Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating the roles of directed breeding and gene flow in animal domestication

For the last 150 y scholars have focused upon the roles of intentional breeding and genetic isolation as fundamental to understanding the process of animal domestication. This analysis of ethnoarchaeological, archaeological, and genetic data suggests that long-term gene flow between wild and domestic stocks was much more common than previously assumed, and that selective breeding of females was largely absent during the early phases of animal domestication. These findings challenge assumptions about severe genetic bottlenecks during domestication, expectations regarding monophyletic origins, and interpretations of multiple domestications. The findings also raise new questions regarding ways in which behavioral and phenotypic domestication traits were developed and maintained.
Hepatitis D virus infection in the Western Brazilian Amazon - far from a vanishing disease.

INTRODUCTION A decline in hepatitis D virus (HDV) occurrence was described in Europe and Asia. We estimated HDV prevalence in the Brazilian Amazon following hepatitis B vaccination. METHODS This is a cross-sectional survey of HDV measured by total antibodies to HDV (anti-HD T). RESULTS HDV prevalence was 41.9% whiting HBsAg carries and was associated with age (PR = 1.96; 95% CI 1.12-3.42; p = 0.01), hepatitis B virus (HBV) infection (PR = 4.38; 95% CI 3.12-6.13; p < 0.001), and clinical hepatitis (PR =1.44; 95% CI 1.03-2.00; p = 0.03). Risk factors were related to HDV biology, clinical or demographic aspects such as underlying HBV infection, clinical hepatitis and age. CONCLUSIONS Our study demonstrated that HDV infection continues to be an important health issue in the Brazilian Amazon and that the implementation of the HBV vaccination in rural Lábrea had little or no impact on the spread of HDV. This shows that HDV has not yet disappeared from HBV hyperendemic areas and reminding that it is far from being a vanishing disease in the Amazon basin.
Simple adult rabbit model for Campylobacter jejuni enteritis

We tested the usefulness of the Removable Intestinal Tie Adult Rabbit Diarrhea model to establish Campylobacter jejuni infection in rabbits. The procedure involved ligation of the cecum, placement of a slip knot at the terminal ileum, and injection of the test inoculum into the mid-small bowel. The ends of the slip knot were externalized, and the tie was released 4 h later. Fifty-five rabbits received C. jejuni, and 16 received uninoculated medium as controls. Daily rectal swabs were positive for 2 weeks in infected rabbits. The diarrheal attack rate was 64% in infected rabbits and 0% in controls. Diarrhea was characterized by loose, mucus-containing stools after an incubation period ranging from 24 h to 6 days. When blood was obtained daily for culture from 30 rabbits for 4 days post-challenge, bacteremia was present in 96.3% 24 h after challenge but diminished to 5 of 19 (26.3%) at 96 h. Death occurred in 53% of rabbits and was always preceded by diarrhea. No control animal died. Only 5 of 35 animals experiencing diarrhea recovered. An indirect whole-cell enzyme-linked immunosorbent assay was used to determine serum immunoglobulin G responses. Mean titers rose from 1:198 preoperatively to 1:9,087 on day 28. Necropsy on eight infected and two control animals showed inflammatory lesions with ulceration in 62.5% and goblet cell hyperplasia in 75% of infected rabbits. We conclude that the Removable Intestinal Tie Adult Rabbit Diarrhea procedure is a simple, effective method to establish C. jejuni infection which mimics human disease.
Pricing commodity bonds using binomial option pricing

Commodity linked bonds have received considerable attention recently as a way to tailor a developing country's debt repayments to its ability to pay. This report presents a method for pricing commodity-linked bonds in the presence of default risk and a commodity price risk. The advantage of this method is that extensions are very simple. Following an introduction, in part 2 of the report a simple version of the bond is priced to make the process transparent. In part 3, the parameters of the model are derived from real world values. In part 4 the model is extended to incorporate the various features that these bonds can include. Part 5 contains come comparisons of the values obtained by the model with those obtained by the Schwartz model.
Inspiratory Muscle Performance of Former Smokers and Nonsmokers Using the Test of Incremental Respiratory Endurance

BACKGROUND: Smoking has potential deleterious effects on respiratory muscle function. Smokers may present with reduced inspiratory muscle strength and endurance. We compared inspiratory muscle performance of nonsmokers with that of former smokers without overt respiratory problems via the Test of Incremental Respiratory Endurance. METHODS: This study was performed on 42 healthy subjects between the ages of 30 and 79 y (mean ± SD of 56.5 ± 14.4 y). Fourteen male and 7 female former smokers were matched to nonsmokers based on sex, age, height, and weight. Subjects completed a questionnaire about their health and current smoking status. Testing included the best of 3 or more consistent trials. The Test of Incremental Respiratory Endurance measurements included maximal inspiratory pressure measured from residual volume as well as sustained maximal inspiratory pressure and inspiratory duration measured from residual volume to total lung capacity during a maximal sustained inhalation. RESULTS: No significant difference in inspiratory performance of the entire group of former smokers compared with nonsmokers was found. However, separate sex analyses found a significant difference in sustained maximal inspiratory pressure between male former smokers and nonsmokers (518.7 ± 205.0 pressure time units vs 676.5 ± 255.2 pressure time units, P = .041). CONCLUSIONS: We found similar maximal inspiratory pressure between former smokers and nonsmokers via the Test of Incremental Respiratory Endurance, but the significant difference in sustained maximal inspiratory pressure between male former smokers and nonsmokers suggests that the sustained maximal inspiratory pressure may have greater discriminatory ability in assessing the effects of smoking on inspiratory muscle performance. Further investigation of the effects of smoking on inspiratory performance via the Test of Incremental Respiratory Endurance is warranted.
Pathological Aspects of Some Problems of Experimental Cancer Research

Although the great possibilities presented by the study of transmissible tumors of lower animals were fully revealed in 1894 by the systematic observations of Morau, it was not until 1901–2 that the work of Loeb in America and Jensen in Denmark attracted universal attention to this field. Especially in the last decade a great number of observations from a host of workers have produced a body of new data which is of first importance in oncology. From this extensive field it is my purpose to select for discussion certain problems which are of special interest to the general pathologist and to attempt to evaluate the new contributions by the old and established pathological criteria. Prominent among the questions raised by the study of transmissible tumors of lower animals is whether these processes are genuine neoplasms. Considering that Virchow once said that no one even under torture could state exactly what a tumor is, this question must appear somewhat academic. Yet to the older pathologists, thoroughly saturated with the conviction that a neoplasm is viable only in its host, the demonstration of successful transfer to a new host naturally raised a lively scepticism. Transmissibility implied to them infectiousness and a granulomatous nature; the transplantable tumors must be shown to grow solely from the transplanted cells, after the manner of metastatic tumors, they must exhibit infiltrative growth, and produce metastases; the striking morphological resemblance to tumors was not universally regarded as decisive evidence. All these essential attributes of true malignant tumors have now been demonstrated for many of the transplantable growths in lower animals.
A Virtual Therapeutic Environment with User Projective Agents

Today, we see the Internet as more than just an information infrastructure, but a socializing place and a safe outlet of inner feelings. Many personalities develop aside from real world life due to its anonymous environment. Virtual world interactions are bringing about new psychological illnesses ranging from netaddiction to technostress, as well as online personality disorders and conflicts in multiple identities that exist in the virtual world. Presently, there are no standard therapy models for the virtual environment. There are very few therapeutic environments, or tools especially made for virtual therapeutic environments. The goal of our research is to provide the therapy model and middleware tools for psychologists to use in virtual therapeutic environments. We propose the Cyber Therapy Model, and Projective Agents, a tool used in the therapeutic environment. To evaluate the effectiveness of the tool, we created a prototype system, called the Virtual Group Counseling System, which is a therapeutic environment that allows the user to participate in group counseling through the eyes of their Projective Agent. Projective Agents inherit the user's personality traits. During the virtual group counseling, the user's Projective Agent interacts and collaborates to recover and increase their psychological growth. The prototype system provides a simulation environment where psychologists can adjust the parameters and customize their own simulation environment. The model and tool is a first attempt toward simulating online personalities that may exist only online, and provide data for observation.
Private Information in M&A Transactions: Evidence from Withdrawn Deals

Based on a large sample of withdrawn mergers over a time period from 1979 until 2003, we examine the informational content revealed to the market by a merger attempt. Using event study methodology, we find that firms that receive a cash offer have a significantly positive price reaction that persists even after the withdrawal of the merger. In contrast, firms that are targets of a stock-financed takeover attempt lose all the abnormal positive return they received at the announcement of the merger once the merger is withdrawn. After controlling for several potential explanations, we find that the financing choice of the bidder significantly affects the overall stock return to the target over the period from announcement to withdrawal. Our findings are consistent with an asymmetric information model, where the bidder has private information about the target that is revealed to the market through the financing choice. This paper is subsumed by the paper: "Target Revaluation after Failed Takeover Attempts Cash versus Stock" joint with Ulrike Malmendier and Farzad Saidi. See http://ssrn.com/abstract=1785942.
Increased Supply Chain Flexibility by Changes in Information Sharing with Suppliers - The FAIS Roadmap

Due to a shifting competitive landscape, companies have realized that in order to meet the new market trends, they need to be flexible not only within their own link but throughout their supply chain. One factor that has proved to have great impact on supply chain flexibility is information sharing. The purpose of this thesis was to add to the knowledge on how organizations can increase their supply chain flexibility by changes in information sharing with suppliers. The objective of this thesis was twofold: To develop a roadmap for analyzing the need and possibilities to increase supply chain flexibility by changes in information sharing with suppliers. With support of this roadmap, present recommendations aiming at increasing the flexibility in Axis’s supply chain by changes in information sharing with suppliers. The study was conducted using a systems approach. Through combining theories about supply chain flexibility, information sharing in supply chains and an empirical investigation in an abductive manner, the FAIS Roadmap was developed. The preliminary FAIS Roadmap was tested using a case study on Axis Communications AB. The developed FAIS Roadmap is a tool that can be used in order to specify what changes that should be made regarding information sharing with suppliers in order to increase the supply chain flexibility. After testing the developed roadmap, some refinements were done, resulting in a final version of the FAIS Roadmap. Furthermore, the test resulted in five recommendations for Axis: understand suppliers’ real need for information, simplify and synchronize internal information processes, make sure that high quality information is passed on further up the chain, benefit from extensive information sharing in early stages of product development, and share additional information in order to decrease lead times.
good enough database caching

Many application systems make use of various forms of asynchronously updated replicas to improve scalability, availability and performance. If an application uses replicas that are not in sync with source data, it is clearly willing to accept results that are not completely current, but typically with some limits on how stale the data can be. Today, such requirements are not explicitly declared anywhere; consequently, the system cannot detect when they are not met and take appropriate action. Instead, data currency requirements are implicitly expressed in the application logic through the choice of data sources. This resembles the situation in the early days of database systems when programmers had to choose what indexes to use and how to join records. This dissertation is about extending DBMS support for relaxed consistency. We envision a scenario where applications are allowed to explicitly express relaxed currency and consistency (CC an administrator can explicitly express the desired local data CC and query processing provides transactional guarantees for the C&C requirements of a query. Our research provides a comprehensive solution to this problem. The first part extends SQL with a new currency clause, allowing queries to explicitly express customized C&C constraints. We suggest a tentative syntax and develop a formal model that rigorously defines the semantics, thereby providing correctness standards for the use of replicated or cached data. The second part develops a data quality-aware, fine-grained cache model based on four fundamental cache properties. Such a model provides an abstract view of the cache to the query processing layer, and opens the door for adaptive cache management. The third part presents query processing methods for enforcing C&C constraints, which is built on the MTCache framework. The optimizer checks most consistency constraints and generates a dynamic plan that includes currency and inexpensive consistency checks. Our solution not only supports transparent caching but also provides transactional data quality guarantees. The last part establishes a realistic model for a database caching system and reports a holistic performance evaluation, offering insights into performance tradeoffs.
The Effect of Flubendazole on Adhesion and Migration in SW480 and SW620 Colon Cancer Cells.

BACKGROUND Colon cancer is the most common type of gastrointestinal cancer. Despite advances during the last two decades, the efficacy of colorectal cancer treatment is still insufficient and new anticancer agents are necessary. METHODS In our study, colon cancer cells derived from a primary tumor (SW480) and lymph node metastasis (SW620) from the same patient were used and compared. The effect of flubendazole (FLU) on cell adhesion and migration was monitored using the x-CELLigence Real-Time Cell Analysis system. Expressions of molecules involved in adhesion and migration were analyzed using RT-PCR and western blot. Furthermore, RNA silencing of nuclear factor-κB in SW620 cells was used to determine the involvement of the NF-κB p65 regulation pathway in FLU action. RESULTS FLU significantly suppressed the adhesion of SW480 cells and reduced the expression of adhesion markers (ICAM-1, αE-catenin; β-catenin; integrin α5 and β1). Moreover, a significant anti-migratory potential of FLU was manifested in the SW620 cells. In addition, FLU suppressed the phosphorylation of NF-κB p65 and potentiated the suppression of several metastatic markers (ICAM-1, EpCAM, integrin α5, β1, α-tubulin) caused by NF-κB p65 silencing. CONCLUSION FLU has a significant anti-migratory effect in intestinal cancer cell SW480 and its lymph node metastatic cells SW620. FLU decreases the expression of some proteins involved in metastatic processes and inhibits activation of NF-κB p65.
Utility estimates for patients with Type 2 diabetes mellitus after experiencing a myocardial infarction or stroke: a systematic review

A systematic review identified studies eliciting utility decrements from myocardial infarction (MI) and stroke in patients with Type 2 diabetes mellitus (T2DM) and examined their use in economic models of new diabetes treatments. In 16 utility studies in patients with T2DM, utility decrements in the first year ranged from 0.017 to 0.226 for MI and from 0.034 to 0.590 for stroke. Sixteen of 19 economic evaluations of new treatments for T2DM included utility decrements for an MI and/or stroke from one of the 16 utility studies. Decrements for MI ranged from 0.012 to 0.180 in the first year. Decrements for stroke ranged from 0.044 to 0.690 in the first year. Utility studies in patients with T2DM provide little information about changes in utility decrements by time since the event and by disease severity. Cost–effectiveness studies do not always indicate how these values were used in the analysis.
Shutdown of an acute T cell immune response to viral infection is mediated by the proapoptotic Bcl-2 homology 3-only protein Bim

We used mutant Fas-deficient (lpr) or Bim-deficient mice to investigate the role of the death receptor and Bcl-2-regulated apoptotic pathways in terminating a physiological T cell response to herpes simplex virus infection. In WT and lpr mice CD8+ antigen-specific T cells were deleted after viral clearance. In contrast, the immune response was not terminated in Bim-deficient mice despite viral clearance, and CD8+ antigen-specific T cells accumulated in the spleen. Thus, Bim is dispensable for viral clearance but is necessary for the death of activated T cells when immune responses are terminated. These findings have implications for the therapeutic manipulation of immune responses to infections and immunization.
Towards industrial products from microalgae

Microalgae show an enormous potential as sustainable feedstock for numerous bioproducts. The current work analyzes the feasibility of business cases for different markets of products from microalgae. We perform a techno-economic evaluation of the whole process chain including cultivation, biorefinery and market exploitation for a 100 hectares facility in six locations. Our projections show a current cost per unit of dry biomass of 3.4 € kg−1 for microalgae cultivation in Spain (excluding biorefining products), with an expected reduction to 0.5 € kg−1 in ten years. A sensitivity analysis reveals the roadmap to achieve this. Production of high-value products (e.g. pigments) would be currently profitable, with a net present value of 657 M€ in 15 years. Markets aimed at food and chemical commodities require further cost reductions for cost competitiveness, reachable in the next decade.
A multi-band body-worn antenna vest

This work discusses the development of a multi-band, body-worn antenna vest (BWAV) that enables the reception of both narrowband and wideband signals, with hands-free operation, needed in military programs such as the joint tactical radio system and joint threat warning system. An array of six tapered slot antenna (TSA) elements covers the 650-2000 MHz range. The TSA element is composed of a printed circuit microstrip feed line that excites the tapered slot pattern etched into the ground plane of the microstrip, providing a self-balanced-feed. The 7 cm/spl times/15 cm TSA circuit boards are positioned in pockets sewn into the outer shell of the vest; one pair in front, one pair in the rear, and one on each side under the wearer's arms.
BiGGER: A new (soft) docking algorithm for predicting protein interactions

A new computationally efficient and automated “soft docking” algorithm is described to assist the prediction of the mode of binding between two proteins, using the three‐dimensional structures of the unbound molecules. The method is implemented in a software package called BiGGER (Bimolecular Complex Generation with Global Evaluation and Ranking) and works in two sequential steps: first, the complete 6‐dimensional binding spaces of both molecules is systematically searched. A population of candidate protein‐protein docked geometries is thus generated and selected on the basis of the geometric complementarity and amino acid pairwise affinities between the two molecular surfaces. Most of the conformational changes observed during protein association are treated in an implicit way and test results are equally satisfactory, regardless of starting from the bound or the unbound forms of known structures of the interacting proteins. In contrast to other methods, the entire molecular surfaces are searched during the simulation, using absolutely no additional information regarding the binding sites. In a second step, an interaction scoring function is used to rank the putative docked structures. The function incorporates interaction terms that are thought to be relevant to the stabilization of protein complexes. These include: geometric complementarity of the surfaces, explicit electrostatic interactions, desolvation energy, and pairwise propensities of the amino acid side chains to contact across the molecular interface. The relative functional contribution of each of these interaction terms to the global scoring function has been empirically adjusted through a neural network optimizer using a learning set of 25 protein‐protein complexes of known crystallographic structures. In 22 out of 25 protein‐protein complexes tested, near‐native docked geometries were found with Cα RMS deviations ≤ 4.0 Å from the experimental structures, of which 14 were found within the 20 top ranking solutions. The program works on widely available personal computers and takes 2 to 8 hours of CPU time to run any of the docking tests herein presented. Finally, the value and limitations of the method for the study of macromolecular interactions, not yet revealed by experimental techniques, are discussed. Proteins 2000;39:372–384. © 2000 Wiley‐Liss, Inc.