Miracle-dz/UniFAR-FTUs huggingface dataset:
Spray-drying process optimization for manufacture of drug–cyclodextrin complex powder using design of experiments

Background: Design of experiments (DOE), a component of Quality by Design, is systematic and simultaneous evaluation of variables (process or formulation) to develop a product with predetermined quality attributes. This study presents a case study to understand the effects of process variables in a spray-drying process used in the manufacture of drug-cyclodextrin complex for a drug that is prone to chemical instability at elevated temperature conditions encountered during processing. Methods: Experiments were designed, and data were collected according to a three-factor, three-level face-centered central composite design. The factors investigated were inlet temperature, spray rate, and batch size. Responses analyzed for computing the interaction effects were drug content, impurities, moisture content, and process yield. The spray-drying process conditions were optimized using DOE to maximize production yields while minimizing moisture content and drug-related impurities. Process validation batches were executed using the optimum process conditions obtained from software Design-Expert® to evaluate both the repeatability and reproducibility of spray-drying technique. Results: Optimization of process variables using DOE resulted in a significant improvement of process yields, above 90% and moisture content below 6% (w/w). The impurities were controlled within acceptable limits. The desirability function used to optimize the response variables and observed responses were in agreement with experimental values. These results demonstrated the reliability of selected model for manufacture of powder complex with predictable quality attributes. Conclusion: The study indicates the general applicability of DOE approach to optimize critical process parameters in the manufacture of drug product with desired quality attributes.
All My People Right Here, Right Now: management of group co-presence on a social networking site

A mundane but theoretically interesting and practically relevant situation presents itself on social networking sites: the co-presence of multiple groups important to an individual. This primarily qualitative study concentrates on the point of view of individual SNS users and their perspectives on multiple group affiliations. After charting the perceived multiplicity of groups on the social networking site Facebook, we investigated the relevance of multiple groups to the users and the effect of group co-presence on psychological identification processes. Users deal with group co-presence by managing the situation to prevent anticipated conflictive and identity-threatening situations. Their behavioral strategies consist of dividing the platform into separate spaces, using suitable channels of communication, and performing self-censorship. Mental strategies include both the creation of more inclusive in-group identities and the reciprocity of trusting other users and being responsible. In addition to giving further evidence of the existence of group co-presence on SNSs, the study sheds light on the management of the phenomenon. Management of group co-presence should be supported, since otherwise users may feel the urge to resort to defensive strategies of social identity protection such as ceasing to use SNSs altogether or, less dramatically, limit their use according to "the least common denominator". Hence, the phenomenon merits the attention of researchers, developers, and designers alike.
Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication

Genomewide scans for natural selection (GWSS) have become increasingly common over the last 15 years due to increased availability of genome‐scale genetic data. Here, we report a representative survey of GWSS from 1999 to present and find that (i) between 1999 and 2009, 35 of 49 (71%) GWSS focused on human, while from 2010 to present, only 38 of 83 (46%) of GWSS focused on human, indicating increased focus on nonmodel organisms; (ii) the large majority of GWSS incorporate interpopulation or interspecific comparisons using, for example FST, cross‐population extended haplotype homozygosity or the ratio of nonsynonymous to synonymous substitutions; (iii) most GWSS focus on detection of directional selection rather than other modes such as balancing selection; and (iv) in human GWSS, there is a clear shift after 2004 from microsatellite markers to dense SNP data. A survey of GWSS meant to identify loci positively selected in response to severe hypoxic conditions support an approach to GWSS in which a list of a priori candidate genes based on potential selective pressures are used to filter the list of significant hits a posteriori. We also discuss four frequently ignored determinants of genomic heterogeneity that complicate GWSS: mutation, recombination, selection and the genetic architecture of adaptive traits. We recommend that GWSS methodology should better incorporate aspects of genomewide heterogeneity using empirical estimates of relevant parameters and/or realistic, whole‐chromosome simulations to improve interpretation of GWSS results. Finally, we argue that knowledge of potential selective agents improves interpretation of GWSS results and that new methods focused on correlations between environmental variables and genetic variation can help automate this approach.
A Novel Downstream Regulatory Element Cooperates with the Silencing Machinery to Repress EPA1 Expression in Candida glabrata

Candida glabrata, an opportunistic fungal pathogen, adheres to mammalian epithelial cells; adherence is mediated primarily by the Epa1 adhesin. EPA1 is a member of a large gene family of ∼23 paralogues, which encode putative adhesins. In this study, we address how EPA1 transcription is regulated. Our data show that EPA1 expression is subject to two distinct negative regulatory mechanisms. EPA1 transcription is repressed by subtelomeric silencing: the Sir complex (Sir2–Sir4), Rap1, Rif1, yKu70, and yKu80 are required for full repression. Activation of EPA1 occurs immediately after dilution of stationary phase (SP) cells into fresh media; however, transcription is rapidly repressed again, limiting expression to lag phase, just as the cells exit stationary phase. This repression following lag phase requires a cis-acting regulatory negative element (NE) located in the EPA1 3′-intergenic region and is independent of telomere proximity. Bioinformatic analysis shows that there are 10 copies of the NE-like sequence in the C. glabrata genome associated with other EPA genes as well as non-EPA genes.
Correct End Use during End Joining of Multiple Chromosomal Double Strand Breaks Is Influenced by Repair Protein RAD50, DNA-dependent Protein Kinase DNA-PKcs, and Transcription Context*

Background: Incorrect end use during repair can cause chromosome rearrangements. Results: DNA-PKcs and RAD50 limit incorrect end use, and a break downstream from an active promoter shows elevated incorrect end use; these factors and conditions have distinct effects on repair requiring end processing. Conclusion: DNA-PKcs, RAD50, and transcription context influence correct end use. Significance: Correct end use and end processing appear distinct processes. During repair of multiple chromosomal double strand breaks (DSBs), matching the correct DSB ends is essential to limit rearrangements. To investigate the maintenance of correct end use, we examined repair of two tandem noncohesive DSBs generated by endonuclease I-SceI and the 3′ nonprocessive exonuclease Trex2, which can be expressed as an I-SceI-Trex2 fusion. We examined end joining (EJ) repair that maintains correct ends (proximal-EJ) versus using incorrect ends (distal-EJ), which provides a relative measure of incorrect end use (distal end use). Previous studies showed that ATM is important to limit distal end use. Here we show that DNA-PKcs kinase activity and RAD50 are also important to limit distal end use, but that H2AX is dispensable. In contrast, we find that ATM, DNA-PKcs, and RAD50 have distinct effects on repair events requiring end processing. Furthermore, we developed reporters to examine the effects of the transcription context on DSB repair, using an inducible promoter. We find that a DSB downstream from an active promoter shows a higher frequency of distal end use, and a greater reliance on ATM for limiting incorrect end use. Conversely, DSB transcription context does not affect end processing during EJ, the frequency of homology-directed repair, or the role of RAD50 and DNA-PKcs in limiting distal end use. We suggest that RAD50, DNA-PKcs kinase activity, and transcription context are each important to limit incorrect end use during EJ repair of multiple DSBs, but that these factors and conditions have distinct roles during repair events requiring end processing.
On the pointwise maximum of convex functions

We study the conjugate of the maximum, f ∨ g, of f and g when f and g are proper convex lower semicontinuous functions on a Banach space E. We show that (f ∨g)∗∗ = f∗∗ ∨g∗∗ on the bidual, E∗∗, of E provided that f and g satisfy the Attouch-Brezis constraint qualification, and we also derive formulae for (f ∨ g)∗ and for the “preconjugate” of f∗ ∨ g∗.
Quantitative ecology of psychropilic bacteria in an aquatic environment and characterization of heterotrophic bacteria from permanently cold sediments.

Aerobic heterotrophic bacteria, anaerobic heterotrophic bacteria, ammonifying bacteria, sulfur-oxidizing bacteria, and sulfate-reducing bacteria were quantitated in Fairbank Lake, an oligotrophic to mesotrophic lake with a permanently cold hypolimnion, as a function of depth in three seasons. Representatives of each physiological group were recovered at an incubation temperature of 2 °C and for all the physiological groups the 2 °C counts were usually higher than the 37 °C counts, although sulfate-reducing bacteria were not recoverable at an incubation temperature of 37 °C. In addition, the numbers of each physiological type were generally higher in the sediments than in the water column, except in the case of sulfate-reducing bacteria for which the counts were low and often below the detection limit. Aerobic heterotrophic bacteria usually outnumbered the other physiological groups surveyed, and winter minima were characteristic of some of the physiological groups. A relatively stable density of anaerobic.
A Powerful Approach to Sub-Phenotype Analysis in Population-Based Genetic Association Studies

The ultimate goal of genome‐wide association (GWA) studies is to identify genetic variants contributing effects to complex phenotypes in order to improve our understanding of the biological architecture underlying the trait. One approach to allow us to meet this challenge is to consider more refined sub‐phenotypes of disease, defined by pattern of symptoms, for example, which may be physiologically distinct, and thus may have different underlying genetic causes. The disadvantage of sub‐phenotype analysis is that large disease cohorts are sub‐divided into smaller case categories, thus reducing power to detect association. To address this issue, we have developed a novel test of association within a multinomial regression modeling framework, allowing for heterogeneity of genetic effects between sub‐phenotypes. The modeling framework is extremely flexible, and can be generalized to any number of distinct sub‐phenotypes. Simulations demonstrate the power of the multinomial regression‐based analysis over existing methods when genetic effects differ between sub‐phenotypes, with minimal loss of power when these effects are homogenous for the unified phenotype. Application of the multinomial regression analysis to a genome‐wide association study of type 2 diabetes, with cases categorized according to body mass index, highlights previously recognized differential mechanisms underlying obese and non‐obese forms of the disease, and provides evidence of a potential novel association that warrants follow‐up in independent replication cohorts. Genet. Epidemiol. 34: 335–343, 2010. © 2009 Wiley‐Liss, Inc.
A Cost-Effective Foundational Certified Code System

Certified code systems enable untrusted programs to be proven safe to execute in a machine–checkable manner. Recent work has focused on building foundational certified code systems, where safety is defined relative to a concrete machine architecture. We wish to build a cost–effective system, with practicality along two dimensions — the intellectual effort to engineer the proofs, and the resource usage by the machine in verifying these proofs. Thus, we factor the proof that a particular program is safe to execute into two parts, a generic part and a program–specific part. These parts are linked by a mediating logic, typically a type system, which we call the safety condition. Consequently, we must prove that all programs that satisfy this condition are safe to execute, and then, we prove that the particular program satisfies this safety condition. Moreover, each of these proofs must be done in a cost–effective manner. In previous work, we have described a machine–checkable proof for the first part, based on defining an operational semantics in LF and using the Twelf metalogic. For the second part, experience has shown that proof terms for a reasonable logic, or type system, are too big to generate, send across the network, and check. We wish to check adherence to the safety condition by an untrusted functional program. It remains to prove (in a machine–checkable manner) that the program implements the logic specified in a LF signature. We propose to accomplish this by static typechecking. We have designed an expressive type system using dependent refinements for this purpose.
Hemoptysis: bronchial and nonbronchial systemic arteries at 16-detector row CT.

PURPOSE To retrospectively evaluate 16-detector row computed tomography (CT) compared with conventional angiography in depiction of bronchial and nonbronchial systemic arteries in patients with hemoptysis. MATERIALS AND METHODS Institutional review board approval was obtained, and informed consent was not required. Sixteen-detector row helical CT and conventional angiography of the thorax were performed in 22 patients (16 men, six women; age range, 18-75 years; mean age, 50 years) with hemoptysis. Three observers in consensus analyzed retrospectively transverse, multiplanar reconstruction, or three-dimensional CT images for visibility, traceability of bronchial arteries from their origin at the aorta or aortic branches to the hilum, and presence of nonbronchial systemic arteries. CT and angiographic findings of bronchial and nonbronchial systemic arteries causing hemoptysis were compared by two radiologists in consensus. Differences in visibility, traceability, and diameter of bronchial arteries causing and those not causing hemoptysis were tested by using generalized estimating equation method or the mixed model. RESULTS Fifty-two (30 right and 22 left) bronchial arteries and 33 nonbronchial systemic arteries were visible at CT. Thirty-four (20 right and 14 left) of 52 bronchial arteries were traceable from their origins to the hilum. Thirty-one (16 right and 15 left) of 46 (27 right and 19 left) bronchial arteries and 26 of 64 nonbronchial systemic arteries evaluated at angiography were causing hemoptysis. Forty (87%, 23 right and 17 left) of 46 bronchial arteries seen at angiography were also detected at CT. All 31 bronchial arteries and sixteen (62%) of 26 nonbronchial systemic arteries causing hemoptysis were detected at CT. Twenty-three (74%) of 31 bronchial arteries causing hemoptysis were traceable from their origins to the hilum, and one (11%) of nine bronchial arteries not causing hemoptysis was traceable (P = .002). CONCLUSION Sixteen-detector row CT provides depiction and traceability of the bronchial arteries in patients with hemoptysis, and in most patients it enables detection of the bronchial and nonbronchial arteries causing hemoptysis.
A PROPOSAL FOR A STANDARD TERMINOLOGY OF ANATOMICAL NOTATION AND ORIENTATION IN FOSSIL VERTEBRATE DENTITIONS

Abstract There is little consistency in the notation and orientation terminology used in discussions of non-mammalian fossil vertebrate dentitions. The standardization of this terminology, as done in the medical and dental sciences, would facilitate all future research on fossil teeth. For mammals, we recommend following convention, where incisors, canines, premolars, and molars are abbreviated as In, Cn, Pn, and Mn (n = tooth number) in upper jaws and as in, cn, pn, and mn in lower jaws. Right, left, and deciduous teeth are indicated by R, L, and D (e.g., DP4, Rp2). For non-mammals, which can have dentigerous premaxillae, maxillae, and dentaries, as well as additional tooth-bearing bones (e.g., vomers, palatines, pterygoids, ectopterygoids, sphenoids, splenials, and even parasphenoids), we encourage identifying teeth using the bone abbreviation (e.g., pmn, mxn, dn, vn, paln). A number and slash (/) combination can be used to distinguish between multiple tooth rows (e.g., Pal1/n, Pal2/n), and specimen-specific maps can be created for very complicated dentitions. We suggest the use of the terms mesial and distal to designate tooth surfaces and directions facing toward and away from the mandibular symphysis. Labial is offered for those surfaces and directions facing the lips or cheeks and lingual for those facing the tongue. We offer the terms basal for the direction toward crown bases, apical for the direction toward crown tips, occlusal for views of the occlusal surfaces, and basal and root apical for views of crown bases and roots, respectively.
Device Technology for embedded DRAM utilizing stacked MIM(Metal-Insulator-Metal) Capacitor

This paper presents embedded DRAM device technology utilizing stacked MIM(metal-insulator-metal) capacitor. Targeted for high random-access performance as well as low-power data-streaming applications, original structure named "full metal DRAM" has been devised and implemented from 150nm generation. This features reduced parasitic resistance of DRAM cell and fully-compatible CMOS Trs. characteristics with that of leading-edge CMOS. In 90nm generation, ZrO 2 is introduced as capacitor dielectric material for cell size reduction. For the next generation of 55nm, high-k gate dielectric(HfSiON) will be introduced in CMOS platform, which can be effectively exploited for embedded DRAM scaling and performance improvement
Sample Complexity of Smooth Stochastic Optimization

Let N( , δ) be the number of samples needed when solving a stochastic program such that the objective function evaluated at the sample optimizer is within of the true optimum with probability 1− δ. Previous results are of the form N( , δ) = O( −2 log δ−1). However, a smooth objective function is often locally quadratic at an interior optimum. For that case we use results on the convergence of the sample optimizers, to show that N( , δ) = O( −1 log δ−1). These results are both bounds and asymptotics. Hence we show for a common case (smooth objective functions with an interior optimum), that the number of samples needed is O( −1). This suggests that stochastic optimization is a practical approach for such problems.
Random web crawls

This paper proposes a random Web crawl model. A Web crawl is a (biased and partial) image of the Web. This paper deals with the hyperlink structure, i.e. a Web crawl is a graph, whose vertices are the pages and whose edges are the hypertextual links. Of course a Web crawl has a very special structure; we recall some known results about it. We then propose a model generating similar structures. Our model simply simulates a crawling, i.e. builds and crawls the graph at the same time. The graphs generated have lot of known properties of Web crawls. Our model is simpler than most random Web graph models, but captures the sames properties. Notice that it models the crawling process instead of the page writing process of Web graph models.
Syntactic Features for Protein-Protein Interaction Extraction

Background: Extracting Protein-Protein Interactions (PPI) from research papers is a way of translating information from English to the language used by the databases that store this information. With recent advances in automatic PPI detection, it is now possible to speed up this process considerably. Syntactic features from different parsers for biomedical English text are readily available, and can be used to improve the performance of such PPI extraction systems. Results: A complete PPI system was built. It uses a deep syntactic parser to capture the semantic meaning of the sentences, and a shallow dependency parser to improve the performance further. Machine learning is used to automatically make rules to extract pairs of interacting proteins from the semantics of the sentences. The results have been evaluated using the AImed corpus, and they are better than earlier published results. The F-score of the current system is 69.5% for cross-validation between pairs that may come from the same abstract, and 52.0% when complete abstracts are hidden until final testing. Automatic 10-fold cross-validation on the entire AImed corpus can be done in less than 45 minutes on a single server. We also present some previously unpublished statistics about the AImed corpus, and a short analysis of the AImed representation language. Conclusions: We present a PPI extraction system, using different syntactic parsers to extract features for SVM with Tree Kernels, in order to automatically create rules to discover protein interactions described in the molecular biology literature. The system performance is better than other published systems, and the implementation is freely available to anyone who is interested in using the system for academic purposes. The system can help researchers quickly discover reported PPIs, and thereby increasing the speed at which databases can be populated and novel signaling pathways can be constructed.
A stability result for RLS adaptive bilinear filters

The article considers recursive least squares (RLS) adaptive nonlinear filtering using bilinear system models. It is shown that the extended RLS adaptive bilinear filter, as well as the equation-error RLS adaptive bilinear filter, are guaranteed to be stable in the sense that the time average of the squared estimation error is bounded whenever the underlying process that generates the input signals is stable in the same sense. <<ETX>>
Identification and control of induction motor stator currents using fast on-line random training of a neural network

Artificial neural networks (ANNs) which have no off-line pre-training, can be trained continually on-line to identify an inverter fed induction motor and control its stator currents. Due to the small time constants of the motor circuits, the time to complete one training cycle has to be extremely small. This paper proposes and evaluates a new, fast, on-line training algorithm which is based on the method of random search training, termed the random weight change (RWC) algorithm. Simulation results show that RWC training of an ANN yields performance very much the same as conventional backpropagation training. Unlike backpropagation, however, the RWC method can be implemented in mixed digital/analog hardware, and still have a sufficiently small training cycle time. The paper also proposes a VLSI implementation which one training cycle in as little as 8 /spl mu/sec. Such a fast ANN can identify and control the motor currents within a few milliseconds and thus provide self-tuning of the drive while the ANN has no prior information whatsoever of the connected inverter and motor.