38 results on '"Allard, Marc"'
Search Results
2. Treatment strategies to resectable metachronous colorectal liver metastases after adjuvant oxaliplatin‐based chemotherapy for primary colorectal cancer.
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Julio, Camille, Benoist, Stephane, Allard, Marc‐Antoine, Navarro, Francis, Pessaux, Patrick, Sa Cunha, Antonio, and Brouquet, Antoine
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- 2022
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3. Impact of the duration of normothermic regional perfusion on the results of liver transplant from controlled circulatory death donors: A retrospective, multicentric study.
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Barbier, Louise, Guillem, Thomas, Savier, Eric, Scatton, Olivier, Dondero, Federica, Si Larbi, Anne‐Gaëlle, Bucur, Petru, Sulpice, Laurent, Robin, Fabien, Goumard, Claire, Muller, Xavier, Venhard, Jean‐Christophe, Allard, Marc‐Antoine, Pittau, Gabriella, Soubrane, Olivier, Mercier, Emmanuelle, Laffon, Marc, Lesurtel, Mickael, and Salamé, Ephrem
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ISOLATION perfusion ,LIVER transplantation ,HOMOGRAFTS ,LIVER ,REPERFUSION injury - Abstract
In France, the program of controlled donation after circulatory death (cDCD) was established with routine use of in situ normothermic regional perfusion (NRP). There is currently no consensus on its optimal duration. The purpose was to assess the impact of NRP duration on liver graft function and biliary outcomes. One‐hundred and fifty‐six liver recipients from NRP‐cDCD donors from six French centers between 2015 and 2019 were included. Primary endpoint was graft function assessed by early allograft dysfunction (EAD, according to Olthoff's criteria) and MEAF (model for early allograft function) score. Overall, three (1.9%) patients had primary non‐function, 30 (19.2%) patients experienced EAD, and MEAF score was 7.3 (±1.7). Mean NRP duration was 179 (±43) min. There was no impact of NRP duration on EAD (170±44 min in patients with EAD vs. 181±42 min in patients without, P =.286). There was no significant association between NRP duration and MEAF score (P =.347). NRP duration did neither impact on overall biliary complications nor on non‐anastomotic biliary strictures (overall rates of 16.7% and 3.9%, respectively). In conclusion, duration of NRP in cDCD donors does not seem to impact liver graft function and biliary outcomes after liver transplantation. A 1 to 4‐h perfusion represents an optimal time window. [ABSTRACT FROM AUTHOR]
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- 2022
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4. Optimal patient selection for successful two‐stage hepatectomy of bilateral colorectal liver metastases.
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Imai, Katsunori, Allard, Marc‐Antoine, Baba, Hideo, and Adam, René
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HEPATECTOMY ,COLORECTAL cancer ,PATIENT selection - Abstract
Two‐stage hepatectomy (TSH) is one of the specific surgical techniques that can expand the pool of resectable patients with initially unresectable colorectal liver metastases (CRLM). The indication of TSH for CRLM is only bilateral, multinodular disease, which cannot be resected by a single hepatectomy. TSH is nowadays considered an effective treatment for selected patients, with acceptable morbidity/mortality rates and promising long‐term outcomes. However, not all eligible patients can benefit from the TSH strategy. One of the most important issues is dropout from the strategy (failure to complete both of the two sequential procedures), because the survival of such patients is drastically worse compared with patients who can complete both stages. Another important issue is the early recurrence rate and subsequent poor survival even after completion of TSH. Thus, the selection of appropriate patients who can really benefit from the TSH strategy is crucial. This review discusses the optimal patient selection for TSH, which should be helpful for the development of treatment strategies for patients with extensive CRLM. Although two‐stage hepatectomy (TSH) for extensive colorectal liver metastases (CRLM) is nowadays considered an effective treatment for selected patients, with acceptable morbidity/mortality rates and promising long‐term outcomes, not all eligible patients can benefit from this strategy. In this review, we discuss the optimal patient selection for TSH, which should be helpful for the development of treatment strategies for patients with extensive CRLM. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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5. Ideal Surgical Margin to Prevent Early Recurrence After Hepatic Resection for Hepatocellular Carcinoma.
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Nitta, Hidetoshi, Allard, Marc-Antoine, Sebagh, Mylène, Golse, Nicolas, Ciacio, Oriana, Pittau, Gabriella, Vibert, Eric, Sa Cunha, Antonio, Cherqui, Daniel, Castaing, Denis, Bismuth, Henri, Baba, Hideo, and Adam, René
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SURGICAL margin , *HEPATOCELLULAR carcinoma , *LOGISTIC regression analysis , *ALPHA fetoproteins , *ODDS ratio - Abstract
Backgrounds and Aims: Postoperative early recurrence after hepatic resection for hepatocellular carcinoma (HCC) poses a challenge to surgeons, and the effect of a surgical margin is still controversial. This study aimed to identify an ideal margin to prevent early recurrence. Methods: A total of 226 consecutive patients who underwent primary curative hepatic resection for solitary and primary HCC were enrolled. The definition of early recurrence was determined using the minimum P value approach. Logistic regression analysis was used to identify the risk factors of early recurrence. The receiver-operating characteristic (ROC) curve was used to identify the optimal cut-off of the surgical margin and early recurrence. Results: Recurrence within 8 months induced the poorest overall survival (P = 2×10−15). ROC analysis showed that the optimal cut-off value of the surgical margin was 7 mm. The risk factors of early recurrence (≤ 8-month recurrence) were preoperative alpha-fetoprotein levels ≥ 100 ng/ml (Odds ratio [OR] 4.92 [2.28–10.77], P < 0.0001) and a surgical margin < 7 mm (OR 3.09 [1.26–8.85], P = 0.01) by multivariable analysis. The probability of early recurrence ranged from 5.0% in the absence of any factors to 43.5% in the presence of both factors. Among patients with alpha-fetoprotein levels ≥ 100 ng/ml, non-capsule formation, or microvascular invasion, there was a significant difference in 5-year overall survival between surgical margins of < 7 mm and ≥ 7 mm. Conclusions: A > 7-mm margin is important to prevent early recurrence. Patients with HCC and alpha-fetoprotein levels > 100 ng/ml, non-capsule formation, or microvascular invasion may have a survival benefit from a ≥ 7-mm margin. [ABSTRACT FROM AUTHOR]
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- 2021
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6. Early‐ and long‐term outcomes of liver transplantation with rescue allocation grafts.
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Kitano, Yuki, Allard, Marc‐Antoine, Nakada, Shinichiro, Beghdadi, Nassiba, Karam, Vincent, Vibert, Eric, Sa Cunha, Antonio, Castaing, Denis, Cherqui, Daniel, Baba, Hideo, and Adam, René
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ALLOCATION of organs, tissues, etc. , *LIVER transplantation - Abstract
In France, liver grafts which have been refused by at least five centers are proposed as rescue allocation (RA). The aim of this study is to clarify the feasibility and safety of RA grafts in liver transplantation (LT). Short‐ and long‐term outcomes of patients who received RA grafts (RA group) were compared with those of patients who received standard allocation (SA) grafts (SA group). From a total of 1635 patients, 102 patients received RA grafts. Before matching, the RA group was characterized primarily by less severe liver disease, but the quality of graft was worse. After matching recipients' characteristics of 102 patients who used RA grafts with 306 patients who used SA grafts, recipients' characteristics were well balanced (1:3 matching). Although the rate of primary dysfunction was significantly higher in the RA group, there is no significant difference in the occurrence of major complications, length of hospitalization, and mortality between two groups. Graft survival (GS) and overall survival (OS) in the RA group were not significantly different from the SA group (GS; HR = 1.03 P =.89, OS; HR = 1.03 P =.90). In the French allocation system, the feasibility and safety of RA grafts might be comparable to SA grafts for carefully selected patients. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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7. Genomics‐based re‐examination of the taxonomy and phylogeny of human and simian Mastadenoviruses: an evolving whole genomes approach, revealing putative zoonosis, anthroponosis, and amphizoonosis.
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Kang, June, Ismail, Ashrafali Mohamed, Dehghan, Shoaleh, Rajaiya, Jaya, Allard, Marc W., Lim, Haw Chuan, Dyer, David W., Chodosh, James, and Seto, Donald
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ADENOVIRUS diseases ,DNA vaccines ,GENETIC transformation ,TAXONOMY ,TRANSLATIONAL research ,GENE therapy - Abstract
With the advent of high‐resolution and cost‐effective genomics and bioinformatics tools and methods contributing to a large database of both human (HAdV) and simian (SAdV) adenoviruses, a genomics‐based re‐evaluation of their taxonomy is warranted. Interest in these particular adenoviruses is growing in part due to the applications of both in gene transfer protocols, including gene therapy and vaccines, as well in oncolytic protocols. In particular, the re‐evaluation of SAdVs as appropriate vectors in humans is important as zoonosis precludes the assumption that human immune system may be naïve to these vectors. Additionally, as important pathogens, adenoviruses are a model organism system for understanding viral pathogen emergence through zoonosis and anthroponosis, particularly among the primate species, along with recombination, host adaptation, and selection, as evidenced by one long‐standing human respiratory pathogen HAdV‐4 and a recent re‐evaluation of another, HAdV‐76. The latter reflects the insights on amphizoonosis, defined as infections in both directions among host species including "other than human", that are possible with the growing database of nonhuman adenovirus genomes. HAdV‐76 is a recombinant that has been isolated from human, chimpanzee, and bonobo hosts. On‐going and potential impacts of adenoviruses on public health and translational medicine drive this evaluation of 174 whole genome sequences from HAdVs and SAdVs archived in GenBank. The conclusion is that rather than separate HAdV and SAdV phylogenetic lineages, a single, intertwined tree is observed with all HAdVs and SAdVs forming mixed clades. Therefore, a single designation of "primate adenovirus" (PrAdV) superseding either HAdV and SAdV is proposed, or alternatively, keeping HAdV for human adenovirus but expanding the SAdV nomenclature officially to include host species identification as in ChAdV for chimpanzee adenovirus, GoAdV for gorilla adenovirus, BoAdV for bonobo adenovirus, and ad libitum. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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8. A Model to Predict Significant Macrosteatosis in Hepatic Grafts.
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Swelam, Ahmed, Adam, René, Lauka, Lelde, Basilio Rodrigues, Luiza, Elgarf, Sherif, Sebagh, Mylène, Golse, Nicolas, Sa Cunha, Antonio, Cherqui, Daniel, Castaing, Denis, and Allard, Marc-Antoine
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BODY mass index ,ALCOHOLISM ,BRAIN death ,LIVER biopsy - Abstract
Background and aims: Assessing the risk of significant macrosteatosis in donors is crucial before considering hepatic graft procurement. We aimed to build a model to predict significant macrosteatosis based on noninvasive methods. Methods: From January 2012 to December 2018, liver attenuation indices and liver-to-spleen (L/S) ratio were measured in 639 brain-dead donors by local radiologists. Quantity and quality of steatosis were evaluated by an expert pathologist, blinded for attenuation indices measurement. Results: Macrosteatosis ≥ 30% was found in 33 donors (5.2%). Body weight, body mass index (BMI), abdominal perimeters, history of alcohol abuse, L/S ratio, and liver parenchyma attenuation were associated with macrosteatosis ≥ 30%. The L/S ratio, BMI, and a history of alcohol abuse remained independent predictors in multivariate analysis and were used to build a predictive model (C-index: 0.77). The optimal cutoff to predict macrosteatosis ≥ 60% was 0.85. Conclusion: Our model, including L/S ratio, BMI, and history of alcohol, might be helpful to refine indication for liver biopsy before donation after brain death. External validation is required. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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9. In‐depth comparative analysis of Illumina® MiSeq run metrics: Development of a wet‐lab quality assessment tool.
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Kastanis, George John, Sanchez‐Leon, Maria, Brown, Eric W., Allard, Marc W., Lomonaco, Sara, and Santana‐Quintero, Luis V.
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NUCLEOTIDE sequencing ,DATA analysis ,BACTERIA ,GENOMES ,PRINCIPAL components analysis ,CLUSTER analysis (Statistics) ,COMPARATIVE studies - Abstract
Whole genome sequencing of bacterial isolates has become a daily task in many laboratories, generating incredible amounts of data. However, data acquisition is not an end in itself; the goal is to acquire high‐quality data useful for understanding genetic relationships. Having a method that could rapidly determine which of the many available run metrics are the most important indicators of overall run quality and having a way to monitor these during a given sequencing run would be extremely helpful to this effect. Therefore, we compared various run metrics across 486 MiSeq runs, from five different machines. By performing a statistical analysis using principal components analysis and a K‐means clustering algorithm of the metrics, we were able to validate metric comparisons among instruments, allowing for the development of a predictive algorithm, which permits one to observe whether a given MiSeq run has performed adequately. This algorithm is available in an Excel spreadsheet: that is, MiSeq Instrument & Run (In‐Run) Forecast. Our tool can help verify that the quantity/quality of the generated sequencing data consistently meets or exceeds recommended manufacturer expectations. Patterns of deviation from those expectations can be used to assess potential run problems and plan preventative maintenance, which can save valuable time and funding resources. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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10. Genomics of Salmonella contaminating backyard production systems reveals persistence and transmission of genetically related Salmonella on a farm basis.
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Toro, Magaly, Rivera, Dácil, Toledo, Viviana, Campos‐Vargas, Reinaldo, Allard, Marc W., Hamilton‐West, Christopher, and Moreno‐Switt, Andrea I.
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SALMONELLA diseases ,ENTEROBACTERIACEAE diseases ,SALMONELLA genetics ,PHYLOGENY ,FOODBORNE diseases - Abstract
Animals raised in backyard productive systems (BPS) have been frequently associated with Salmonella outbreaks. Several serovars have caused these events, showing that different BPSs can be contaminated by distinct Salmonella serovars. The aim of this study was to characterize the genomic diversity of Salmonella isolates obtained from BPSs in Central Chile to understand their genomic relatedness. A whole‐genome SNP‐based phylogenetic analysis of 22 Salmonella isolates from 12 locations revealed that S. Typhimurium isolates clustered based on the BPS that they were originally isolated from, and the same was established for S. Enteritidis isolates. Furthermore, our genomic analysis shows that animals from different species (i.e., a chicken, a duck and a pig) carried genetically related S. Typhimurium strains within the same BPS. Moreover, some of these genetically related isolates were obtained in different years (2013 and 2014), indicating that farm‐specific Salmonella can persist in BPSs for multiple years and that interspecies transmission is plausible in this environment. Understanding the dynamics of interspecies transmission of Salmonella serovars within a contaminated BPS is fundamental to the design of mitigation strategies to reduce outbreaks of human Salmonella associated with backyard production systems. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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11. γ-Aminobutyric acid receptor alpha 1 subunit loss of function causes genetic generalized epilepsy by impairing inhibitory network neurodevelopment.
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Samarut, Éric, Swaminathan, Amrutha, Riché, Raphaëlle, Meijiang Liao, Hassan-Abdi, Rahma, Renault, Solène, Allard, Marc, Dufour, Liselotte, Cossette, Patrick, Soussi-Yanicostas, Nadia, and Drapeau, Pierre
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GABA receptors ,AMINOBUTYRIC acid ,EPILEPSY ,NEURAL development ,NEURODEVELOPMENTAL treatment ,GENETIC mutation - Abstract
Objective: In humans, mutations of the γ-aminobutyric acid receptor subunit 1 (GABRA1) cause either mild or severe generalized epilepsy. Although these epilepsy-causing mutations have been shown to disrupt the receptor activity in vitro, their in vivo consequences on brain development and activity are not known. Here, we aim at unraveling the epileptogenesis mechanisms of GABRA1 loss of function. Methods: We generated a gabra1-/- zebrafish mutant line displaying highly penetrant epileptic seizures. We sought to identify the underlying molecular mechanisms through unbiased whole transcriptomic assay of gabra1-/- larval brains. Results: Interestingly, mutant fish show fully penetrant seizures at juvenile stages that accurately mimic tonic-clonic generalized seizures observed in patients. Moreover, highly penetrant seizures can be induced by light stimulation, thus providing us with the first zebrafish model in which evident epileptic seizures can be induced by nonchemical agents. Our transcriptomic assay identified misregulated genes in several pathways essential for correct brain development. More specifically, we show that the early development of the brain inhibitory network is specifically affected. Although the number of GABAergic neurons is not altered, we observed a drastic reduction in the number of inhibitory synapses and a decreased complexity of the GABAergic network. This is consistent with the disruption in expression of many genes involved in axon guidance and synapse formation. Significance: Together with the role of GABA in neurodevelopment, our data identify a novel aspect of epileptogenesis, suggesting that the substratum of GABRA1-deficiency epilepsy is a consequence of early brain neurodevelopmental defects, in particular at the level of inhibitory network wiring. [ABSTRACT FROM AUTHOR]
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- 2018
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12. Epidemiology needs more interdisciplinary teams with expertise in molecular systematics, public health and food safety.
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Allard, Marc W. and Brown, Eric W.
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FOOD safety , *PUBLIC health , *NATURAL history museums , *SCHOOL discipline , *AQUATIC sports safety measures - Abstract
What are considered fundamental principles within the Willi Hennig Society and published in their journal are not always fully appreciated by many other biological fields that have not been schooled in these disciplines of systematics principles and the reasons for why these principles are important (Wenzel, Cladistics, 2020, in press). Natural history museums and their associated programs have been a traditional source of the dissemination and training on the uses of phylogenetic systematics. Systematists should do more to expand these interdisciplinary collaborations by reaching out and supporting their local and international collaborators in public health, food and water safety, and other microbiology applications so that critical life‐saving and timely phylogenetic‐based decisions can be made. [ABSTRACT FROM AUTHOR]
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- 2020
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13. Suitability of livers for transplantation when treated by normothermic machine perfusion.
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Allard, Marc‐Antoine, Castro‐Benitez, Carlos, Imai, Katsunori, Selten, Jasmijn, Lopez, Alexandre, Sebagh, Mylène, Lemoine, Antoinette, Sa Cunha, Antonio, Cherqui, Daniel, Castaing, Denis, Vibert, Eric, and Adam, René
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LIVER transplantation , *PRESERVATION of organs, tissues, etc. , *ALLOCATION of organs, tissues, etc. , *ISCHEMIA , *BLOOD flow - Abstract
Abstract: Background: Many factors may compromise the functional recovery of a harvested potential liver for engraftment. Normothermic machine perfusion (NMP) can revive hepatic metabolism ex vivo enabling subsequent transplantation. In this study, we evaluated the recovery of 11 discarded livers’ function utilizing NMP. Materials and methods: Eleven consecutive discarded livers underwent NMP for 6 hours. Liver function recovery was defined by lactate levels of ≤3 mmol/L and continuous bile production. Results: Ten of 11 livers perfused were fatty. The median percentage of macrosteatosis (MaS) and microsteatosis (MiS) was 40% (10%‐90%) and 40% (20%‐50%), respectively, based on a review of paraffin‐embedded sections of preperfusion biopsies. A discarded “amyloid” liver from an HIV‐positive donor was also studied. Recovery of liver function was observed in 4 livers, including that with the amyloid deposition. These livers sustained shorter cold ischemia times and seemed to have increased portal and arterial blood flow. No significant change in MiS or MaS was observed before and after perfusion. Conclusion: Our results suggest that some discarded grafts might have been salvaged for transplantation. Further studies utilizing NMP with subsequent transplantation would validate this strategy. [ABSTRACT FROM AUTHOR]
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- 2018
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14. Is Routine Intraoperative Contrast-Enhanced Ultrasonography Useful During Whole Liver Transplantation?
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Golse, Nicolas, Santoni, Simone, Karam, Vincent, Ciacio, Oriana, Pittau, Gabriella, Allard, Marc-Antoine, Cherqui, Daniel, Sa Cunha, Antonio, Adam, René, Castaing, Denis, and Vibert, Eric
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ULTRASONIC imaging ,LIVER transplantation ,LIVER diseases ,ABDOMINAL surgery ,SURGICAL complications ,ARTERIOVENOUS anastomosis ,CATHETER ablation - Abstract
Background: Vascular complications following liver transplantation (LT) may result from technical deficiencies. Intraoperative diagnosis remains challenging but can prevent serious delayed complications. Intraoperative Doppler ultrasonography (IOUS) represents the gold standard for imaging, although it requires radiological skills. Contrast-enhanced ultrasonography has been reported during postoperative assessments, but never intraoperatively (CE-IOUS). The aim of this study was to assess the feasibility of routine CE-IOUS, to evaluate its impact on surgical strategy and its usefulness.Methods: All 553 whole LTs performed in our tertiary centre between 01/2010 and 12/2014 were reviewed. We compared perioperative outcomes and long-term survival in IOUS (
n = 370) versus CE-IOUS (n = 103) groups. Secondarily, the seven cases where the two imaging findings conflicted (CE+ Group) were matched 1:2 and compared with an exclusively IOUS procedure (CE− Group,n = 14) to assess the consequences of a specific CE-guided strategy. Results: CE-IOUS assessments were successful in 100% of cases, without any adverse effects. Vascular complications and patient/graft survival rates were identical in the IOUS and CE-IOUS groups (p = 0.65, 0.95 and 0.86, respectively). CE-IOUS confirmed IOUS findings in 93% of cases (n = 96) and led to the realization of an additional procedure (median arcuate ligament lysis) and six conservative strategies despite poor arterial (n = 5) or venous flow (n = 1) under Doppler analysis. The CE+ and CE− groups presented statistically identical perioperative and long-term outcomes.Conclusion: This study demonstrated the feasibility of CE-IOUS during whole LT. However, we failed to demonstrate any advantages of CE-IOUS over IOUS. Therefore, IOUS currently remains the gold-standard imaging technique for the intraoperative assessment of vascular patency. [ABSTRACT FROM AUTHOR]- Published
- 2018
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15. Management of the Open Abdomen after Liver Transplantation.
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Hobeika, Christian, Allard, Marc-Antoine, Bucur, Petru-Octav, Naili, Salima, Sa Cunha, Antonio, Cherqui, Daniel, Castaing, Denis, Adam, René, and Vibert, Eric
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ABDOMINAL surgery , *LIVER transplantation , *NEGATIVE-pressure wound therapy , *WOUND care , *THERAPEUTIC use of vacuums - Abstract
Introduction: The optimal management of the open abdomen (OA) after liver transplantation (LT) is unclear. The negative pressure wound therapy (NPWT) has been shown to be safe and can increase the chance for early fascial closure in trauma or septic patients. However, little data are available on the specific setting of LT. We aimed to report our experience of OA after LT, marked by the recent use of NPWT. Methods: All patients with postponed wall closure after LT, from 2002 to 2014, in a single institution were included and retrospectively analyzed. Our management of OA after LT has shifted from skin-only closure (SOC) followed by abdominal wall reconstruction at a distance to the use of NPWT with early fascial closure. Results: Of the 1559 LTs performed during the study period, immediate abdominal wall closure at the end of transplantation could not be achieved in 46 (2.9%) patients. Of them, SOC was performed in 22 (47.8%) patients, whereas vacuum-assisted closure (VAC) therapy was used in 24 (52.1%) patients. The comprehensive complication indexes (CCI) were similar [CCI: 66 (0-100) in the SOC group vs. 56 (0-100) in the VAC group; p = 0.55]. No evisceration or fistula occurred in both groups. One (4.2%) postoperative bleeding case was reported in the VAC group. Early fascial closure was achieved within a median of 5.5 days (1-12) for the 24 patients (100%) of the VAC group. In four of them, a biological mesh was necessary. Only nine patients (52.9%) of the survivors in the SOC group underwent abdominal reconstruction. Conclusion: The NPWT in patients with OA after LT enables early fascial closure with limited morbidity provided a specific attention is given to the risk of bleeding. These results support the use of NPWT as the first option in OA patients after LT. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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16. Potential of a cure in patients with colorectal liver metastases and concomitant extrahepatic disease.
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Imai, Katsunori, Castro Benitez, Carlos, Allard, Marc‐Antoine, Vibert, Eric, Sa Cunha, Antonio, Cherqui, Daniel, Castaing, Denis, Bismuth, Henri, Baba, Hideo, and Adam, René
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- 2017
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17. The forensic analysis of foodborne bacterial pathogens in the age of whole-genome sequencing.
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Wilson, Mark R., Allard, Marc W., and Brown, Eric W.
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NUCLEOTIDE sequence , *PATHOGENIC microorganisms , *DNA analysis , *MITOCHONDRIAL DNA , *GENOMES - Abstract
The forensic evaluation of bacterial pathogens presents new challenges to the forensic science community. This review examines bacterial pathogens as objects of forensic comparison, focusing on their nucleic acid sequences as an important aspect of the comparison process. Because of the clonal propagation of most bacterial pathogens, a phylogenetic approach to understanding the diversity and using this understanding to address common forensic questions is explored. As a general phylogenetic framework is now employed in human mitochondrial DNA analysis, we will use the relevant concepts and approaches common in this area to develop this approach further. We also address the impact of the current ease and prevalence of whole-genome DNA sequence analysis in the forensic comparison process. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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18. Liver Packing During Elective Surgery: An Option that can be Considered.
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Allard, Marc, Dondero, Federica, Sommacale, Daniel, Dokmak, Safi, Belghiti, Jacques, and Farges, Olivier
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ELECTIVE surgery , *LIVER surgery , *BLOOD coagulation disorders , *HEMORRHAGE , *CATECHOLAMINES - Abstract
Background: Packing is a life-saving procedure in patients undergoing emergency surgery for blunt hepatic trauma, especially when massive blood transfusions, acidosis, or hypothermia have resulted in coagulation disorders. The purpose of this study was to apply this concept to the setting of elective liver surgery. Methods: Elective packing was performed in 7 patients who had sustained prolonged bleeding mainly related to partial outflow obstruction during the course of liver resection ( n = 3) or transplantation ( n = 4). At the time of packing, conventional methods of hemostasis had failed and surgery had lasted for 490 (range, 380-695) minutes, blood loss was 5,700 (range, 2,100-13,700) ml, and all patients had coagulation disorders (prothrombin time PT <30%, platelets <45 g/l), hypothermia (body temperature 35.4°C), acidosis (median blood pH 7.24; serum lactate 6.5 mmol/l) and required catecholamine support. Results: Unpacking was performed after a median of 37 (range, 26-60) hours. At that time, all patients were normothermic, with platelet counts >45 g/l, PT >30%, and restored acid-base balance. Active bleeding had stopped, and secondary fascia closure was feasible. With a minimum follow-up of 6 months, all patients are alive without sequel. Conclusions: Packing is a safe and efficient means to control venous bleeding when conventional methods of hemostasis have failed, knowing that commonly the reason for failure of conventional method of hemostasis is partial outflow obstruction. [ABSTRACT FROM AUTHOR]
- Published
- 2011
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19. The mega-matrix tree of life: using genome-scale horizontal gene transfer and sequence evolution data as information about the vertical history of life.
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Kurt Lienau, E., DeSalle, Rob, Allard, Marc, Brown, Eric W., Swofford, David, Rosenfeld, Jeffrey A., Sarkar, Indra N., and Planet, Paul J.
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GENETIC transformation ,GENOMES ,PROKARYOTES ,AMINO acid sequence ,PHYLOGENY - Abstract
Because horizontal gene transfer can confound the recovery of the largely prokaryotic tree of life (ToL), most genome-based techniques seek to eliminate horizontal signal from ToL analyses, commonly by sieving out incongruent genes and data. This approach greatly limits the number of gene families analysedto a subset thought to be representative of vertical evolutionary history. However, formalized tests have not been performed to determine whether combining the massive amounts of information available in fully sequenced genomes can recover a reasonable ToL. Consequently, we used empirically defined gene homology definitions from a previous study that delineate xenologous gene families (gene families derived from a common transfer event) to generate amassively concatenated, combined-data ToL matrix derived from 323 404 translated open reading frames arranged into 12 381 gene homologue groups coded as amino acid data and 63 336, 64 105, 65 153, 66 922 and 67 109 gene homologue groups coded as gene presence ⁄ absence data for 166 fully sequenced genomes. This whole-genome gene presence ⁄ absence and amino acid sequence ToL data matrix is composed of 4867 184 characters (a combined data-type mega-matrix). Phylogenetic analysis of this mega-matrix yielded a fully resolved ToL that classifies all three commonly accepted domains of life as monophyletic and groups most taxa in traditionally recognized locations with high support. Most importantly, these resultscorroborate the existence of a common evolutionary history for these taxa present in both data types that is evident only when these data are analyzed in combination. [ABSTRACT FROM AUTHOR]
- Published
- 2011
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20. Mitochondrial Genome DNA Analysis of the Domestic Dog: Identifying Informative SNPs Outside of the Control Region.
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Webb, Kristen M. and Allard, Marc W.
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DOMESTIC animals , *DOGS , *MITOCHONDRIAL DNA , *ANIMAL breeds , *MITOCHONDRIA , *GENETIC polymorphisms , *NUCLEOTIDES , *EVALUATION , *POPULATION - Abstract
While the mitochondrial control region has proven successful for human forensic evaluations by indicating ethnic origin, domestic dogs ( Canis lupus familiaris) of seemingly unrelated breeds often form large groups based on identical control region sequences. In an attempt to break up these large haplotype groups, we have analyzed the remaining c. 15,484 base pairs of the canine mitochondrial genome for 79 dogs and used phylogenetic and population genetic methods to search for additional variability in the form of single nucleotide polymorphisms (SNPs). We have identified 356 SNPs and 65 haplotypes in the remainder of the mitochondrial genome excluding the control region. The exclusion capacity was found to be 0.018. The mitochondrial control region was also evaluated for the same 79 dogs. The signals from the different fragments do not conflict, but instead support one another and provide a larger fragment of DNA that can be analyzed as forensic evidence. [ABSTRACT FROM AUTHOR]
- Published
- 2009
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21. Identification of Forensically Informative SNPs in the Domestic Dog Mitochondrial Control Region.
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Webb, Kristen M. and Allard, Marc W.
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DOGS , *HAIR , *MITOCHONDRIA , *ANIMAL breeds , *DNA , *GENETIC polymorphisms , *NUCLEOTIDES , *SURVEYS - Abstract
Dog hair is often found at crime scenes either due to the dog’s involvement in the crime or secondary transfer. As little nuclear DNA is present in shed hair, a 1000 base pair fragment of the mitochondrial control region (mtCR) from 552 dogs was assessed for forensically useful sequence variation. Through pairwise alignment to a standard reference sequence, existing haplotypes were further described and 36 new haplotypes and 24 new single nucleotide polymorphisms were identified. The probability of exclusion was found to be 0.957. Breeds were found to have similar sequences, although not identical. No genetic basis was found for grouping dogs by either purebred or mixed or geographic location within the continental United States. Our research demonstrates that the domestic dog mtCR has not been thoroughly surveyed for sequence variation and that a single database comprised of purebred and mixed breed dogs is sufficient for the continental United States. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
22. Forensic Utility of the Mitochondrial Hypervariable Region 1 of Domestic Dogs, in Conjunction with Breed and Geographic Information.
- Author
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Himmelberger, Andrea L., Spear, Theresa F., Satkoski, Jessica A., George, Debra A., Garnica, Wendy T., Malladi, Venkat S., Smith, David G., Webb, Kristen M., Allard, Marc W., and Kanthaswamy, Sreetharan
- Subjects
FORENSIC sciences ,MITOCHONDRIAL DNA ,COYOTE ,DOGS ,DNA damage ,BIOCHEMICAL genetics ,GENES ,DEOXYRIBOSE ,NUCLEIC acids - Abstract
The 608-bp hypervariable region 1 (HV1) sequences from 36 local dogs were analyzed to characterize the population genetic structure of canid mitochondrial DNA (mtDNA). Sixteen haplotypes were identified. A 417-bp segment of this sequence was compared with GenBank sequences from a geographically representative sample of 201 dogs, two coyotes, and two wolves. Sixty-six haplotypes were identified including 62 found only in domestic dogs. Fourteen of these correspond to the 16 local haplotypes and were among the most frequent haplotypes. The local sample was judged to be representative of the much broader geographic sample. No correlation was observed between local haplotypes and the owner’s characterization of dog breed. A 60-bp variation “hotspot” within the canid HV1 was identified as a potentially valuable molecular tool, particularly for assaying limited or degraded DNA samples. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
23. Mitochondrial DNA Analysis of the Domestic Dog: Control Region Variation Within and Among Breeds.
- Author
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Gundry, Rebekah L., Allard, Marc W., Moretti, Tamyra R., Honeycutt, Rodney L., Wilson, Mark R., Monson, Keith L., and Foran, David R.
- Subjects
- *
FORENSIC sciences , *MITOCHONDRIA , *DNA , *DOGS , *DOMESTIC animals , *CANIS - Abstract
The mitochondrial DNA (mtDNA) control regions of 125 domestic dogs ( Canis familiaris) encompassing 43 breeds, as well as one coyote and two wolves were sequenced and subsequently examined for sequence variation in an effort to construct a reference dog mtDNA data set for forensic analysis. Forty informative variable sites were identified that described 45 haplotypes, 29 of which were observed only once. Substantial variation was found both within and among breeds in the mtDNA derived from tissue, indicating that analysis of the mtDNA derived from dog hairs could be a valuable, discriminating piece of evidence in forensic investigations. The dog data set single nucleotide polymorphisms (SNPs) ranged from having one to six changes on a phylogenetic tree. On average, there were 1.9 character changes for each variable position on the tree. The most variable sites (with four or more changes each, listed from the most changes to the fewest) observed were 15,639 ( L=6), 16,672 ( L=5), 15,955 ( L=4), 15,627 ( L=3), 16,431 ( L=3), and 16,439 ( L=3). These sites were consistent with other reports on variable positions in the dog mtDNA genome. A total of 26 SNPs were chosen to best identify all major clusters in the domestic dog data set. The descriptive analyses revealed that this data set is similar to other published canine data sets and further demonstrates that this domestic dog data set is a useful resource for forensic applications. This reference data set has been compiled and validated against the published dog genetic literature with an aim to aid forensic investigations that seek to incorporate mtDNA sequences and SNPs from trace evidence such as dog hair. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
24. Evaluation of Variation in Control Region Sequences for Hispanic Individuals in the SWGDAM mtDNA Data Set.
- Author
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Allard, Marc W., Polanskey, Deborah, Wilson, Mark R., Monson, Keith L., and Budowle, Bruce
- Subjects
- *
HISPANIC Americans , *FORENSIC sciences , *MITOCHONDRIAL DNA , *GENETIC polymorphisms , *DNA - Abstract
The Scientific Working Group on DNA Analysis Methods (SWGDAM) Hispanic data set was analyzed to determine the diversity, phylogeny, and relevant single nucleotide polymorphisms (SNPs) that describe haplogroup patterns for Hispanic Americans ( N=686), and to assess the degree of admixture regarding mitochondrial DNA (mtDNA). The largest component of admixture based on mtDNA analysis derives from the four major haplogroups previously observed in Native American ancestry, including A (29.3%), B (15.7%), C (20.6%), and D (4.8%). European (17.8%) and African (11.8%) haplogroups also were observed within this data set. Hispanic SWGDAM samples from the southwest, compared with other SWGDAM Hispanic samples, were observed to have a greater percent of Native American haplogroups present (79.9%), and fewer African American haplogroups (4.5%). A total of 234 SNPs were observed in the data set, including 36 newly reported variable positions. These SWGDAM Hispanic data set SNPs ranged from having 1 to 31 changes (Length= L) on the phylogenetic tree, with site 16519 being the most variable. On average, there were 3.9 character changes for each variable position on the tree. The most variable sites (with 13 or more changes each listed from fastest to slowest) observed were 16519 ( L=31), 16189 ( L=23), 152 ( L=23), 16311 ( L=19), 146 ( L=17), 195 ( L=17), 16093 ( L=15), 16362 ( L=14), 16129 ( L=13), 150 ( L=13), and 153 ( L=13). These sites are consistent with other reports on highly variable positions. A total of 27 SNPs were chosen to identify all clusters containing 1% ( N=7) or more individuals in the SWGDAM Hispanic data set. The descriptive analyses revealed that the SWGDAM Hispanic data set is similar to published Native American and Hispanic data sets. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
25. Addressing the Use of Phylogenetics for identification of Sequences in Error in the SWGDAM Mitochondrial DNA Database.
- Author
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Budowle, Bruce, Polanskey, Deborah, Allard, Marc W., and Chakraborzty, Ranajit
- Subjects
MITOCHONDRIAL DNA ,DNA fingerprinting ,FORENSIC genetics ,IDENTIFICATION ,FORENSIC sciences ,PHYLOGENY - Abstract
Discusses the use of phylogenetics for the identification of sequences in error in the Scientific Working Group on DNA Analysis Methods' mitochondrial DNA database. Suggestion that the majority of errors are due to human error and are transcriptional in nature; Need to evaluate evolutionary and anthropological data for confirming the relevance and representativeness of forensic databases.
- Published
- 2004
- Full Text
- View/download PDF
26. A Test of Archonta Monophyly and the Phylogenetic Utility of the Mitochondrial Gene 12S rRNA.
- Author
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McNiff, Barbara E. and Allard, Marc W.
- Subjects
- *
MAMMALS , *MITOCHONDRIAL DNA - Abstract
Presents the results of a study which examined the relationships between various mammals, such as Dermoptera, Scandentia, Chiroptera and Primates and the phylogenetic utility of the mitochondrial 12S rRNA gene. Methodology used in the study; Types of transversion analyses performed on the 12S rRNA sequence data.
- Published
- 1998
- Full Text
- View/download PDF
27. Phylogenetic Relationships of the Order Insectivora Based on Complete 12S rRNA Sequences from Mitochondria.
- Author
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Emerson, Ginny L., Kilpatrick, C.W., McNiff, B.E., Ottenwalder, J., and Allard, Marc W.
- Published
- 1999
- Full Text
- View/download PDF
28. The Random Cladist: A Review of the Software Package RANDOM CLADISTICS.
- Author
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Allard, Marc W., Kearney, Maureen, Kivimaki, K. Lindholm, Meisner, Amy Downing, and Strong, Ellen E.
- Published
- 1999
- Full Text
- View/download PDF
29. Congruence among Mammalian Mitochondrial Genes.
- Author
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Allard, Marc W., Farris, J.S., and Carpenter, James M.
- Published
- 1999
- Full Text
- View/download PDF
30. Phylogenetic Characterization lcrD Gene Family: Molecular Evolutionary Aspects of Pathogen-Induced Hypersensitivity in plants.
- Author
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Brown, Eric W., Allard, Marc W., and Zwet, Tom
- Published
- 1998
- Full Text
- View/download PDF
31. ON WEIGHTING AND CONGRUENCE.
- Author
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Allard, Marc W. and Carpenter, James M.
- Published
- 1996
- Full Text
- View/download PDF
32. EXPLANATION.
- Author
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Farris, James S., Källersjö, Mari, Albert, Victor A., Allard, Marc, Anderberg, Arne, Bowditch, Brunella, Bult, Carol, Carpenter, James M., Crowe, Timothy M., Laet, Jan, Fitzhugh, Kirk, Frost, Darryl, Goloboff, Pablo, Humphries, Christopher J., Jondelius, Ulf, Judd, Darlene, Karis, Per Ola, Lipscomb, Diana, Luckow, Melissa, and Mindell, David
- Published
- 1995
- Full Text
- View/download PDF
33. TESTING THE VALIDITY OF THE CYTOCHROME B SEQUENCE FROM CRETACEOUS PERIOD BONE FRAGMENTS AS DINOSAUR DNA.
- Author
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Young, Deshea L., Huyen, Yentram, and Allard, Marc W.
- Published
- 1995
- Full Text
- View/download PDF
34. FURTHER COMMENTS ON GOODMAN'S MAXIMUM PARSIMONY PROCEDURE.
- Author
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Allard, Marc W.
- Published
- 1990
- Full Text
- View/download PDF
35. Hepaticocholecystic duct: A pitfall of cholecystectomy.
- Author
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Laurenzi, Andrea, Allard, Marc‐Antoine, and Vibert, Eric
- Subjects
- *
ANATOMICAL variation , *INJURY complications , *SURGICAL complications , *CHOLECYSTECTOMY , *BILE ducts - Abstract
Key Clinical Message: The anatomical variations of accessory biliary ducts account for up to 2% of the population. The two types of ducts are the: subvescical and hepaticocholecystic. The knowledge of such variations is extremely important during cholecystectomy in order to avoid possible postoperative complications such as biliary injury or choleperitoneum. The anatomical variations of accessory biliary ducts account for up to 2% of the population. The two types of ducts are the: subvescical and hepatocholecystic. The knowledge of such variations is extremely important during cholecystectomy in order to avoid possible postoperative complications such as biliary injury or choleperitoneum. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
36. DNA Fingerprint Variation and Reproductive Fitness in the Plain Pigeon.
- Author
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Young, Deshea L., Allard, Marc W., Moreno, Jorge A., Miyamoto, Michael M., Ruiz, Carlos R., and Pérez‐Rivera, Raul A.
- Subjects
- *
PIGEONS , *DNA fingerprinting , *REPRODUCTION - Abstract
Examines the genetic fingerprint variation and reproductive fitness in the Plain Pigeon in Puerto Rico. Estimation of DNA fingerprint variation among the existing founders of the Plain Pigeon breeding program; Positive relationship between the reproductive variables and Hae scores; Facilitation of the pairing of birds by DNA fingerprints.
- Published
- 1998
- Full Text
- View/download PDF
37. Note on Hemostatic Devices in Liver Surgery: Reply.
- Author
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Farges, Olivier and Allard, Marc Antoine
- Subjects
- *
LETTERS to the editor , *LIVER surgery - Abstract
A response by Olivier Farges and Marc Antoine Allard about their article regarding hemostatic agents in the context of liver surgery is presented.
- Published
- 2011
- Full Text
- View/download PDF
38. Book reviews: The tree of life: A phylogenetic classification.
- Author
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Allard, Marc W.
- Published
- 2007
- Full Text
- View/download PDF
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