bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted genomic sequencing of pediatric Burkitt lymphoma identifies recurrent alterations in antiapoptotic and chromatin-remodeling genes
Authors: Giulino-Roth Lisa , Wang Kai , MacDonald Theresa Y. , Mathew Susan , Tam Yifang , Cronin Maureen T. , Palmer Gary , Lucena-Silva Norma , Pedrosa Francisco , Pedrosa Marcia , Teruya-Feldstein Julie , Bhagat Govind , Alobeid Bachir , Leoncini Lorenzo , Bellan Cristiana , Rogena Emily , Pinkney Kerice A. , Rubin Mark A. , Ribeiro Raul C. , Yelensky Roman , Tam Wayne , Stephens Philip J. , Cesarman Ethel 
Published: October 2012

Abstract
To ascertain the genetic basis of pediatric Burkitt lymphoma (pBL), we performed clinical-grade next-generation sequencing of 182 cancer-related genes on 29 formalin-fixed, paraffin embedded primary pBL samples. Ninety percent of cases had at least one mutation or genetic alteration, most commonly involving MYC and TP53. EBV(−) cases were more likely than EBV(+) cases to have multiple mutations (P < .0001). Alterations in tumor-related genes not previously described in BL were identified. Truncating mutations in ARID1A, a member of the SWI/SNF nucleosome remodeling complex, were seen in 17% of cases. MCL1 pathway alterations were found in 22% of cases and confirmed in an expanded panel. Other clinically relevant genomic alterations were found in 20% of cases. Our data suggest the roles of MCL1 and ARID1A in BL pathogenesis and demonstrate that comprehensive genomic profiling may identify additional treatment options in refractory disease.
Analysis of a slow-growing line reveals wide genetic variability of carcass and meat quality-related traits
Authors: Chabault Marie , Baéza Elisabeth , Gigaud Vérane , Chartrin Pascal , Chapuis Hervé , Boulay Maryse , Arnould Cécile , D’Abbadie François , Berri Cécile , Le Bihan-Duval Elisabeth 
Published: October 2012

Abstract

Background
Slow-growing lines are widely used in France for the production of high quality free-range chickens. While such production is mainly dedicated to the whole carcass market, new prospects are opening up for the development of cuts and processed products. Whether the body composition and meat quality of slow-growing birds can be improved by selection has thus become an important issue. The genetic parameters of growth, body composition and breast meat quality traits were evaluated in relation to behaviour at slaughter in a large pedigree population including 1022 male and female slow-growing birds.

Results
The heritability coefficients (h2) of body weight and body composition traits varied from 0.3 to 0.5. Abdominal fat percentage was genetically positively correlated with body weight but negatively correlated with breast muscle yield. The characteristics of the breast meat (i.e., post-mortem fall in pH, colour, drip loss, shear-force and lipid content) were all heritable, with h2 estimates ranging from 0.18 to 0.48. The rate and extent of the fall in pH were under different genetic control. Strong negative genetic correlations were found between the ultimate pH and the lightness, yellowness and drip loss of the meat. Wing flapping on the shackle line was significantly heritable and exhibited marked genetic correlations with the pH at 15 min post-slaughter and the redness of the meat. The genetic relationships between meat quality traits, body weight and body composition appeared slightly different between males and females.

Conclusion
This study suggested that there are a number of important criteria for selection on carcass and breast meat quality in slow-growing birds. Selection for reduced abdominal fatness and increased breast muscle yield should be effective as both traits were found to be highly heritable and favourably correlated. Substantial improvement in meat quality could be achieved by selection on ultimate pH which was highly heritable and strongly correlated with the colour and water-holding capacity of the meat. Moreover, this study revealed for the first time that the behaviour at slaughter is partly genetically determined in the chicken.
Controllable fabrication of PS/Ag core-shell-shaped nanostructures
Authors: Zhang Chunjing , Zhu Xianfang , Li Haixia , Khan Imran , Imran Muhammad , Wang Lianzhou , Bao Jianjun , Cheng Xuan 
Published: October 2012

Abstract
In this paper, based on the previous steps, a facile in situ reduction method was developed to controllably prepare polystyrene/Ag (PS/Ag) core-shell-shaped nanostructures. The crucial procedure includes surface treatment of polystyrene core particles by cationic polyelectrolyte polyethyleneimine, in situ formation of Ag nanoparticles, and immobilization of the Ag nanoparticles onto the surface of the polystyrene colloids via functional group NH from the polyethyleneimine. The experimental parameters, such as the reaction temperature, the reaction time, and the silver precursors were optimized for improvement of dispersion and Ag coat coverage of the core-shell-shaped nanostructures. Ultimately, the optimum parameters were obtained through a series of experiments, and well-dispersed, uniformly coated PS/Ag core-shell-shaped nanostructures were successfully fabricated. The formation mechanism of the PS/Ag core-shell-shaped nanostructures was also explained.
Opposing effects of Toll-like receptors 2 and 4 on synaptic stability in the spinal cord after peripheral nerve injury
Authors: Freria Camila Marques , Velloso Licio Augusto , Oliveira Alexandre LR 
Published: October 2012

AbstractBackgroundGlial cells are involved in the synaptic elimination process that follows neuronal lesions, and are also responsible for mediating the interaction between the nervous and immune systems. Neurons and glial cells express Toll-like receptors (TLRs), which may affect the plasticity of the central nervous system (CNS). Because TLRs might also have non-immune functions in spinal-cord injury (SCI), we aimed to investigate the influence of TLR2 and TLR4 on synaptic plasticity and glial reactivity after peripheral nerve axotomy.MethodsThe lumbar spinal cords of C3H/HePas wild-type (WT) mice, C3H/HeJ TLR4-mutant mice, C57BL/6J WT mice, and C57BL/6J TLR2 knockout (KO) mice were studied after unilateral sciatic nerve transection. The mice were killed via intracardiac perfusion, and the spinal cord was processed for immunohistochemistry, transmission electron microscopy (TEM), western blotting, cell culture, and reverse transcriptase PCR. Primary cultures of astrocytes from newborn mice were established to study the astrocyte response in the absence of TLR2 and the deficiency of TLR4 expression.ResultsThe results showed that TLR4 and TLR2 expression in the CNS may have opposite effects on the stability of presynaptic terminals in the spinal cord. First, TLR4 contributed to synaptic preservation of terminals in apposition to lesioned motor neurons after peripheral injury, regardless of major histocompatibility complex class I (MHC I) expression. In addition, in the presence of TLR4, there was upregulation of glial cell-derived neurotrophic factor and downregulation of interleukin-6, but no morphological differences in glial reactivity were seen. By contrast, TLR2 expression led to greater synaptic loss, correlating with increased astrogliosis and upregulation of pro-inflammatory interleukins. Moreover, the absence of TLR2 resulted in the upregulation of neurotrophic factors and MHC I expression.ConclusionTLR4 and TLR2 in the CNS may have opposite effects on the stability of presynaptic terminals in the spinal cord and in astroglial reactions, indicating possible roles for these proteins in neuronal and glial responses to injury.
Ano-genital human papillomavirus type 97 infection is detected in Canadian men but not women at risk or infected with the human immunodeficiency virus
Authors: Landry Marie-Eve , Salit Irving E , Rodrigues-Coutlée Catherine , Money Deborah , Rebbapragada Anu , Tinmouth Jill , Hankins Catherine , Gorska-Flipot Isabelle , Archambault Jacques , Franco Eduardo L , Coutlée François 
Published: October 2012

Abstract

Background
Human papillomavirus type 97 (HPV97) DNA was detected in nearly 5% of anal samples collected from HIV-seropositive men living in Montreal, Canada. The rate of detection of HPV97 in the genital tract of Canadian women is unknown. Whether HPV97 is a local epidemic in HIV-seropositive men living in Montreal is also unknown. The prevalence of human papillomavirus type 97 (HPV97) was assessed in cervicovaginal cells from women living in Canada and in anal samples from HIV-seropositive men living in Toronto.

Findings
Cervicovaginal lavages collected from 904 women (678 HIV-seropositive, 226 HIV-seronegative) women living in Canada and anal cells collected from 123 HIV-seropositive men living in Toronto were tested for the presence of HPV97 with PCR. HPV97-positive samples were further tested by PCR-sequencing for molecular variant analysis to assess if all HPV97-positive men were infected with the same strain. All cervicovaginal samples were negative for HPV97. HPV97 was detected in anal samples from 6 HIV-seropositive men (4.9%, 95% confidence interval 2.0-10.5%), of whom five had high-grade and one had low-grade anal intraepithelial neoplasia, in addition to 2 to 8 HPV genital genotypes per sample. Four HPV97 variants were defined by four variation sites in the viral control region.

Conclusion
These findings indicate that HPV97 infects in the anal canal of HIV-seropositive men but is not detected in the genital tract of women.
N-Acetyl-Cysteine Causes Analgesia by Reinforcing the Endogenous Activation of Type-2 Metabotropic Glutamate Receptors
Authors: Bernabucci Matteo , Notartomaso Serena , Zappulla Cristina , Fazio Francesco , Cannella Milena , Motolese Marta , Battaglia Giuseppe , Bruno Valeria , Gradini Roberto , Nicoletti Ferdinando 
Published: October 2012

Background: Pharmacological activation of type-2 metabotropic glutamate receptors (mGlu2 receptors) causes analgesia in experimental models of inflammatory and neuropathic pain. Presynaptic mGlu2 receptors are activated by the glutamate released from astrocytes by means of the cystine/glutamate antiporter (System x−c or Sx−c). We examined the analgesic activity of the Sx−c activator, N-acetyl-cysteine (NAC), in mice developing inflammatory or neuropathic pain. Results: A single injection of NAC (100 mg/kg, i.p.) reduced nocifensive behavior in the second phase of the formalin test. NAC-induced analgesia was abrogated by the Sx−c inhibitor, sulphasalazine (8 mg/kg, i.p.) or by the mGlu2/3 receptor antagonist, LY341495 (1 mg/kg, i.p.). NAC still caused analgesia in mGlu3−/− mice, but was inactive in mGlu2−/− mice. In wild-type mice, NAC retained the analgesic activity in the formalin test when injected daily for 7 days, indicating the lack of tolerance. Both single and repeated injections of NAC also caused analgesia in the complete Freund's adjuvant (CFA) model of chronic inflammatory pain, and, again, analgesia was abolished by LY341495. Data obtained in mice developing neuropathic pain in response to chronic constriction injury (CCI) of the sciatic nerve were divergent. In this model, a single injection of NAC caused analgesia that was reversed by LY341495, whereas repeated injections of NAC were ineffective. Thus, tolerance to NAC-induced analgesia developed in the CCI model, but not in models of inflammatory pain. The CFA and CCI models differed with respect to the expression levels of xCT (the catalytic subunit of Sx−c) and activator of G-protein signaling type-3 (AGS3) in the dorsal portion of the lumbar spinal cord. CFA-treated mice showed no change in either protein, whereas CCI mice showed an ipislateral reduction in xCT levels and a bilateral increase in AGS3 levels in the spinal cord. Conclusions: These data demonstrate that pharmacological activation of Sx−c causes analgesia by reinforcing the endogenous activation of mGlu2 receptors. NAC has an excellent profile of safety and tolerability when clinically used as a mucolytic agent or in the management of acetaminophen overdose. Thus, our data encourage the use of NAC for the experimental treatment of inflammatory pain in humans.
Trigeminal-Rostral Ventromedial Medulla Circuitry is Involved in Orofacial Hyperalgesia Contralateral to Tissue Injury
Authors: Chai Bryan , Guo Wei , Wei Feng , Dubner Ronald , Ren Ke 
Published: October 2012

Background: Our previous studies have shown that complete Freund's adjuvant (CFA)-induced masseter inflammation and microinjection of the pro-inflammatory cytokine interleukin-1β (IL-1β) into the subnucleus interpolaris/subnucleus caudalis transition zone of the spinal trigeminal nucleus (Vi/Vc) can induce contralateral orofacial hyperalgesia in rat models. We have also shown that contralateral hyperalgesia is attenuated with a lesion of the rostral ventromedial medulla (RVM), a critical site of descending pain modulation. Here we investigated the involvement of the RVM-Vi/Vc circuitry in mediating contralateral orofacial hyperalgesia after an injection of CFA into the masseter muscle. Results: Microinjection of the IL-1 receptor antagonist (5 nmol, n=6) into the ipsilateral Vi/Vc attenuated the CFA-induced contralateral hyperalgesia but not the ipsilateral hyperalgesia. Intra-RVM post-treatment injection of the NK1 receptor antagonists, RP67580 (0.5-11.4 nmol) and L-733,060 (0.5-11.4 nmol), attenuated CFA-induced bilateral hyperalgesia and IL-1β induced bilateral hyperalgesia. Serotonin depletion in RVM neurons prior to intra-masseter CFA injection prevented the development of contralateral hyperalgesia 1–3 days after CFA injection. Inhibition of 5-HT3 receptors in the contralateral Vi/Vc with direct microinjection of the select 5-HT3 receptor antagonist, Y-25130 (2.6-12.9 nmol), attenuated CFA-induced contralateral hyperalgesia. Lesions to the ipsilateral Vc prevented the development of ipsilateral hyperalgesia but did not prevent the development of contralateral hyperalgesia. Conclusions: These results suggest that the development of CFA-induced contralateral orofacial hyperalgesia is mediated through descending facilitatory mechanisms of the RVM-Vi/Vc circuitry.
Estimates of marker effects for measures of milk flow in the Italian brown Swiss dairy cattle population
Authors: Gray Kent A , Maltecca Christian , Bagnato Alessandro , Dolezal Marlies , Rossoni Attilio , Samore Antonia B , Cassady Joseph P 
Published: October 2012

Abstract

Background
Milkability is a complex trait that is characterized by milk flow traits including average milk flow rate, maximum milk flow rate and total milking time. Milkability has long been recognized as an economically important trait that can be improved through selection. By improving milkability, management costs of milking decrease through reduced labor and improved efficiency of the automatic milking system, which has been identified as an important factor affecting net profit. The objective of this study was to identify markers associated with electronically measured milk flow traits, in the Italian Brown Swiss population that could potentially improve selection based on genomic predictions.

Results
Sires (n = 1351) of cows with milk flow information were genotyped for 33,074 single nucleotide polymorphism (SNP) markers distributed across 29 Bos taurus autosomes (BTA). Among the six milk flow traits collected, ascending time, time of plateau, descending time, total milking time, maximum milk flow and average milk flow, there were 6,929 (time of plateau) to 14,585 (maximum milk flow) significant SNP markers identified for each trait across all BTA. Unique regions were found for each of the 6 traits providing evidence that each individual milk flow trait offers distinct genetic information about milk flow. This study was also successful in identifying functional processes and genes associated with SNPs that influences milk flow.

Conclusions
In addition to verifying the presence of previously identified milking speed quantitative trait loci (QTL) within the Italian Brown Swiss population, this study revealed a number of genomic regions associated with milk flow traits that have never been reported as milking speed QTL. While several of these regions were not associated with a known gene or QTL, a number of regions were associated with QTL that have been formerly reported as regions associated with somatic cell count, somatic cell score and udder morphometrics. This provides further evidence of the complexity of milk flow traits and the underlying relationship it has with other economically important traits for dairy cattle. Improved understanding of the overall milking pattern will aid in identification of cows with lower management costs and improved udder health.
Nutritive quality of romanian hemp varieties (Cannabis sativa L.) with special focus on oil and metal contents of seeds
Authors: Mihoc Marcela , Pop Georgeta , Alexa Ersilia , Radulov Isidora 
Published: October 2012

Abstract

Background
The study aims to determine the nutritional value of hemp seed expressed by the oil content and by the concentration of metals (Ca, Mg, K, Fe, Mn, Zn and Cd), for five varieties of monoecious and dioecious hemp seeds approved in Romania, comparative with the concentration of these metals in the soil.

Results
The content of oil in hempseed registers a slight decrease in the production records of 2011, losses due to drought and low levels of precipitation during the growth period. The greatest loss is found in Diana monoecious variety (26.54-20.82%) followed by Zenit varieties (27.37-22.97%), Armanca (29.27-25.32%), Silvana (28.89-25.04%) and Denise (26.96-25.30%). Siccative hemp oil has a yellowish green color and an iodine index of 140–156 g I2/100 g oil. Hemp seed are rich in mineral based Ca (144–955 mg/100 g seed), Mg (237–694 mg/100 g seed), K (463–2821 mg/100 g seed), Fe (1133-2400 mg.kg-1), Mn (63–110 mg.kg-1) and Zn (42-94 mg.kg-1). For the soil the following macroelements concentrations were determined: Ca (2100–2520 mg.kg-1), Mg (320–376 mg.kg-1) and K (232–257 mg.kg-1). Mn (156–197 mg.kg-1) and Zn (54–67 mg.kg-1) remain within normal limits for Romania. The soils in the experience area contain large amounts of Fe (19000–20430 mg.kg-1). The presence of K in large quantities determines the accumulation of large quantities of Fe in the soil.

Conclusion
Hempseed belonging to the five Romanian varieties are rich source of nutrients (Ca, Mg, K) and unsaturated oil easily digestible by the body, but the presence of Cd concentrations above the upper limit puts a question mark over the use of seeds in various food products. Hemp extracts easily certain metals from the soil. Significant amounts of Fe (1133–2400 mg.kg-1), Mn (63–110 mg.kg-1), Zn (42–94 mg.kg-1) and Cd (1.3-4.0 mg.kg-1) are found in hemp seeds. Hemp (Cannabis sativa L.) is included among plants suitable for phytoremediation of soil contaminated with cadmium, zinc and iron.
Bacillus coagulans GBI-30, 6086 limits the recurrence of Clostridium difficile-Induced colitis following vancomycin withdrawal in mice
Authors: Fitzpatrick Leo R , Small Jeffrey S , Greene Wallace H , Karpa Kelly D , Farmer Sean , Keller David 
Published: October 2012

AbstractBackgroundRecently, we found that the probiotic strainBacillus coagulansGBI-30, 6086 (GanedenBC30) improved indices ofClostridium difficile (C. difficile)-induced colitis in mice (Fitzpatrick et al.,Gut Pathogens, 2011). Our goal was to determine if BC30 could also prevent the recurrence ofC. difficile-induced colitis in mice, following initial treatment with vancomycin. During study days 0 through 5, mice were treated with antibiotics. On day 6, theC. difficilestrain VPI 10463 was given by oro-gastric gavage at ≈ 5x104CFU to induce colitis. Mice were treated on study days 6 to 10 with vancomycin (50 mg/kg) (vanco) or vehicle (saline) by gavage. On days 10 to16, mice were dosed by gavage with saline vehicle or BC30 (2 x 109CFU per day). Mice were monitored for mortality, weight loss and diarrhea. On study days 14, 16 and 17, stools and colons were collected for analyzing other parameters of colitis.ResultsThe mean stool consistency score in Vehicle/C.difficile/Vanco mice increased from 0.4 (day 10) to a range of 1.1 to 1.4 (days 14 to 17), indicating the recurrence of colitis. On days 13 through 17, the stool consistency scores for the vancomycin/BC30 mice were significantly lower (p< 0.05) than for the vancomycin/vehicle cohort of animals. On day 17, 88.9% of mice treated with BC30 had normal stools, while this value was 0% with vehicle treatment (p value = 0.0004). Colonic myeloperoxidase (Units/2 cm colon) was significantly (p < 0.05) reduced from 4.3 ± 0.7 (Vehicle/C.difficile/Vanco) to 2.6 ± 0.2 (BC30/C. Difficle/Vanco). The colonic histology score and Keratinocyte derived-chemokine level in the colon were also lower in BC30 treated mice.SummaryIn BC30-treated mice, there was evidence of better stool consistency, as well as improved biochemical and histological indices of colitis, following initial treatment of animals with vancomycin.ConclusionBC30 limited the recurrence ofCD-induced colitis following vancomycin withdrawal in mice.
Decolorization and biodegradation of reactive sulfonated azo dyes by a newly isolated Brevibacterium sp. strain VN-15
Authors: Franciscon Elisangela , Grossman Matthew James , Paschoal Jonas Augusto Rizzato , Reyes Felix Guillermo Reyes , Durrant Lucia Regina 
Published: October 2012

Abstract
Azo dyes constitute the largest and most versatile class of synthetic dyes used in the textile, pharmaceutical, food and cosmetics industries and represent major components in wastewater from these industrial dying processes. Biological decolorization of azo dyes occurs efficiently under low oxygen to anaerobic conditions. However, this process results in the formation of toxic and carcinogenic amines that are resistant to further detoxification under low oxygen conditions. Moreover, the ability to detoxify these amines under aerobic conditions is not a wide spread metabolic activity. In this study we describe the use of Brevibacterium sp. strain VN-15, isolated from an activated sludge process of a textile company, for the sequential decolorization and detoxification of the azo dyes Reactive Yellow 107 (RY107), Reactive Black 5 (RB5), Reactive Red 198 (RR198) and Direct Blue 71 (DB71). Tyrosinase activity was observed during the biotreatment process suggesting the role of this enzyme in the decolorization and degradation process, but no-activity was observed for laccase and peroxidase. Toxicity, measured using Daphnia magna, was completely eliminated.