Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring complex protein-ligand recognition mechanisms with coarse metadynamics.

The metadynamics method has been shown to be a valuable tool to study the mechanism of molecular recognition in atomistic detail [Gervasio, F. L. ; et al. J. Am. Chem. Soc. 2005, 127, 2600]. However, it requires an a priori knowledge of all slow degrees of freedom relevant to the docking/undocking mechanism. Here we investigate a combination of docking/clustering with metadynamics performed with a subset of the necessary degrees of freedom (coarse metadynamics), and show that it provides a full mechanistic insight on the protein-ligand docking mechanism. Moreover, the proposed protocol is able to clearly distinguish between crystallographic and noncrystallographic poses of protein-ligand complexes, and also to find the transition state of the full undocking mechanism, thus giving an indication on the binding free energy.
A high performance configurable storage manager

Presents the architecture of /spl Bscr/eSS (Bell Laboratories Storage System)-a high-performance configurable database storage manager providing key facilities for the fast development of object-oriented, relational or home-grown database management systems. /spl Bscr/eSS is based on a multi-client multi-server architecture offering distributed transaction management facilities and extensible support for persistence. We present some novel aspects of the /spl Bscr/eSS architecture, including a fast object reference technique that allows re-organization of databases without affecting existing references, and two operation modes that an application running on a client or server machine can use to interact with the storage system-(i) copy on access and (ii) shared memory. <<ETX>>
gp63 in Stable Cationic Liposomes Confers Sustained Vaccine Immunity to Susceptible BALB/c Mice Infected with Leishmania donovani

ABSTRACT Visceral leishmaniasis is deadly if not treated, and development of a vaccine with long-term immunity remains a challenge. In this study, we showed that cationic distearoyl phosphatidylcholine (DSPC) liposomes, when used as vaccine adjuvant with the immunodominant 63-kDa glycoprotein (gp63) of Leishmania donovani promastigotes, induced significant protection against progressive visceral leishmaniasis in susceptible BALB/c mice. gp63 used without adjuvant elicited partial protection but in association with liposomes exhibited marked resistance in both the livers and spleens of the mice challenged 10 days after the last vaccination. The protective efficacy of liposomal gp63 vaccination was dose dependent, with 2.5 μg of protein showing optimal protection. The immunity conferred by this vaccine formulation was durable, as mice challenged 12 weeks after immunization were still protected, and the infection was controlled for at least 3 months postchallenge. Production of gamma interferon (IFN-γ) and interleukin-4 (IL-4) by splenic T cells, and of serum immunoglobulin G1 (IgG1) and IgG2a following immunization, suggested that a mixed Th1/Th2 response had been induced following immunization. However, control of disease progression and parasitic burden in mice vaccinated with gp63 in cationic DSPC liposomes was associated with enhancement of antigen-specific IFN-γ and downregulation of IL-4, demonstrating a Th1 bias. Long-term immunity elicited by this vaccine corresponded to, in addition to the presence of antigen-specific Th1, CD8+ T-cell responses. Our results demonstrated that stable cationic liposomes containing gp63 acted as a potent adjuvant for protein antigen to induce long-term protection against L. donovani that represents an alternative to DNA vaccination.
Relationship of Adolescent Perceptions of Racial Socialization to Racial Identity

The reklaonship between racial sociadization attitudes and racial identity stages is the subject of this article, with racial socialization hypothesized as one key variable to link the literatures in childhood racial awareness ad young adult racial identity. A teenage sample was selected to compare measures of racial socialization and racial identity processes. The Scale of Racial Socilizationfor Adolescents and the 50-item Racial Identity Attitude Scale (RIAS) based on Nigrescence theory were administered to 287 African American adolescents between the ages of 14 and 15 years. A principal components analysis was conducted on the RIAS to assess its appropriateness with a younger adolescent population. The factor analytic procedure yielded a three-factor solution with moderately reliablefactors. Thefactors corresponded to the Nigrescence stages of preencounter, immersion, and internalization. Results indicate that specific factors of racial socialization differentially predict all of the racial identiy stages for females and the preencounter and internalization identity stages for males. Findings also suggest that racial socialization is multidimensional, and implications for integrating it with revised multidimensional conceptualizations of racial identity are raised.
Making Object Oriented Efficient for Embedded System Applications

Nowadays, with the growing complexity of embedded systems, it is necessary to use techniques and methodologies that in the same time increase the software productivity, while being still able to manipulate physical embedded systems constraints like memory footprint, real-time behavior, power dissipation and so on. Object-oriented modeling and design is a widely-known methodology in software engineering. This paradigm may satisfy the software portability and maintainability requirements, but it presents an overhead in terms of memory, performance and code size. This paper proposes a pragmatic approach, consisting in the use design space exploration tool (DESEJOS Tool) to allow an automatic selection of the best object organization. This tool tries to transform, in an automatic way, as many dynamic objects to static ones, in the goal to reduce execution time, while maintaining memory costs as low as possible. Experimental results are presented and demonstrate that a one can increase by 24% the performance of an MP3 player while paying just 0.3% increase in memory size
Global shifts, theoretical shifts: Changing geographies of religion

The paper evaluates the burst in geographical research on religion in the last decade. It examines: (1) the relative emphases and silences in analyses of different sites of religious practice, sensuous geographies, population constituents, religions, geographies and scales of analyses; (2) the rise in the discourse of postsecularization; and (3) four contemporary global shifts (growing urbanization and social inequality, deteriorating environments, ageing populations, and increasing human mobilities), the ways in which religion shapes human response to them, and the implications for new research agendas.
Pharmacist participation on physician rounds and adverse drug events in the intensive care unit.

CONTEXT Pharmacist review of medication orders in the intensive care unit (ICU) has been shown to prevent errors, and pharmacist consultation has reduced drug costs. However, whether pharmacist participation in the ICU at the time of drug prescribing reduces adverse events has not been studied. OBJECTIVE To measure the effect of pharmacist participation on medical rounds in the ICU on the rate of preventable adverse drug events (ADEs) caused by ordering errors. DESIGN Before-after comparison between phase 1 (baseline) and phase 2 (after intervention implemented) and phase 2 comparison with a control unit that did not receive the intervention. SETTING A medical ICU (study unit) and a coronary care unit (control unit) in a large urban teaching hospital. PATIENTS Seventy-five patients randomly selected from each of 3 groups: all admissions to the study unit from February 1, 1993, through July 31, 1993 (baseline) and all admissions to the study unit (postintervention) and control unit from October 1, 1994, through July 7, 1995. In addition, 50 patients were selected at random from the control unit during the baseline period. INTERVENTION A senior pharmacist made rounds with the ICU team and remained in the ICU for consultation in the morning, and was available on call throughout the day. MAIN OUTCOME MEASURES Preventable ADEs due to ordering (prescribing) errors and the number, type, and acceptance of interventions made by the pharmacist. Preventable ADEs were identified by review of medical records of the randomly selected patients during both preintervention and postintervention phases. Pharmacists recorded all recommendations, which were then analyzed by type and acceptance. RESULTS The rate of preventable ordering ADEs decreased by 66% from 10.4 per 1000 patient-days (95% confidence interval [CI], 7-14) before the intervention to 3.5 (95% CI, 1-5; P<.001) after the intervention. In the control unit, the rate was essentially unchanged during the same time periods: 10.9 (95% CI, 6-16) and 12.4 (95% CI, 8-17) per 1000 patient-days. The pharmacist made 366 recommendations related to drug ordering, of which 362 (99%) were accepted by physicians. CONCLUSIONS The presence of a pharmacist on rounds as a full member of the patient care team in a medical ICU was associated with a substantially lower rate of ADEs caused by prescribing errors. Nearly all the changes were readily accepted by physicians.
New construction of algebraic manipulation detection codes based on wavelet transform

This article presents the new construction of security-oriented codes that provides protection of device against algebraic manipulations. New construction of algebraic manipulation detection codes based on wavelet decomposition. The proposed error-detecting schemes can significantly improves the reliability of storage systems and channels of information transmission. The presented code constructions provides a significant gain in the systems that are already has wavelet transformation. In these systems the coefficients of scaling functions are already calculated and it can be used in the proposed constructions, it gives the gain in rate of information processing and have lower maximum of error masking probability.
The role of preoperative embolization for intracranial meningiomas.

OBJECT As endovascular techniques have become more advanced, preoperative embolization has become an increasingly used intervention in the management of meningiomas. To date, however, no consensus has been reached on the use of this technique. To clarify the role of preoperative embolization in the management of meningiomas, the authors conducted a systematic review of case reports, case series, and prospective studies to increase the current understanding of the management options for these common lesions and complications associated with preoperative embolization. METHODS A PubMed search was performed to include all relevant studies in which the management of intracranial meningiomas with preoperative embolization was reported. Immediate complications of embolization were reported as major (sustained) or minor (transient) deficits, death, or no neurological deficits. RESULTS A total of 36 studies comprising 459 patients were included in the review. Among patients receiving preoperative embolization for meningiomas, 4.6% (n = 21) sustained complications as a direct result of embolization. Of the 21 patients with embolization-induced complications, the incidence of major complications was 4.8% (n = 1) and the mortality rate was 9.5% (n = 2). CONCLUSIONS Preoperative embolization is associated with an added risk for morbidity and mortality. Preoperative embolization may be associated with significant complications, but careful selection of ideal cases for embolization may help reduce any added morbidity with this procedure. Although not analyzed in the authors' study, embolization may still reduce rates of surgical morbidity and mortality and therefore may still have a potential benefit for selected patients. Future prospective studies involving the use of preoperative embolization in certain cases of meningiomas may further elucidate its potential benefit and risks.
Cross‐Coupling Modification of Nucleoside Triphosphates, PEX, and PCR Construction of Base‐Modified DNA

A novel, efficient, two‐step methodology is presented for construction of base‐modified oligonucleotides or DNA, involving aqueous cross‐coupling reactions of halogenated nucleoside triphosphates (dNTPs) with terminal acetylenes or arylboronic acids, followed by polymerase incorporation of the modified dNTPs either using primer extension (PEX) or polymerase chain reaction (PCR). Curr. Protoc. Chem Biol. 2:1‐14. © 2010 by John Wiley & Sons, Inc.
Management strategies for gastrointestinal, erectile, bladder, and sudomotor dysfunction in patients with diabetes

There are substantial advances in understanding disordered gastrointestinal autonomic dysfunction in diabetes. It occurs frequently. The underlying pathogenesis is complex involving defects in multiple interacting cell types of the myenteric plexus as well. These defects may be irreversible or reversible. Gastrointestinal symptoms represent a major and generally underestimated source of morbidity for escalating health care costs in diabetes. Acute changes in glycaemia are both determinants and consequences of altered gastrointestinal motility. 35–90% of diabetic men have moderate‐to‐severe erectile dysfunction (ED). ED shares common risk factors with CVD. Diagnosis is based on medical/sexual history, including validated questionnaires. Physical examination and laboratory testing must be tailored to patient's complaints and risk factors. Treatment is based on PDE5‐inhibitors (PDE5‐I). Other explorations may be useful in patients who do not respond to PDE5‐I. Patients at high cardiovascular risk should be stabilized by their cardiologists before sexual activity is considered or ED treatment is recommended.
AIDS and Sexually Transmitted Diseases in the Rural South

S ince the mid-1980's more cases of AIDS have been reported in the South a than in any other region of the United States, 1 and the rise of the epidemic in rural b America has been widely recognized 2-4 and documented (see other RCAP Fact Sheets, especially " HIV/AIDS in Rural America, " 1996). Rural Southerners are, therefore, assumed to be especially at risk. Our understanding of the unique risks of rural Southerners is limited, however, because few surveillance studies have targeted this population, necessitating a review of other less narrowly targeted studies of the South, rural populations, and selected minorities. In 1996 c there were nearly four to five times as many rural AIDS cases in the South as in any other region of the United States; among rural blacks the number of AIDS cases is 9 to 44 times higher in the South. 4 More than half of all rural cases (54%) reported through 1997 were in the southern region. 5,d Just over 1 in 50 (2.2% of) child-bearing women in five rural Georgia hospitals from 1993 to 1997 were HIV positive. 6 Three quarters of patients attending one of four urban academic ID clinics in North Carolina, South Carolina, Alabama, and Florida in 1997 were from rural zip codes. 7 Given that ulcerative sexually transmitted diseases (STDs) promote HIV infection and that sexual risk taking leads to both kinds of infections, the high rates of STDs in the rural South are also of concern. For example, in 1991 through 1993, syphilis rates were markedly higher in North Carolinian rural counties compared to NC urban counties. 8 The South has been especially affected by the " second wave " of the HIV/AIDS epidemic—affecting mostly young, nonwhite, heterosexual women not living in " first wave " epicenters. 9 Women in the South are especially at risk for HIV/AIDS. 7, 9-14 Heterosexual sex accounted for 18% and 60% of AIDS cases reported in 1999 among rural Southern males and females, respectively compared to 40% in the combined U.S. population. 2 Although a substantial proportion of rural people with AIDS (PWAs) have used injection drugs, this behavior is less common than in urban settings and accounts for a smaller proportion of HIV transmission in rural settings. 15, 16 Non-injection drug use, particularly alcohol and swapping sex for crack cocaine, however, has been clearly linked to HIV transmission in studies of …
Retail Interest Rate Pass-Through - The Irish Experience

Most central banks use a short-term interest rate such as the one-month money market interest rate as their main instrument of monetary policy. Changes to this short-term interest rate are the first important step in the transmission of monetary policy. Consumption and investment decisions made by households and firms will be affected by the rate of interest rate charged to them by banks and other financial intermediaries. A critical element of the transmission of monetary policy is the degree and speed at which changes in the short-term policy rate are transmitted to retail rates faced by firms and households. The term pass through refers to the extent to which changes in money market rates are reflected in changes in retail rates. This paper aims at increasing our understanding of this particular aspect of the monetary transmission mechanism in an Irish context between 1980 and 2001. In particular, we seek to answer two questions. 1) To what extent are changes in the one-month money-market rate passed through to various retail lending rates? 2) What is the speed at which changes in this money market rate transmitted to these lending rates? Understanding this process is important since it will determine in part how sensitive the domestic economy is to monetary policy changes as well as determining the speed at which the real economy responds to such policy rate changes. One of our main findings is that pass through from the money market rates to retail lending rates is not complete. In other words, lending rates respond less than one for one to changes in money market rates. For example, a one per cent change in the money market rate results in less than 0.8 of one per cent pass through to mortgage rates. Our results for the speed of adjustment are consistent with those of previous international studies. A significant part of our analysis is that we document the effect of a number of the more substantial developments in the financial environment over the sample period, namely, the institutional arrangements regarding the setting of retail rates, changes in competition and regulatory regimes in financial markets and changes in the conduct and operation of monetary policy. We find that such structural change has had a significant effect on the relationship between the money market rate and the various lending rates both in terms of pass through and speed of adjustment during this period. For example, we find that the dismantling of so called ‘matrix’ (an agreement on the setttng of various retail rates between the Central Bank and the Associated Banks) led to an increase in the degree of pass through between the money market rate and all lending rates considered. Failure to account for such change will lead to biased estimates of both the degree of and speed of pass through from money market rates to lending rates.
Cocoonase. II. Substrate specificity, inhibitors, and classification of the enzyme.

Abstract Cocoonase, a proteolytic enzyme produced by silk moths, is active toward a variety of proteins. It also hydrolyzes specifically esters of basic amino acids, thus showing specificity characteristic of trypsin. Kinetic constants for the hydrolysis of synthetic substrates are remarkably similar to those of trypsin and thrombin. Diisopropyl fluorophosphate is a potent inhibitor of cocoonase, suggesting the presence of a serine in the active site. Heavy metal ions and sulfhydryl reagents have little inhibitory effect. 1-Chloro-3-tosylamido-7-amino-2-heptanone is inhibitory, indicating that histidine may participate in the active site. Soybean trypsin inhibitor blocks the action of cocoonase to a degree intermediate between its actions on trypsin and chymotrypsin. A comparison is made among cocoonase, other insect proteases, and the better known mammalian proteases.
Plagiarism Detection for Indonesian Texts

In this paper, we describe a view of our research method on the Plagiarism Detection for Indonesian texts that we are working on. This method should address the problems of handling the equivalence class of Indonesian tokens, selecting the targeted source documents, and minimizing the gap of similarity measurement between the selection and the comparison modules. For these reasons, we propose a novel document representation in the candidate document retrieval module and the hybrid of segmentation and similarity of hashing technique in the comparison module.
Alkaloids from the Roots of Senecio macedonicus Griseb

The new alkaloids 7-,9-diangeloylplatynecine (1) and 8-episarracine N-oxide (2), were isolated and identified from the roots of Senecio macedonicus. Another one, 8-epineosarracine was detected by GC/MS analyses of the crude alkaloid mixture. The cytotoxicity and biological activity of the alkaloids were tested on normal murine spleen lymphocytes and P3U1 mouse myeloma.
The EMG-UKA corpus for electromyographic speech processing

This article gives an overview of the EMG-UKA corpus, a corpus of electromyographic (EMG) recordings of articulatory activity enabling speech processing (in particular speech recognition and synthesis) based on EMG signals, with the purpose of building Silent Speech interfaces. Data is available in multiple speaking modes, namely audibly spoken, whispered, and silently articulated speech. Besides the EMG data, synchronous acoustic data was additionally recorded to serve as a reference. The corpus comprises 63 recorded sessions from 8 speakers, the total amount of data is 7:32 hours. A trial subset, consisting of 1:52 hours of data, is freely available for download.
Commutative law for products of infinitely large isotropic random matrices.

Ensembles of isotropic random matrices are defined by the invariance of the probability measure under the left (and right) multiplication by an arbitrary unitary matrix. We show that the multiplication of large isotropic random matrices is spectrally commutative and self-averaging in the limit of infinite matrix size N→∞. The notion of spectral commutativity means that the eigenvalue density of a product ABC. of such matrices is independent of the order of matrix multiplication, for example, the matrix ABCD has the same eigenvalue density as ADCB. In turn, the notion of self-averaging means that the product of n independent but identically distributed random matrices, which we symbolically denote by AAA. , has the same eigenvalue density as the corresponding power A(n) of a single matrix drawn from the underlying matrix ensemble. For example, the eigenvalue density of ABCCABC is the same as that of A(2)B(2)C(3). We also discuss the singular behavior of the eigenvalue and singular value densities of isotropic matrices and their products for small eigenvalues λ→0. We show that the singularities at the origin of the eigenvalue density and of the singular value density are in one-to-one correspondence in the limit N→∞: The eigenvalue density of an isotropic random matrix has a power-law singularity at the origin ~|λ|(-s) with a power sε(0,2) when and only when the density of its singular values has a power-law singularity ~λ(-σ) with a power σ=s/(4-s). These results are obtained analytically in the limit N→∞. We supplement these results with numerical simulations for large but finite N and discuss finite-size effects for the most common ensembles of isotropic random matrices.