Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonsmooth Optimization : Thinking Outside of the Black Box

This issue of SIAG/OPT Views-and-News is dedicated to the 2011 SIAM Conference on Optimization. Claudia Sagastizábal has written a beautiful and elegant survey of nonsmooth optimization showing how traditional methods can be cleverly improved by exploiting structure beyond the black box. Don’t miss her plenary presentation on Wednesday at 1pm! Other highlights of OP11 include the SIAG/OPT business meeting on Wednesday (6:45-7:15pm) and a mini-tutorial on Convex Relaxation and Applications (Thu. 9:30–11:30am) presented by Michael Friedlander, Maryam Fazel, and Etienne de Klerk. I am grateful to two “Heiners” (or local heroes), Stefan Ulbrich and Kai Habermehl, for providing at very short notice a great guide of things-to-do in Darmstadt. I am sure their ideas will make the already excellent OP11 meeting even more enjoyable!
Neighbourhood characteristics and mental disorders in three Chinese cities: multilevel models from the World Mental Health Surveys

Objectives The rapid growth of urban areas in China in the past few decades has introduced profound changes in family structure and income distribution that could plausibly affect mental health. Although multilevel studies of the influence of area-level socioeconomic factors on mental health have become more common in other parts of the world, a study of this sort has not been carried out in Chinese cities. Our objectives were to examine the associations of two key neighbourhood-level variables—median income and percentage of married individuals living in the neighbourhood—with mental disorders net of individual-level income and marital status in three Chinese cities. Setting Household interviews in Beijing, Shanghai and Shenzhen, PRC, as part of the cross-sectional World Mental Health Surveys. Participants 4072 men and women aged 18–88 years. Primary and secondary outcome measures Lifetime and past-year internalising and externalising mental disorders. Results Each one-point increase in neighbourhood-level percentage of married residents was associated with a 1% lower odds of lifetime (p=0.024) and 2% lower odds of past-year (p=0.008) individual-level externalising disorder, net of individual-level marital status. When split into tertiles, individuals living in neighbourhoods in the top tertile of percentage of married residents had 54% lower odds of a past-year externalising disorder (OR=0.46, 95% CI: 0.24 to 0.87) compared with those in the bottom tertile. Neighbourhood-level marital status was not statistically associated with either lifetime or past-year internalising disorders. Neighbourhood-level income was not statistically associated with odds of either internalising or externalising disorders. Conclusions The proportion of married residents in respondents’ neighbourhoods was significantly inversely associated with having externalising mental disorders in this sample of Chinese cities. Possible mechanisms for this finding are discussed and related to social causation, social selection and social control theories. Future work should examine these relationships longitudinally.
Supervised Machine Learning Methods Applied to Predict Ligand- Binding Affinity.

BACKGROUND Calculation of ligand-binding affinity is an open problem in computational medicinal chemistry. The ability to computationally predict affinities has a beneficial impact in the early stages of drug development, since it allows a mathematical model to assess protein-ligand interactions. Due to the availability of structural and binding information, machine learning methods have been applied to generate scoring functions with good predictive power. OBJECTIVE Our goal here is to review recent developments in the application of machine learning methods to predict ligand-binding affinity. METHOD We focus our review on the application of computational methods to predict binding affinity for protein targets. In addition, we also describe the major available databases for experimental binding constants and protein structures. Furthermore, we explain the most successful methods to evaluate the predictive power of scoring functions. RESULTS Association of structural information with ligand-binding affinity makes it possible to generate scoring functions targeted to a specific biological system. Through regression analysis, this data can be used as a base to generate mathematical models to predict ligandbinding affinities, such as inhibition constant, dissociation constant and binding energy. CONCLUSION Experimental biophysical techniques were able to determine the structures of over 120,000 macromolecules. Considering also the evolution of binding affinity information, we may say that we have a promising scenario for development of scoring functions, making use of machine learning techniques. Recent developments in this area indicate that building scoring functions targeted to the biological systems of interest shows superior predictive performance, when compared with other approaches.
Association between Increased Emergency Contraception Availability and Risky Sexual Practices

OBJECTIVE We studied whether increased emergency contraception availability for women over age 18 was associated with a higher probability of risky sexual practices. DATA A total of 34,030 individual/year observations on 3,786 women aged 18 and older were extracted from the National Longitudinal Survey of Youth, 1997 from October 1999 through November 2009. STUDY DESIGN We modeled three binary outcome variables: any sexual activity; sexual activity with more than one partner; and any sex without a condom for women with multiple partners for women in states with state-level policy changes (prior to the 2006 FDA ruling) and for women in states subject to only the national policy change both jointly and separately. FINDINGS We found different results when estimating the state and federal changes separately. The national change was associated with a reduction in the probability of sexual activity, a reduction in the likelihood of reporting multiple partnerships, and there was no relationship between the national policy change and unprotected sexual activity. There was no relationship between the probability of sexual activity or multiple partnerships for women in states with their own policy changes, but we did find that women in these states were more likely to report unprotected sex.
Realtime PCI Express monitoring for self adaptive reconfigurable systems

In this paper we introduce the concept for an embedded performance monitor of PCI Express links. This PCI Express Performance Monitor (PPM) enables the analysis of several properties (e.g. amount of available credits), without affecting the performance of the monitored link. By including a PPM in an embedded system it is possible to avoid the need for high cost PCI Express measurement and analyzing equipment. The concept was implemented on a rapid prototyping system to monitor several PCI Express links that connect an Intel Atom processor with an Altera Field Programmable Gate Array (FPGA). In addition we present a framework of functions, which makes it easy to use the utilization of a monitored PCI Express link as trigger condition for self adaptive systems.
Response to Dr. Losanoff et al.

TO THE EDITOR: We thank Losanoff et al. for their interest in our recent review on complications of gallstone disease (1). We agree with their statement in reference to the definition of ileus as derived from Dorland’s medical dictionary (2). However, we disagree with their conclusions, because the term ileus is commonly used in both medical and surgical textbooks to imply “decreased intestinal motility. ” In fact, a recent major gastroenterology textbook (3) dedicated a chapter to “Intestinal Obstruction and Ileus” and defined ileus as “failure of normal intestinal motility in the absence of an obstructing lesion. ” In another major surgical textbook (4), the authors defined ileus as “intestinal distention and the slowing or absence of passage of luminal contents without a demonstrable mechanical obstruction” and said that “gallstone ileus” was “incorrectly termed”; they also cautioned about the need to distinguish “functional [ileus] from mechanical obstruction” in elderly patients with suspected small bowel obstruction. We also agree with Losanoff et al. about the role and value of endoscopy in the diagnosis and management of patients with Bouveret’s syndrome, because endoscopic methods can be effective when the stone is within the reach of the endoscope. It is our hope that our review will further increase physician awareness of the many important and less known complications of gallstone disease, especially in elderly patients.
Effects of feed restriction and subsequent refeeding on energy utilization in growing pigs.

An experiment was carried out to evaluate the metabolic utilization of energy in crossbred barrows during feed restriction and subsequent refeeding. Ten pigs, initially weighing 52 kg, were used in 5 blocks of 2 littermates each. A 7-d adaptation period (P1) was used in which pigs were offered feed at 2.60 MJ of ME.kg of BW(-0.60). d(-1). This adaptation period was followed by a 7-d period (P2), in which 1 pig of each block continued to receive feed at the same level of feeding, whereas for its littermate a 40% reduction in feed intake was imposed (i.e., 1.55 MJ of ME.kg of BW(-0.60). d(-1)). During the subsequent 7-d period (P3), both pigs were offered feed at 2.60 MJ of ME.kg of BW(-0.60). d(-1). After P3, pigs were fasted for 1 d. Heat production (HP) was measured for all pigs during the last 3 d of P1 and on all days for P2 and P3. Heat production was measured using an open-circuit respiration chamber. Energy and N balances were determined for P1, P2, and P3. The HP was partitioned into HP due to physical activity, the short-term thermic effect of feeding, and resting HP. Feed restriction during P2 decreased (P < 0.01) total HP, resting HP, short-term thermic effect of feeding, and retained energy, whereas HP due to physical activity was not affected by feed restriction (P = 0.50). Likewise, fecal and urinary N loss, protein gain, lipid gain, and ADG were reduced during feed restriction (P < 0.01). There were no differences in components of HP and metabolic utilization of energy between the 2 groups during P1 and P3. Nevertheless, urinary N loss was decreased (P < 0.05) and ADG increased (P < 0.01) during P3 for pigs that were restricted in P2. Compensatory growth after a period of feed restriction does not seem to be related to a change in the metabolic utilization of energy for gain but more likely is due to gain in water and gut contents.
A Complete Natural Deduction System for the Relational Calculus

A relational calculus is a formal system in which relation is the fundamental concept. The simplest relational calcu1us, that of ordinary binary relations, was introduced by Tarski in [4]. Tarski's system is essentially an algebra in which the operations are the usual Boolean operations (on sets of ordered pairs) together with the two special operations converse (denoted by u) and composition (denoted by ";" or by juxtaposition).
Generation of Pure-State Single-Photon Wavepackets by Conditional Preparation Based on Spontaneous Parametric Downconversion

We study the conditional preparation of single photons based on parametric downconversion, where the detection of one photon from a given pair heralds the existence of a single photon in the conjugate mode. We derive conditions on the modal characteristics of the photon pairs, which ensure that the conditionally prepared single photons are quantum-mechanically pure. We propose specific experimental techniques that yield photon pairs ideally suited for single-photon conditional preparation.
Dense Wavelength Division Multiplexing Networks: Principles and Applications

The very broad bandwidth of low-loss optical transmission in a single-mode fiber and the recent improvements in single-frequency tunable lasers have stimulated significant advances in dense wavelength division multiplexed optical networks. This technology, including wavelength-sensitive optical switching and routing elements and passive optical elements, has made it possible to consider the use of wavelength as another dimension, in addition to time and space, in network and switch design. The independence of optical signals at different wavelengths makes this a natural choice for multiple-access networks, for applications which benefit from shared transmission media, and for networks in which very large throughputs are required. Recent progress in multiwavelength networks are reviewed, some of the limitations which affect the performance of such networks are discussed, and examples of several network and switch proposals based on these ideas are presented. Discussed also are critical technologies that are essential to progress in this field. >
Data-driven kinodynamic RRT

We present a novel, data-driven kinodynamic motion planner. Our sampling-based planner is based on using a physics simulator as a black box to compute a trajectory considering dynamics, even when we cannot derive exact propagation functions. To improve its overall efficiency, we pre-compute a motion database containing different motions simulated with different controls and states defined in the local frame of a robot. We then use the motion database to efficiently estimate the simulated trajectory during iterations of our planner. When the planner requests the best control to reach a desired state from a query state, we retrieve nearby motions that are close to the query state and pick the motion that is closest to the desired state for the tree extension. To control accuracy of our planner with a high efficiency, we lazily validate retrieved motions. The pre-constructed motion database contains modular trajectories and thus can be reused for other test cases, where we have different composition of obstacles or different start/goal states.
Efficient Area Minimization with High Speed and Low Power Multiplier Structural Design for Multirate Filter Design

In Multi-rate Signal processing studies used in Digital Signal processing systems include sample rate conversion. This technique is used for systems with different input and output sample rates. Interpolation and Decimation is very effective and popular in multi rate signal processing applications. This paper proposes a high speed, area and power efficient VLSI architecture for polyphase decimation filter with decimation factor of three (D=3) using Booth multiplier. By using booth multiplier to multiply signed numbers also. Various key performance metrics such as number of slices, maximum operating frequency, number of LUT’s, input output bonds, power consumption, setup time, hold time, propagation delay between source and destinations are estimated for the filter of length nine (N=9). The power dissipation is reduced in polyphase decimation filter using Booth multiplier which consumes low-power when compared to the conventional multiplier. The speed is improved by using carry look-ahead adder. It was observed that the proposed scheme provides increase in speed, reduction in area and slight reduction in power dissipation when compared to conventional and BFD multiplier and low complexity.
Alpha-factor-leader-directed secretion of recombinant human-insulin-like growth factor I from Saccharomyces cerevisiae. Precursor formation and processing in the yeast secretory pathway.

A synthetic gene coding for human-insulin-like growth factor I (IGFI) was fused to the leader sequence of yeast prepro-alpha-factor and expressed in Saccharomyces cerevisiae under the control of a glyceraldehyde-3-phosphate dehydrogenase promoter fragment. Recombinant IGFI was found inside yeast cells and secreted into the medium. The secreted IGFI migrated on SDS gels with the same electrophoretic mobility as authentic IGFI, i.e. at about 7.5 kDa. HPLC analysis of secreted IGFI revealed the presence of the correctly folded, genuine molecule as well as an isomeric byproduct of equal molecular mass but with two of the three disulfide bonds interchanged. Inside exponentially growing cells the 7.5-kDa IGFI was also found, along with up to four additional IGFI-related polypeptides of higher molecular mass. By endoglycosidase F treatment the three polypeptides between 19-26 kDa were converted to a single peptide of 17 kDa. Since this peptide also reacted with an anti-alpha-factor antibody, it represents most likely the unglycosylated alpha-factor--IGFI fusion precursor. Pulse-chase experiments established the precursor nature of the intracellular higher-molecular-mass IGFI species. Conversion of the primary translation product to the differently glycosylated IGFI precursor proteins and into the mature form occurred very rapidly, within 2 min. Rapid maturation was, however, not followed by an equally rapid secretion of the mature form into the medium: only after 30-40 min did IGFI appear outside the cells. We therefore postulate the presence of an as yet undefined Golgi or post-Golgi bottleneck representing a major obstacle in secretion of recombinant IGFI from S. cerevisiae cells.
Variants of vaccinia virus hemagglutinin altered in intracellular transport

Two classes of revertants were isolated from a vaccinia virus mutant whose hemagglutinins (HAs) accumulate on nuclear envelopes and rough endoplasmic reticulums. The HAs of one of the revertants had the same phenotype as the wild type, i.e., rapid and efficient movement to the cell surface. The HAs of the second class had biphasic transport: rapid export to the cell surface as in the wild type and slow movement to the medial cisternae of the Golgi apparatus. Biochemical and nucleotide sequence analyses showed that the HAs of all the mutants examined that have defects in transport from the rough endoplasmic reticulum to the Golgi apparatus have altered cytoplasmic domains and that the HAs of the second class of revertants lack the whole cytoplasmic domain, while the HAs of the first class of revertants have a wild-type cytoplasmic domain.
Study of MA Protection Technology Based Extending Inheritance Trees

Mobile agents ( MA ) are autonomous software entities that are able to migrate across heterogeneous network execution environments, they have wide application prospects. The security issues are becoming obstacles for the application of mobile agents. Compared with host protection, the research of mobile agents active protection is at the beginning stage. Obfuscation is a technique in which the mobile code producer enforces the security policy by applying a behavior transformation to the code before sending it to run on different platforms. This paper presents a protection scheme of mobile agent in network management application, which combining method of extending inheritance hierarchy tree and time checking technology to protect the security of MA. The protection scheme is tested in actual network management environment, which can effectively identify the malicious host.
Severe Depletion of CD4+ CD25+ Regulatory T Cells from the Intestinal Lamina Propria but Not Peripheral Blood or Lymph Nodes during Acute Simian Immunodeficiency Virus Infection

ABSTRACT CD4+ CD25+ regulatory T cells (Tregs) suppress the activation and proliferation of effector lymphocytes. In human immunodeficiency virus type 1 (HIV-1) infection, Tregs play a significant role in controlling the apoptotic loss of uninfected CD4+ T cells resulting from high levels of generalized immune activation. During acute HIV-1 infection, more than 50% of CD4+ T cells are depleted from the gastrointestinal lamina propria. To elucidate the role of Tregs in HIV-1-induced depletion of CD4+ T cells in the gut-associated lymphoid tissue (GALT), we first determine the distribution of Tregs in a setting of acute infection using the simian immunodeficiency virus (SIV)/pigtailed macaque model of HIV-1 disease. CD4+ T cells from the GALT, lymph nodes, and peripheral blood were isolated from SIV-infected pigtailed macaques on days 4, 14, and 114 postinoculation. Quantitative real-time reverse transcription-PCR was used to quantitate FOXP3 copy numbers in SIV-infected and uninfected control macaques. Expression of FOXP3 in the ileal lamina propria was significantly decreased at all stages of infection compared to levels in uninfected control macaques. In addition, functional analysis of ileal CD4+ T cells from SIV-infected macaques revealed a lack of suppressive activity suggestive of the absence of Tregs in that compartment. These results indicate that Tregs are rapidly depleted in the GALT of SIV-infected macaques, defining a role for the loss of Treg-mediated suppression in early events in the pathogenesis of the disease.
Políticas públicas de la sociedad de la información en América Latina: ¿una misma visión?

El rapido desarrollo de las Tecnologias de Informacion y Comunicaciones (TIC), en cuanto al acceso a servicios de telefonia movil e Internet, a la incorporacion de computadores en las actividades cotidianas, y al desarrollo de servicios y aplicaciones electronicas, tomo de sorpresa a las sociedades y gobiernos de America Latina puesto que su irrupcion a partir de la segunda mitad de la decada de los noventa planteo un nuevo foco de politicas publicas, cuando aun no habian sido cubiertas areas tradicionalmente consideradas como prioritarias para el desarrollo. Si bien los paises compartian la vision de considerar a las TIC como insumos para el desarrollo economico y social, el enfoque prevaleciente fue el de masificacion de estas tecnologias, mas que el de su incorporacion y asimilacion en las distintas actividades de la vida en sociedad. De esta forma, primo un enfoque de desarrollo de las TIC por sobre el desarrollo sustentado en estas tecnologias.Para los paises de la region, el llevar a cabo politicas publicas en este ambito ha constituido un proceso de aprendizaje, que con mas o menos altibajos continua hasta el dia de hoy. Esta tarea implica la maduracion y reformulacion de las politicas tradicionalmente concebidas, para hacer frente a una tematica altamente dinamica, que impone retos a la gestion e institucionalidad publica, y que es afectada por distintos factores, tanto endogenos como exogenos a dicho proceso.A fin de comprender como se ha dado este fenomeno en la region, en la primera parte de este documento se identificaran las razones por las cuales las TIC son un objetivo de politica publica, ilustrando la situacion de la region en terminos de las brechas existentes entre America Latina y los paises desarrollados de Europa, asi como tambien al interior de los paises. Posteriormente se identificaran los principales elementos que distinguen una politica TIC, dadas las particularidades de la tematica, que alejan estas politicas de los disenos tradicionales, para culminar la primera seccion con la identificacion de los determinantes del avance de las agendas digitales en la region. En la segunda parte se describe el grado de desarrollo en la implementacion de estas politicas en los paises de la region -con la incorporacion de Espana y Portugal- identificando distintos niveles de esfuerzo para impulsar acciones en TIC, como son las agendas digitales propias de los paises y el Plan de Accion regional para America Latina y el Caribe eLAC. Se procede a identificar distintos elementos que permiten su caracterizacion, mismos que se consideran para un posterior analisis comparativo.