Long-term results of concurrent chemoradiotherapy with daily-low-dose continuous infusion of 5-fluorouracil and cisplatin (LDFP) for Stage I-II esophageal carcinoma.

We investigated long-term treatment outcomes and the feasibility of chemoradiotherapy consisting of daily-low-dose 5-fluorouracil and cisplatin (LDFP) chemotherapy plus radiotherapy for Stage I-II squamous cell esophageal cancer. Treatment records from the 2000 through 2008 period were reviewed retrospectively. Fractionated radiotherapy was performed with a total dose of 60 Gy delivered in 2 Gy per fraction. LDFP chemotherapy, as continuous infusion of 200 mg/m2 5-fluorouracil combined with one hour infusion of 4 mg/m2 cisplatin, was administered on the same days as radiotherapy. Survival was calculated by the Kaplan-Meier method. Survival, responses, failure patterns, and toxicities were evaluated. Seventy-six (47 stage I and 29 stage II) patients were analyzed with a median follow-up of 93.6 months. The 8-year overall survival (OS), progression-free survival (PFS) and cause-specific survival (CSS) rates were 63.4%, 49.8%, and 76.7%, respectively. The 8-year OS, PFS, and CSS for stage I and stage II patients were 71.0%/56.1%/82.9% and 45.2%/40.2%/66.6%, respectively. Sixty-eight patients (89.5%) completed the treatment regimen. A complete response (CR) was achieved in 68 patients (89.5%). Twenty-five patients (36.8%) experienced recurrence after CR. The failure patterns were (overlap included): local failure (n = 12), nodal metastasis (n = 12), distant metastasis (n = 3), details unknown (n = 2). Salvage therapy was performed for local failure; endoscopic therapy (n = 7) or surgery (n = 2). Six patients remain alive without relapse after salvage endoscopic therapy. Major Grade 3 or higher acute adverse events were leukopenia (22%), anorexia (17%), and esophagitis (11%). Major late toxicities (Grade 3 or 4) involved pericardial effusion (12%), pleural effusion (4%), and esophageal stenosis (3%). Chemoradiotherapy with LDFP provided favorable long-term survival with acceptable toxicity for Stage I-II squamous cell esophageal cancer. The tumor response was excellent, but close endoscopic follow-up is essential for detecting and treating local recurrence.

Fluctuation Spectroscopy Analysis of Glucose Capped Gold Nanoparticles.

In this work, we report the synthesis and biophysical studies carried out on a new kind of biocompatible and very stable gold nanoparticle (GNP) stabilized with glucose through a PEG linker (AuNP-PEG-Glu). The synthetic path was optimized to obtain nanoparticles of controlled sizes. ζ-potential and dynamic light scattering measurements allowed assessment of the nanodimension, dispersity, surface charge, and stability of our GNPs. Confocal microscopy demonstrated qualitatively that glucose molecules are successfully bonded to GNP surfaces. For our study, we selected nanoparticles with diameter in a range that maximizes the internalization efficiency in cells (40 nm). A detailed investigation about the biophysical proprieties of AuNP-PEG-Glu was carried out by means of fluorescence correlation spectroscopy (FCS) and orbital tracking techniques. This work gives new insights about the uptake mechanism of gold nanoparticles capped with glucose molecules.

Molecular evidence for BDNF- and GABA-related dysfunctions in the amygdala of female subjects with major depression.

Women are twice as likely as men to develop major depressive disorder (MDD) and are more prone to recurring episodes. Hence, we tested the hypothesis that the illness may associate with robust molecular changes in female subjects, and investigated large-scale gene expression in the post-mortem brain of MDD subjects paired with matched controls (n=21 pairs). We focused on the lateral/basolateral/basomedian complex of the amygdala as a neural hub of mood regulation affected in MDD. Among the most robust findings were downregulated transcripts for genes coding for γ-aminobutyric acid (GABA) interneuron-related peptides, including somatostatin (SST), tachykinin, neuropeptide Y (NPY) and cortistatin, in a pattern reminiscent to that previously reported in mice with low brain-derived neurotrophic factor (BDNF). Changes were confirmed by quantitative PCR and not explained by demographic, technical or known clinical parameters. BDNF itself was significantly downregulated at the RNA and protein levels in MDD subjects. Investigating putative mechanisms, we show that this core MDD-related gene profile (including SST, NPY, TAC1, RGS4 and CORT) is recapitulated by complementary patterns in mice with constitutive (BDNF-heterozygous) or activity-dependent (exon IV knockout) decreases in BDNF function, with a common effect on SST and NPY. Together, these results provide both direct (low RNA/protein) and indirect (low BDNF-dependent gene pattern) evidence for reduced BDNF function in the amygdala of female subjects with MDD. Supporting studies in mutant mice models suggest a complex mechanism of low constitutive and activity-dependent BDNF function in MDD, particularly affecting SST/NPY-related GABA neurons, thus linking the neurotrophic and GABA hypotheses of depression.

A multiple resistance locus on chromosome arm 3BS in wheat confers resistance to stem rust (Sr2), leaf rust (Lr27) and powdery mildew.

Sr2 is the only known durable, race non-specific adult plant stem rust resistance gene in wheat. The Sr2 gene was shown to be tightly linked to the leaf rust resistance gene Lr27 and to powdery mildew resistance. An analysis of recombinants and mutants suggests that a single gene on chromosome arm 3BS may be responsible for resistance to these three fungal pathogens. The resistance functions of the Sr2 locus are compared and contrasted with those of the adult plant resistance gene Lr34.

EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome.

In a panel of seven genotypes, 437 expressed sequence tag (EST)-derived DNA fragments were sequenced. Single nucleotide polymorphisms (SNPs) that were polymorphic between the parents of three mapping populations were mapped by heteroduplex analysis and a genome-wide consensus map comprising 216 EST-derived SNPs and 4 InDel (insertion/deletion) markers was constructed. The average frequency of SNPs amounted to 1/130 bp and 1/107.8 bp for a set of randomly selected and a set of mapped ESTs, respectively. The calculated nucleotide diversities (pi) ranged from 0 to 40.0 x 10(-3) (average 3.1 x 10(-3)) and 0.52 x 10(-3) to 39.51 x 10(-3) (average 4.37 x 10(-3)) for random and mapped ESTs, respectively. The polymorphism information content value for mapped SNPs ranged from 0.24 to 0.50 with an average of 0.34. As expected, combination of SNPs present in an amplicon (haplotype) exhibited a higher information content ranging from 0.24 to 0.85 with an average of 0.50. Cleaved amplified polymorphic sequence assays (including InDels) were designed for a total of 87 (39.5%) SNP markers. The high abundance of SNPs in the barley genome provides avenues for the systematic development of saturated genetic maps and their integration with physical maps.

Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies.

To elucidate the potential of single nucleotide polymorphism (SNP) markers in rye, a set of 48 barley EST (expressed sequence tag) primer pairs was employed to amplify from DNA prepared from five rye inbred lines. A total of 96 SNPs and 26 indels (insertion-deletions) were defined from the sequences of 14 of the resulting amplicons, giving an estimated frequency of 1 SNP per 58 bp and 1 indel per 214 bp in the rye transcriptome. A mean of 3.4 haplotypes per marker with a mean expected heterozygosity of 0.66 were observed. The nucleotide diversity index (pi) was estimated to be in the range 0.0059-0.0530. To improve assay cost-effectiveness, 12 of the 14 SNPs were converted to a cleaved amplified polymorphic sequence (CAPS) format. The resulting 12 SNP loci mapped to chromosomes 1R, 3R, 4R, 5R, 6R, and 7R, at locations consistent with their known map positions in barley. SNP genotypic data were compared with genomic simple sequence repeat (SSR) and EST-derived SSR genotypic data collected from the same templates. This showed a broad equivalence with respect to genetic diversity between these different data types.

Penetrating gastric ulcer presenting as a subcapsular liver abscess.

This report describes a subcapsular liver abscess secondary to a penetrating gastric ulcer. The initial read on the CT scan misinterpreted the abscess cavity as an opacified loop of bowel, although it was very conspicuous on a retrospective review. A penetrating gastric ulcer was identified with esophagogastroduodenoscopy and the subcapsular liver abscess was subsequently detected using MRI. Although the conventional treatment of this condition is surgery, successful management was accomplished with a combination of percutaneous drainage, Helicobacter pylori eradication, and acid-suppressive therapy. A review of the literature is provided, including associated cases and the diagnostic modalities used in the evaluation of this condition. This case illustrates how one can arrive at the correct diagnosis with the use of multiple complementary modalities of investigation.

Outcomes of management in stable children with intra-abdominal free fluid without solid organ injury after blunt abdominal injury.

BACKGROUND: The optimal management of hemodynamically stable children without solid-organ injury and with intra-abdominal free fluid on computed tomographic (CT) scan is highly debatable. The possibility of hollow viscus injury in this setting has led many to propose mandatory exploration. We think that stable children with intra-abdominal fluid without solid organ injury can be managed nonoperatively. METHODS: The charts of all children less than 18 years of age who had an abdominopelvic CT scan after a blunt abdominal trauma between January 2001 and July 2004 were queried. Patient demographics, mechanism of injury, vital signs, physical examination, laboratory data, CT findings, and outcomes of management were reviewed. RESULTS: There were 37 pediatric patients identified during the study period who met the selection criteria. Twenty were boys and 17 were girls. Thirty-one patients had a small amount of fluid and six had a moderate amount of fluid. The most common mechanism of injury was motor vehicle crash (MVC). Thirty-one patients were successfully managed nonoperatively. Six patients received an exploratory laparotomy. Intraoperative findings included mesenteric injuries with or without ischemic bowel. There were no cases of hollow viscus perforation. CONCLUSIONS: Nonoperative management of stable patients with small amounts of free fluid in the absence of significant abdominal findings is appropriate in the pediatric population. Increasing amounts of tenderness elicited on physical examination correlates well with the presence of more than a small amount of fluid. The presence of seat belt sign and more than a small amount of fluid may be associated with an increased likelihood of operative intervention.

Fine genetic mapping fails to dissociate durable stem rust resistance gene Sr2 from pseudo-black chaff in common wheat (Triticum aestivum L.).

The broad-spectrum stem rust resistance gene Sr2 has provided protection in wheat against Puccinia graminis Pers. f. sp. tritici for over 80 years. The Sr2 gene and an associated dark pigmentation trait, pseudo-black chaff (PBC), have previously been localized to the short arm of chromosome 3B. In a first step towards the positional-based cloning of Sr2, we constructed a high-resolution map of this region. The wheat EST (wEST) deletion bin mapping project provided tightly linked cDNA markers. The rice genome sequence was used to infer the putative gene order for orthologous wheat genes and provide additional markers once the syntenic interval in rice was identified. We used this approach to map six wESTs that were collinear with the physical order of the corresponding genes on rice chromosome 1 suggesting there are no major re-arrangements between wheat and rice in this region. We were unable to separate by recombination the tightly linked morphological trait, PBC from the stem rust resistance gene suggesting that either a single gene or two tightly linked genes control both traits.

Farmers and formulations--rural health perspective.

Conventional farming demands excessive use of chemicals in the form of synthetic fertilizers and pesticides, confirming to the norms of Green Revolution. Farmers in general, specifically in the developing countries resort to injudicious and excessive use of pesticides which is linked to the illiteracy and poverty of the rural farming community. Their overriding concern for profitable agriculture, has rendered the health of the farmers at a greater risk of developing dreadful maladies including various type of cancers, reproductive disorders, respiratory, dermal, and neuropsychological problems etc. The possible means of reducing the health risks are discussed, including the global effort to regulate the manufacture, transport and use of highly toxic pesticides. Slow and programmed transition to alternative agriculture and strengthening of farmers' knowledge on health, ecosystem and environment will prove effective.

Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.).

The public EST (expressed sequence tag) databases represent an enormous but heterogeneous repository of sequences, including many from a broad selection of plant species and a wide range of distinct varieties. The significant redundancy within large EST collections makes them an attractive resource for rapid pre-selection of candidate sequence polymorphisms. Here we present a strategy that allows rapid identification of candidate SNPs in barley (Hordeum vulgare L.) using publicly available EST databases. Analysis of 271,630 EST sequences from different cDNA libraries, representing 23 different barley varieties, resulted in the generation of 56,302 tentative consensus sequences. In all, 8171 of these unigene sequences are members of clusters with six or more ESTs. By applying a novel SNP detection algorithm (SNiPpER) to these sequences, we identified 3069 candidate inter-varietal SNPs. In order to verify these candidate SNPs, we selected a small subset of 63 present in 36 ESTs. Of the 63 SNPs selected, we were able to validate 54 (86%) using a direct sequencing approach. For further verification, 28 ESTs were mapped to distinct loci within the barley genome. The polymorphism information content (PIC) and nucleotide diversity (pi) values of the SNPs identified by the SNiPpER algorithm are significantly higher than those that were obtained by random sequencing. This demonstrates the efficiency of our strategy for SNP identification and the cost-efficient development of EST-based SNP-markers.

Gastric bypass for morbid obesity in patients 50 years or older: is laparoscopic technique safer?

Some physicians have considered age > or = 50 years as a relative contraindication for bariatric surgery. Recent reports demonstrated the safety and efficacy of Roux-en-Y gastric bypass (RYGB) in this patient subgroup, but comparisons between laparoscopic technique (LT) and open technique (OT) have not been reported. A review of 52 patients > or = 50 years old who underwent RYGB between January 1999 and April 2002 was conducted. Demographics, operative data, and outcomes were assessed. Preoperative and postoperative renal and hepatic functions, electrolytes, anemia studies, and hematology results were compared. Patients were divided into LT and OT groups and operative outcomes were compared. The percentage of excess body weight loss was 66 +/- 4 per cent at mean follow-up of 12 months. Blood samples drawn after a mean of 8 +/- 2 months revealed no postoperative metabolic alterations. RYGB resulted in a reduction of the number of patients with hyperglycemia, hypertension, degenerative joint disease, gastroesophageal reflux disease, and continuous positive airway pressure-dependent sleep apnea (P < 0.05). The LT resulted in fewer intensive care unit admissions and shorter length of stay. RYGB is safe and well tolerated in patients > or = 50 years resulting in no renal, hepatic, or electrolytic alterations. Weight loss and control of obesity-related comorbidities are satisfactory. The LT results in fewer intensive care unit admissions and shorter length of stay than the OT.

Gastrojejunostomy during laparoscopic gastric bypass: analysis of 3 techniques.

HYPOTHESIS: Although perceived as a more technically demanding and time-consuming technique, the hand-sewn gastrojejunostomy during laparoscopic Roux-en-Y gastric bypass (RYGB) is associated with fewer complications and lower costs than stapled techniques. DESIGN: A retrospective medical record review of prospectively collected data. SETTING: University hospital. PATIENTS: One hundred eight consecutive patients undergoing laparoscopic RYGB between January 1, 1999, and December 31, 2001. INTERVENTION: Three techniques were compared: hand-sewn anastomosis (HSA), circular-stapled anastomosis (CSA), and linear-stapled anastomosis (LSA). MAIN OUTCOME MEASURES: Operative costs, including the cost of stapling devices, the cost of sutures, and operative times, were compared. Rates of anastomotic strictures, leaks, marginal ulcers, bleeding, and wound infections were determined. RESULTS: Eighty-seven patients underwent HSA; 13, CSA; and 8, LSA. Supply costs per patient were higher for CSA ($955) and LSA ($435) than for HSA ($2) (P<.001). The mean +/- SEM operative time for laparoscopic RYGB was longer when performing CSA than HSA or LSA (285 +/- 22 vs 215 +/- 8 and 204 +/- 28 minutes, respectively; P<.001). Stricture rates were higher after CSA than HSA and LSA (4 [31%] of 13 patients vs 3 [3%] of 87 patients and 0 of 8 patients, respectively; P<.01). The wound infection rate was higher after CSA than HSA and LSA (3 [23%] of 13 patients vs 1 [1%] of 87 patients and 0 of 8 patients, respectively; P<.001). There was no difference in anastomotic bleeding, and no anastomotic leaks occurred. CONCLUSIONS: In this experience, hand-sewn gastrojejunostomy during laparoscopic RYGB reduced operating room supply costs and was completed faster than stapled techniques. However, these differences may reflect the learning curve because these techniques were used early in our experience. Lower postoperative stricture and wound infection rates seem to be the primary benefits of the HSA technique.

Application of denaturing high-performance liquid chromatography for mapping of single nucleotide polymorphisms in barley (Hordeum vulgare L.).

Recent advances in DNA sequence analysis and the establishment of high-throughput assays have provided the framework for large-scale discovery and analysis of DNA sequence variation. In this context, single nucleotide polymorphisms (SNPs) are of particular interest. To initiate a systematic approach to develop an SNP map of barley (Hordeum vulgare L.), we have employed denaturing high-performance liquid chromatography (DHPLC) to analyse segregating SNP patterns in a doubled-haploid (DH) mapping population. To this end, SNPs between the parental genotypes were identified using a direct sequencing approach. Once a SNP was established between the parents, the optimal melting temperature of the PCR fragment containing the SNP was predicted for its analysis by DHPLC. Following the detection of the optimal temperature, the DH lines were analysed for the presence of either of the alleles. To test the utility of the analysis, data from previously mapped RFLP markers from which these SNPs were derived were compared. Results from these experiments indicate that DHPLC can be efficiently employed in analysing SNPs on a high-throughput scale.

Parallel computation of a maximum-likelihood estimator of a physical map.

Reconstructing a physical map of a chromosome from a genomic library presents a central computational problem in genetics. Physical map reconstruction in the presence of errors is a problem of high computational complexity that provides the motivation for parallel computing. Parallelization strategies for a maximum-likelihood estimation-based approach to physical map reconstruction are presented. The estimation procedure entails a gradient descent search for determining the optimal spacings between probes for a given probe ordering. The optimal probe ordering is determined using a stochastic optimization algorithm such as simulated annealing or microcanonical annealing. A two-level parallelization strategy is proposed wherein the gradient descent search is parallelized at the lower level and the stochastic optimization algorithm is simultaneously parallelized at the higher level. Implementation and experimental results on a distributed-memory multiprocessor cluster running the parallel virtual machine (PVM) environment are presented using simulated and real hybridization data.

Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.).

The progress of genome sequencing projects of model plants like barley, combined with the recent advances of high throughput assays, has provided a wealth of sequence information. This information is being employed to develop a high density transcript map of barley (Hordeum vulgare L.). To achieve this goal, the available EST database is being used as a resource for the development of novel microsatellite (SSR) and single nucleotide polymorphism (SNP) markers. So far, a total of 692 microsatellites representing different di-, tri- and tetra-nucleotide repeats were identified from a set of 19,000 EST sequences. Non-redundant SSRs have been used for mapping and so far 76 microsatellite loci were mapped. In addition to the 180 SNP primer pairs, which were designed to target specific ESTs, 72 were polymorphic among the seven genotypes examined here. Of these, 60 SNPs have been mapped applying a denaturing HPLC approach. To examine the potential of the EST-derived markers for pedigree studies, EST-derived SSRs (75 loci) and SNPs (72 loci) were used to fingerprint a set of seven genotypes. The results show that although both marker types yielded similar groupings, a larger data set of both SSRs and SNPs is necessary to obtain stable clusters in unrelated germplasm.

Recombination of chromosomes 3A(m) and 5A(m) of Triticum monococcum with homeologous chromosomes 3A and 5A of wheat: the distribution of recombination across chromosomes.

Recombination of chromosomes 3A(m) and 5A(m) of Triticum monococcum with closely homeologous chromosomes 3A and 5A of T. aestivum was compared with recombination across corresponding homologous chromosome pairs. Differentiation between the homeologues impacted recombination in the proximal regions of the long arms the most and in the distal regions of the long arms the least. It is concluded that this variation principally reflects allocation of multiple crossovers across an arm and positive crossover interference across chromosome arms. Recombination rates between homeologous chromosomes 5A(m) and 5A differed in the opposite sexes.

Tel2p, a regulator of yeast telomeric length in vivo, binds to single-stranded telomeric DNA in vitro.

The telomeres of the yeast Saccharomyces cerevisiae consist of a duplex region of TG(1-3) repeats that acquire a single-stranded 3' extension of the TG(1-3) strand at the end of S-phase. The length of these repeats is kept within a defined range by regulators such as the TEL2-encoded protein (Tel2p). Here we show that Tel2p can specifically bind to single-stranded TG(1-3). Tel2p binding produced several shifted bands; however, only the slowest migrating band contained Tel2p. Methylation protection and interference experiments as well as gel shift experiments using inosine-containing probes indicated that the faster migrating bands resulted from Tel2p-mediated formation of DNA secondary structures held together by G-G interactions. Tel2p bound to single-stranded substrates that were at least 19 bases in length and contained 14 bases of TG(1-3), and also to double-stranded/single-stranded hybrid substrates with a 3' TG(1-3) overhang. Tel2p binding to a hybrid substrate with a 24 base single-stranded TG(1-3) extension also produced a band characteristic of G-G-mediated secondary structures. These data suggest that Tel2p could regulate telomeric length by binding to the 3' single-stranded TG(1-3) extension present at yeast telomeres.