and mineral availability. Previous work has shown that phytate solubility is strongly affected by calcium in the feed and by pH in the gastrointestinal (GI) tract, which may have an effect on phytase efficacy. An in vitro model simulating the GI tract of pigs was used to study the survival of Peniophora lycii phytase and the effect of the phytase on phytate degradation, inositol phosphate formation and mineral solubilisation during in vitro digestion of a 30:70 soybean meal/maize meal blend with different calcium levels.RESULTS: The phytase retained 76 and 80% of its initial activity throughout the gastric in vitro digestion. Total phytate hydrolysis by P. lycii phytase was in the same range at total calcium levels of 1.2 and 6.2 mg g−1 dry matter (DM), despite very large differences in phytate solubility at these calcium levels. However, at 11.2 and 21.2 mg Ca g−1 DM, phytate hydrolysis was significantly lower. The amount of soluble mineral was generally increased by P. lycii phytase.CONCLUSION: Stability of P. lycii phytase during gastric digestion was not found to be critical for phytate hydrolysis. Furthermore, original phytate solubility was not an absolute requirement for phytate degradation; phytate solubility seemed to be in a steady state, allowing insoluble phytate to solubilise as soluble phytate was degraded. This is new and interesting knowledge that adds to the current understanding of phytate–phytase interaction. Copyright © 2007 Society of Chemical Industry
Interaction between nitrogen and sulfur by foliar application and its effects on flour bread‐making quality
Authors: Tea Illa , Genter Thierry , Naulet Norbert , Lummerzheim Marie , Kleiber Didier 
Published: September 2007

AbstractBACKGROUND: Optimization of nitrogen (N) and sulfur (S) nutrition of wheat influences the bread‐making quality of grain. This study was conducted to determine whether the application of N and S in winter wheat at anthesis stage during two field trials could influence the absorption and distribution of N and S in grain and flour bread‐making qualityRESULTS: The incorporation of 15N and 34S tracers in various plant parts (leaves, stems, spikes) was determined by isotopic ratio mass spectrometry coupled with an elemental analyser (EA‐IRMS). The effects of foliar fertilization on percentage of 15N and 34S recovery in various plant parts, grain yield, flour protein content, and dough properties were investigated after a combination of treatments: N (urea), S (micronized elemental S) and NS (both urea and micronized elemental S). Nitrogen (70–80%) and S (35–55%) were quickly assimilated during the days following application. Sixty days after application, 42–68% N and 6–12% S were recovered in the grain. When N and S fertilizers were applied simultaneously, N and S recoveries (68% and 12%), N/S ratios (11–14), flour protein content (115 g kg−1) and dough strength (310 × 10−4 J), swelling (21.8 mmH2O) and extensibility (96.4 mm) were increased.CONCLUSION: A synergistic effect between the foliar applied N and S fertilizers appears to increase N and S assimilation in grain and may improve bread‐making qualities. Copyright © 2007 Society of Chemical Industry