Computing accurate forces in quantum Monte Carlo using Pulay's corrections and energy minimization

3In order to overcome the difficulty of optimizing molecular geometry using quantum Monte Carlo methods, we introduce various approximations to the exact force expectation value. We follow Pulay's suggestion [Mol. Phys. 17, 153 (1969)] to correct the Hellmann-Feynman estimator by introducing the contributions due to the changes in the wave function with respect to the nuclear positions. When used in conjunction with energy-optimized explicitly correlated trial wave functions for H-2 and LiH, these approximations appear to yield accurate forces using both the variational and diffusion Monte Carlo methods. Also, the accuracy of the second-order estimate of the Hellmann-Feynman force estimator was investigated employing our energy-optimized trial wave functions, and an erratic behavior was uncovered for some of the studied bond lengths. The additional computational cost required to compute the corrections to the Hellmann-Feynman estimator was found to be only a small fraction of the cost for a simple mean energy calculation. The same approach could be exploited also in computing the derivative of other energy-dependent quantum-mechanical observables. (C) 2003 American Institute of Physics.openM. Casalegno;M. Mella;A. M. RappeM., Casalegno; Mella, Massimo; A. M., Rapp

A novel protein isoform of the RON tyrosine kinase receptor transforms human pancreatic duct epithelial cells.

The MST1R gene is overexpressed in pancreatic cancer producing elevated levels of the RON tyrosine kinase receptor protein. While mutations in MST1R are rare, alternative splice variants have been previously reported in epithelial cancers. We report the discovery of a novel RON isoform discovered in human pancreatic cancer. Partial splicing of exons 5 and 6 (P5P6) produces a RON isoform that lacks the first extracellular immunoglobulin-plexin-transcription domain. The splice variant is detected in 73% of xenografts derived from pancreatic adenocarcinoma patients and 71% of pancreatic cancer cell lines. Peptides specific to RON P5P6 detected in human pancreatic cancer specimens by mass spectrometry confirm translation of the protein isoform. The P5P6 isoform is found to be constitutively phosphorylated, present in the cytoplasm, and it traffics to the plasma membrane. Expression of P5P6 in immortalized human pancreatic duct epithelial (HPDE) cells activates downstream AKT, and in human pancreatic epithelial nestin-expressing cells, activates both the AKT and MAPK pathways. Inhibiting RON P5P6 in HPDE cells using a small molecule inhibitor BMS-777607 blocked constitutive activation and decreased AKT signaling. P5P6 transforms NIH3T3 cells and induces tumorigenicity in HPDE cells. Resultant HPDE-P5P6 tumors develop a dense stromal compartment similar to that seen in pancreatic cancer. In summary, we have identified a novel and constitutively active isoform of the RON tyrosine kinase receptor that has transforming activity and is expressed in human pancreatic cancer. These findings provide additional insight into the biology of the RON receptor in pancreatic cancer and are clinically relevant to the study of RON as a potential therapeutic target

Economics of Insecticide use and Potential for Bt Maize Varieties in the Control of Stalkborer in Kenya.

Maize is the staple food crop and source of income for majority of the Kenyan population and many sub-Saharan African countries. The increasing Kenyan population demands an increase in maize production if intermittent food deficits have to be averted. Since the introduction of improved maize varieties in mid-1960, the start of Green Revolution period, maize yields increased drastically up to 1970s and started declining from 1980s to-date. The key contributory factors are nutrient mining, sub-optimal input use and insect pest damage. Of the insect pests, stalk borer is of economic importance. Currently, KARI and CIMMYT are developing maize varieties that are tolerant to stalk borer damage. In order to evaluate the potential impact of these interventions economics of stalk borer control at farm level was evaluated. Surveys complemented with on-farm trials were executed in six major maize growing zones of Kenya. Farmers were randomly selected and a sample-frame established after which a total of 1854 households were randomly selected using random sampling technique. Each household was interviewed using structured questionnaire. Data on method of stalk borer control and the type insecticides used was collected. Partial budget and economic surplus models were used. The results indicated that very few farmers control stalk borer in maize despite significant stalk borer losses of about 15%. Therefore if Bt maize is introduced in Kenya it is likely to reduce these losses. This will benefit many hungry and poor Kenyans with improved household food supply and on farm incomes, in line with Government policy of food security and poverty eradication.Crop Production/Industries,

Generation of orthotopic patient-derived xenografts from gastrointestinal stromal tumor.

BackgroundGastrointestinal stromal tumor (GIST) is the most common sarcoma and its treatment with imatinib has served as the paradigm for developing targeted anti-cancer therapies. Despite this success, imatinib-resistance has emerged as a major problem and therefore, the clinical efficacy of other drugs has been investigated. Unfortunately, most clinical trials have failed to identify efficacious drugs despite promising in vitro data and pathological responses in subcutaneous xenografts. We hypothesized that it was feasible to develop orthotopic patient-derived xenografts (PDXs) from resected GIST that could recapitulate the genetic heterogeneity and biology of the human disease.MethodsFresh tumor tissue from three patients with pathologically confirmed GISTs was obtained immediately following tumor resection. Tumor fragments (4.2-mm3) were surgically xenografted into the liver, gastric wall, renal capsule, and pancreas of immunodeficient mice. Tumor growth was serially assessed with ultrasonography (US) every 3-4 weeks. Tumors were also evaluated with positron emission tomography (PET). Animals were sacrificed when they became moribund or their tumors reached a threshold size of 2500-mm3. Tumors were subsequently passaged, as well as immunohistochemically and histologically analyzed.ResultsHerein, we describe the first model for generating orthotopic GIST PDXs. We have successfully xenografted three unique KIT-mutated tumors into a total of 25 mice with an overall success rate of 84% (21/25). We serially followed tumor growth with US to describe the natural history of PDX growth. Successful PDXs resulted in 12 primary xenografts in NOD-scid gamma or NOD-scid mice while subsequent successful passages resulted in 9 tumors. At a median of 7.9 weeks (range 2.9-33.1 weeks), tumor size averaged 473 ± 695-mm³ (median 199-mm3, range 12.6-2682.5-mm³) by US. Furthermore, tumor size on US within 14 days of death correlated with gross tumor size on necropsy. We also demonstrated that these tumors are FDG-avid on PET imaging, while immunohistochemically and histologically the PDXs resembled the primary tumors.ConclusionsWe report the first orthotopic model of human GIST using patient-derived tumor tissue. This novel, reproducible in vivo model of human GIST may enhance the study of GIST biology, biomarkers, personalized cancer treatments, and provide a preclinical platform to evaluate new therapeutic agents for GIST

Participation in environmental health research by placenta donation – a perception study

<p>Abstract</p> <p>Background</p> <p>Much environmental health research depends on human volunteers participating with biological samples. The perception study explores why and how people participate in a placenta perfusion study in Copenhagen. The participation implies donation of the placenta after birth and some background information but no follow up.</p> <p>Methods</p> <p>Nineteen semi-structured qualitative interviews were conducted with participants in the placenta perfusion study after donation of placenta. Observation studies were made of recruitment sessions.</p> <p>Results</p> <p>The interviewed participants are generally in favour of medical research. They participated in the placenta perfusion study due to a belief that societal progress follows medical research. They also felt that participating was a way of giving something back to the Danish health care system. The participants have trust in medical science and scientists, but trust is something which needs to be created through "trust-work". Face-to-face interaction, written information material and informed consent forms play important parts in creating trusting relationships in medical research.</p> <p>Conclusion</p> <p>Medical research ethics do not only amount to specific types of written information material but should also be seen as a number of trust making performances involving researchers as well as research participants.</p

Consumers’ salient beliefs regarding foods from edible insects in Kenya: a qualitative study using concepts from the theory of planned behaviour

Population growth, urbanization and climate change, are among the factors that have created uncertainties and pressures on current global food and economic systems. Agricultural intensification can no longer support the increasing demand for food, especially of protein origin. Consequently, pressure is mounting on the supply side (private sector) to develop viable alternative sources of protein’ foods. Insects as food and consumption of foods from edible insects (FEI) are being promoted as one potential solution to the declining access to protein foods. However, one of the challenges facing the private sector is to demonstrate the efficacy of FEI programmes in the face of limited information regarding consumer - psychographic characteristics including their attitudes, values, interests and beliefs. The aim of the study was to explore the salient beliefs underlying consumer attitudes towards FEI consumption in Kenya. To achieve this objective, six focus group discussions (FGDs) were conducted (n= 43), three with only female participants and the other three with a mixed gender. The FGD script was coded using the Theory of Planned Behaviour theoretical framework. The results show that, salient beliefs related to taste, availability, convenience, affordability and other benefits beyond nutrition, are the main determinants of the participants’ intentions to consume FEI. Intentions are also influenced by the perceived feelings regarding the social referents, including family members, peers, religious leaders and health officials; and perceived behavioural control factors such as perceived risks on their food choices, perceived convenience and availability. While designing local programmes to promote FEI consumption, participants support the idea of small groups, but expresses concern about the time of day (evening preferred), length and location of the group session. However, many participants are not receptive to receiving telephone messages, although they are open to the idea of receiving phone calls. The study findings provide unique insights, among them, cultural beliefs that underlies consumer attitudes towards consuming FEI. Additionally, the results suggest possible approaches and practical interventions that can be used to promote FEI consumption in specific regions of Kenya.Key words: Foods from edible insects, theory of planned behaviour, Salient belief

Some basement rocks from Bear Mountain to the Housatonic Highlands

Guidebook for field trips in western Massachusetts, northern Connecticut and adjacent areas of New York: 67th annual meeting October 10, 11, and 12, 1975: Trip A-1; C-

SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling

TCGA head and neck squamous cell carcinoma clinical information of tumors used in comparisons (n = 100). (XLSX 55 kb

Placental transfer of the polybrominated diphenyl ethers BDE-47, BDE-99 and BDE-209 in a human placenta perfusion system: an experimental study

<p>Abstract</p> <p>Background</p> <p>Polybrominated diphenyl ethers (PBDEs) have been widely used as flame retardants in consumer products. PBDEs may affect thyroid hormone homeostasis, which can result in irreversible damage of cognitive performance, motor skills and altered behaviour. Thus, in utero exposure is of very high concern due to critical windows in fetal development.</p> <p>Methods</p> <p>A human ex vivo placenta perfusion system was used to study the kinetics and extent of the placental transfer of BDE-47, BDE-99 and BDE-209 during four-hour perfusions. The PBDEs were added to the maternal circulation and monitored in the maternal and fetal compartments. In addition, the perfused cotyledon, the surrounding placental tissue as well as pre-perfusion placental tissue and umbilical cord plasma were also analysed. The PBDE analysis included Soxhlet extraction, clean-up by adsorption chromatography and GC-MS analysis.</p> <p>Results and Discussion</p> <p>Placental transfer of BDE-47 was faster and more extensive than for BDE-99. The fetal-maternal ratios (FM-ratio) after four hours of perfusion were 0.47 and 0.25 for BDE-47 and BDE-99, respectively, while the indicative permeability coefficient (IPC) measured after 60 minutes of perfusion was 0.26 h^-1and 0.10 h^-1, respectively. The transport of BDE-209 seemed to be limited. These differences between the congeners may be related to the degree of bromination. Significant accumulation was observed for all congeners in the perfused cotyledon as well as in the surrounding placental tissue.</p> <p>Conclusion</p> <p>The transport of BDE-47 and BDE-99 indicates in utero exposure to these congeners. Although the transport of BDE-209 was limited, however, possible metabolic debromination may lead to products which are both more toxic and transportable. Our study demonstrates fetal exposure to PBDEs, which should be included in risk assessment of PBDE exposure of women of child-bearing age.</p