cssi/SciSciGPT-SciSciNet huggingface dataset:
Basker: A Threaded Sparse LU Factorization Utilizing Hierarchical Parallelism and Data Layouts

Scalable sparse LU factorization is critical for efficient numerical simulation of circuits and electrical power grids. In this work, we present a new scalable sparse direct solver called Basker. Basker introduces a new algorithm to parallelize the Gilbert-Peierls algorithm for sparse LU factorization. As architectures evolve, there exists a need for algorithms that are hierarchical in nature to match the hierarchy in thread teams, individual threads, and vector level parallelism. Basker is designed to map well to this hierarchy in architectures. There is also a need for data layouts to match multiple levels of hierarchy in memory. Basker uses a two-dimensional hierarchical structure of sparse matrices that maps to the hierarchy in the memory architectures and to the hierarchy in parallelism. We present performance evaluations of Basker on the Intel SandyBridge and Xeon Phi platforms using circuit and power grid matrices taken from the University of Florida sparse matrix collection and from Xyce circuit simulations. Basker achieves a geometric mean speedup of 5.91× on CPU (16 cores) and 7.4× on Xeon Phi (32 cores) relative to KLU. Basker outperforms Intel MKL Pardiso (PMKL) by as much as 30× on CPU (16 cores) and 7.5× on Xeon Phi (32 cores) for low fill-in circuit matrices. Furthermore, Basker provides 5.4× speedup on a challenging matrix sequence taken from an actual Xyce simulation.
On the Disambiguation of Weighted Automata

We present a disambiguation algorithm for weighted automata. The algorithm admits two main stages: a pre-disambiguation stage followed by a transition removal stage. We give a detailed description of the algorithm and the proof of its correctness. The algorithm is not applicable to all weighted automata but we prove sufficient conditions for its applicability in the case of the tropical semiring by introducing the weak twins property. In particular, the algorithm can be used with all acyclic weighted automata and more generally any determinizable weighted automata. While disambiguation can sometimes be achieved using determinization, our disambiguation algorithm in some cases can return a result that is exponentially smaller than any equivalent deterministic automaton. We also present some empirical evidence of the space benefits of disambiguation over determinization in speech recognition and machine translation applications.
Lattice Study of the Extent of the Conformal Window in Two-Color Yang-Mills Theory

We perform a lattice calculation of the Schr\"odinger functional running coupling in SU(2) Yang-Mills theory with six massless Wilson fermions in the fundamental representation. The aim of this work is to determine whether the above theory has an infrared fixed point. Due to sensitivity of the $SF$ renormalized coupling to the tuning of the fermion bare mass we were unable to reliably extract the running coupling for stronger bare couplings.
Enchanted and Disenchanted International Law

Scholars and activists commonly see international law in a privileged normative and political position in world politics, where international legal institutions are assumed to advance important goals such as international stability, human justice and even global order as a whole. I explore this attitude toward international law, which I call an ‘enchanted’ view, and contrast it to the ‘disenchanted’ alternative. Where the enchanted attitude presumes the normative valence and political wisdom of following international law, the disenchanted approach treats these as open questions for inquiry and discussion. The disenchanted approach is more empirically minded, and more politically open, than the enchanted, and leads to a distinct research program on legalization in international affairs – one that is attentive to the politics of law, the connections between law and power, the ambiguity that exists between legality and policy wisdom.
Poor people׳s money: The politics of mobile money in Mexico and Kenya

Abstract The diffusion of mobile money (also mobile payments) has so far been uneven by country. While in Kenya upwards of 50 percent of the population uses mobile payments platforms, in Mexico the proportion is barely above 2 percent. Drawing on interviews and secondary sources, this paper finds that the actors and the politics surrounding diffusion are key to success. Specifically, regulatory capture sheds light on the extent to which a highly regulated financial sector may seek to protect itself from competition from the telecommunication sector via mobile payments regulation they advocate for and even help formulate. In Mexico, the bank-led regulatory model of mobile payments has limited the diffusion of the service to the unbanked population because of regulatory capture by the banking industry. In Kenya, by contrast, the Mobile Network Operator (MNO)-led model has resulted in much higher rates of diffusion and reflects the extent to which telecommunications firms have played a decisive role in designing the regulatory regime and the limiting the impact of financial industry capture in that country. The implications for policymaking and regulation are discussed.
MR and CT of Occult Vascular Malformations of the Brain

The need for improved specificity in the diagnosis of “occult” vascular malformations led to the use of MR in suspected cases in order to determine MR9s potential for improved diagnostic accuracy. Six patients with six lesions histologically diagnosed as vascular malformation after partial (1) or complete (5) microsurgical excision were studied by CT, MR, and selective magnification subtraction angiography. In all cases, the cerebral lesions were apparently solitary and were visible as focal lesions on both CT and MR. Since angiography failed to reveal the pathologic blood vessels of the lesions, and no arteriovenous shunting was evident, these lesions were termed vascular malformations occult to angiography (VMOTA), Angiography revealed a mass effect in only two cases. MR did not reveal additional vascular malformations missed by CT. In each case, MR, which was performed in an attempt to support the diagnosis suggested by CT, did in fact do so by revealing signal abnormalities indicative of nonacute hemorrhage within the lesion on T1- and T2-weighted pulse sequences. Although, as on CT, MR features of these lesions were found to be nonspecific, the MR criteria reinforced the probable diagnosis of VMOTA in an additional 30 cases that had shown similar nonspecific CT features. In this second group, excluded from this study, in which histologic verification was not obtained because of perceived hazards of surgery, the increased assurance regarding the diagnosis led to proton-beam therapy without histologic verification in 18 cases. It is concluded that MR can provide significant improvement in the accuracy of diagnosing VMOTA beyond that obtainable just by plain and contrast-enhanced CT.
Gaucher's disease.

PHYSICIANS often regard Gaucher's disease as a rare, esoteric, untreatable disorder. Fortunately, the more severe forms of the disease are indeed quite uncommon, but milder forms of Gaucher's disease are encountered frequently, particularly in the Jewish population. Moreover, effective treatment has recently become available, and the prospects for ultimately treating this relatively common disease with the use of gene transfer are quite promising. Cause Gaucher's disease is an autosomal recessive disorder caused by a deficiency of glucocerebrosidase (glucosylceramidase),1 the enzyme required for the lysosomal degradation of lipids containing covalently bound sugars (glycolipids). In its absence the extremely insoluble glucocerebroside (glucosylceramide) . . .
Melting Phenomena and Impurity Redistribution During Pulsed Laser Irradiation of Amorphous Silicon Layers

We have investigated microstructural changes and phase transformations in 30Si+, 75As+, 63Cu+, and 115In+ implanted amorphous silicon layers as a function of pulse energy density. Cross-section electron microscopy studies have revealed the formation of two distinct regions, large and fine polycrystalline regions below the threshold for “defect-free” annealing. The fine polycrystalline region is formed primarily by explosive recrystallization, and occasionally by bulk nucleation and growth. The impurity redistribution in the large and fine polycrystalline regions were determined by Rutherford backscattering measurements. Large redistributions of impurities in the large poly region are consistent with velocity of solidifications of 3—5 ms−1. The nature of impurity redistributions in the fine poly region as a function of distribution coefficient provides information on the details of liguid phase crystallization phenomena.
Android-Stego: a novel service provider imperceptible MMS steganography technique robust to message loss

Information hiding techniques, specifically steganography, have been extensively researched for over two decades. However, steganography on smartphones over cellular carrier networks is yet to be fully explored. Today, smartphones which are at the epitome of ubiquitous and pervasive computing, make steganography an easily accessible covert communication channel. In this paper, we propose Android-Stego -- a framework for steganography employing smartphones. Android-Stego has been evaluated and confirmed to achieve covert communication over real world cellular service providers' communication networks such as Verizon and Sprint. A key contribution of our research presented in this paper is the benchmark results we have provided by analyzing real world cellular carriers' network restrictions on MMS message size. We have also analyzed the actions the carriers take -- such as compression and/or format conversion -- on MMS messages that fall outside the established MMS communication norm, which varies for each service provider. Finally, we have used these benchmark results in implementing Android-Stego such that it is sensitive to carrier restrictions and robust to message loss.
Selective Lewis Acid Catalyzed Assembly of Phosphonomethyl Ethers: Three-Step Synthesis of Tenofovir

Described herein is a novel Lewis acid catalyzed rearrangement–coupling of oxygen heterocycles and bis(diethylamino)chlorophosphine that provides direct formation of the phosphonomethyl ether functionality found in several important antiretroviral agents. A wide range of dioxolanes and 1,3-dioxanes may be employed, furnishing the desired products in good yield. The utility of this method is demonstrated in a novel synthesis of tenofovir, an antiretroviral drug used in the treatment of HIV/AIDS and hepatitis B.
Chiral Phosphoric Acid-Catalyzed Enantioselective and Diastereoselective Spiroketalizations

Catalytic enantioselective and diastereoselective spiroketalizations with BINOL-derived chiral phosphoric acids are reported. The chiral catalyst can override the inherent preference for the formation of thermodynamic spiroketals, and highly selective formation of nonthermodynamic spiroketals could be achieved under the reaction conditions.
THE IMPORTANCE OF STUPIDITY IN SCIENTIFIC RESEARCH

I recently saw an old friend for the first time in many years. We had been Ph.D. students at the same time, both studying science, though in different areas. She later dropped out of graduate school, went to Harvard Law School, and is now a senior lawyer for a major environmental organization. At some point, the conversation turned to why she left grad school. To my utter astonishment, she said it was because it made her feel stupid. After a couple of years of feeling stupid every day, she was ready to do something else. I had thought of her as one of the brightest people I knew, and her subsequent career supports that view. What she said bothered me. I kept thinking about it and sometime the next day, it hit me. Science makes me feel stupid, too. It's just that I've gotten used to it. So used to it, in fact, that I actively seek out new opportunities to feel stupid. I wouldn't know what to do without it. I even think it's supposed to be this way. I don't think students are made to understand how hard it is to do research, and how very, very hard it is to do important research. It's a lot harder than taking even very …
TARGET‐MANAGEMENT‐INVOLVED BUYOUTS: IMPACT ON TAKEOVER COMPETITION, LITIGATION RISK, AND SHAREHOLDER RETURNS

We examine the impact of target management involvement as bidders in a sample of completed going-private buyouts. Announcement-period and long-run target shareholder returns do not appear to be lower in management-involved deals. We attempt to identify disciplining mechanisms in the takeover process that can explain this result. We find that target shareholder lawsuits are more likely when management is involved, and litigation risk appears to positively affect target returns. We also study a sample of withdrawn buyout deals and find that a significant number of management bids are unsuccessful, further suggesting that safeguards exist in management-involved deals.
Joint Data Purchasing and Data Placement in a Geo-Distributed Data Market

This paper studies design challenges faced by a geo-distributed cloud data market: which data to purchase (data purchasing) and where to place/replicate the data (data placement). We show that the joint problem of data purchasing and data placement within a cloud data market is NP-hard in general. However, we give a provably optimal algorithm for the case of a data market made up of a single data center, and then generalize the structure from the single data center setting and propose Datum, a near-optimal, polynomial-time algorithm for a geo-distributed data market.
On Weak and Strong $2^{k}$ -Bent Boolean Functions

In this paper, we introduce a sequence of discrete Fourier transforms and define new versions of bent functions, which we shall call (weak and strong) octa/hexadeca and, in general, $2^{k}$ -bent functions. We investigate relationships between these classes and completely characterize the octabent and hexadecabent functions in terms of bent functions. We further find relative difference sets based upon these functions.
The Cerebellum in Sagittal Plane—Anatomic-MR Correlation: 2. The Cerebellar Hemispheres

Thin (5-mm) sagittal high-field (1.5-T) MR images of the cerebellar hemispheres display (1) the superior, middle, and inferior cerebellar peduncles; (2) the primary white-matter branches to the hemispheric lobules including the central, anterior, and posterior quadrangular, superior and inferior semilunar, gracile, biventer, tonsil, and flocculus; and (3) several finer secondary white-matter branches to individual folia within the lobules. Surface features of the hemispheres including the deeper fissures (e.g., horizontal, posterolateral, inferior posterior, and inferior anterior) and shallower sulci are best delineated on T1-weighted (short TR/short TE) and T2-weighted (long TR/long TE) sequences, which provide greatest contrast between CSF and parenchyma. Correlation of MR studies of three brain specimens and 11 normal volunteers with microtome sections of the anatomic specimens provides criteria for identifying confidently these structures on routine clinical MR. MR should be useful in identifying, localizing, and quantifying cerebellar disease in patients with clinical deficits.
Organocatalyzed Enantioselective Direct Mannich Reaction of α-Styrylacetates

An organocatalyzed direct Mannich reaction of unactivated α-styrylacetates was realized for the first time. By using a quinidine-derived C6′-urea catalyst, the direct Mannich reaction of α-styrylacetates and N-tosylimines gave the desired β-amino esters in high yields, diastereoselectivities, and ee values. The reaction provides a highly stereoselective (up to 96:4 dr and 97% ee) and the most straightforward synthesis of functionalized N-tosylated β-amino esters. The products can be used as precursors for the highly selective synthesis of tetrahydrofuran derivatives.
Conditioning, thickening, and dewatering: research update/research needs

The production of sludges that are amenable to beneficial reuse (and thereby merit the term “biosolids”) has become a high priority concern in wastewater treatment. Regulations in many countries have become stringent in this regard, and the production of suitable biosolids now influences the selection, design, and operation of upstream processes. Among these are the conditioning, thickening, and dewatering of sludges. This paper briefly reviews current technology trends in these process areas, placing them in the context of overall needs for improved biosolids management. It is foreseen that conditioning, thickening and dewatering processes will need to operate at higher performance and reliability levels to maintain disposal and reuse flexibility. The chemistry of conditioning must be more clearly determined since secondary interactions of the conditioning additives may be important in ways that are not currently recognized.
Characteristics of Voluntary Behavior in the Neighborhood Commons: The Case of Dog Parks

The neighborhood commons, and dog parks in particular, provide a good laboratory to explore the drivers of voluntarism and trust, as well as the situational and demographic correlates that promote or inhibit voluntarism. This analysis connects a central theme of Ostrom’s work on institutions for overcoming social dilemmas to the literature on voluntary actions and the health of small communities. Survey results from more than 500 users of 14 dog parks in the Atlanta area are examined to understand how variation in park and user characteristics predict variation in individual contributions to the commons, including pro-social attitudes and behavior and dispute resolution behavior. Our analysis shows how institutions foster community commons, which are correlated with both voluntarism and the voluntary enforcement of norms on users. These results from a study in the field contribute to a growing literature that explores the circumstances for successful voluntary supply and maintenance of public goods.
Geometric median in nearly linear time

In this paper we provide faster algorithms for solving the geometric median problem: given n points in d compute a point that minimizes the sum of Euclidean distances to the points. This is one of the oldest non-trivial problems in computational geometry yet despite a long history of research the previous fastest running times for computing a (1+є)-approximate geometric median were O(d· n4/3є−8/3) by Chin et. al, O(dexpє−4logє−1) by Badoiu et. al, O(nd+poly(d,є−1)) by Feldman and Langberg, and the polynomial running time of O((nd)O(1)log1/є) by Parrilo and Sturmfels and Xue and Ye. In this paper we show how to compute such an approximate geometric median in time O(ndlog3n/є) and O(dє−2). While our O(dє−2) is a fairly straightforward application of stochastic subgradient descent, our O(ndlog3n/є) time algorithm is a novel long step interior point method. We start with a simple O((nd)O(1)log1/є) time interior point method and show how to improve it, ultimately building an algorithm that is quite non-standard from the perspective of interior point literature. Our result is one of few cases of outperforming standard interior point theory. Furthermore, it is the only case we know of where interior point methods yield a nearly linear time algorithm for a canonical optimization problem that traditionally requires superlinear time.
Psychotherapy with schizophrenics in team groups: a systems model.

Treating schizophrenic patients in a heterogeneous group in the inpatient setting poses numerous challenges. The author describes a developmental model based on systems theory to understand the dyn...
Anemia of prematurity.

In addition to the question of whether the postnatal fall in hemoglobin of premature infants is a physiologic event, several other problems considered are: the lowest level of hemoglobin which should be permitted before transfusion becomes necessary, institution of iron supplementation, and the role of vitamin E deficiency in the anemia of prematurity.
Cyclooxygenase-2-Specific Inhibitors and Cardiorenal Function: A Randomized, Controlled Trial of Celecoxib and Rofecoxib in Older Hypertensive Osteoarthritis Patients

Background Arthritis and hypertension are common comorbid conditions affecting elderly adults. Use of nonsteroidal anti-inflammatory drugs in patients treated with antihypertensive medication can lead to destabilization of blood pressure control and other cardiorenal events. The potential for similar interactions with cyclooxygenase-2-specific inhibitors has not been fully explored. The authors evaluated the cardiorenal safety of two new cyclooxygenase-2-specific inhibitors, celecoxib and rofecoxib. Methods This study was a 6-week, randomized, parallel-group, double-blind trial in patients with osteoarthritis who were > or =65 years of age and were taking antihypertensive agents. Patients received once-daily celecoxib 200 mg or rofecoxib 25 mg. The primary endpoints were the development of edema, changes in systolic blood pressure, and changes in diastolic blood pressure as measured at any time point in the study. Measurements occurred at baseline and after 1, 2, and 6 weeks of treatment. Findings Eight hundred ten patients received study medication (celecoxib, n = 411; rofecoxib, n = 399). Nearly twice as many rofecoxib- compared with celecoxib-treated patients experienced edema (9.5% vs. 4.9%, P = 0.014). Systolic blood pressure increased significantly in 17% of rofecoxib- compared with 11% of celecoxib-treated patients (P = 0.032) at any study time point. Diastolic blood pressure increased in 2.3% of rofecoxib- compared with 1.5% of celecoxib-treated patients (P = 0.44). At week 6, the change from baseline in mean systolic blood pressure was +2.6 mmHg for rofecoxib compared with -0.5 mmHg for celecoxib (P = 0.007). Conclusions Patients taking antihypertensive therapy and receiving cyclooxygenase-2-specific inhibitors should be monitored for the development of cardiorenal events. Patients receiving celecoxib experienced less edema and less destabilization of blood pressure control compared with those receiving rofecoxib.
Pay for value.

Texas Bix Bender is not a known health economist. In fact, he's not an economist at all. He is the author of "Don't Squat with Yer Spurs On! The Cowboy's Guide to Life", and in that book he provides some insight into the issues that affect improving healthcare effectiveness and efficiency. One of his guides to life is as follows: "If you find yourself in a hole, the first thing to do is stop digging" [3].
Synthesis of Ethers via Reaction of Carbanions and Monoperoxyacetals

Although transfer of electrophilic alkoxyl (“RO+”) from organic peroxides to organometallics offers a complement to traditional methods for etherification, application has been limited by constraints associated with peroxide reactivity and stability. We now demonstrate that readily prepared tetrahydropyranyl monoperoxyacetals react with sp3 and sp2 organolithium and organomagnesium reagents to furnish moderate to high yields of ethers. The method is successfully applied to the synthesis of alkyl, alkenyl, aryl, heteroaryl, and cyclopropyl ethers, mixed O,O-acetals, and S,S,O-orthoesters. In contrast to reactions of dialkyl and alkyl/silyl peroxides, the displacements of monoperoxyacetals provide no evidence for alkoxy radical intermediates. At the same time, the high yields observed for transfer of primary, secondary, or tertiary alkoxides, the latter involving attack on neopentyl oxygen, are inconsistent with an SN2 mechanism. Theoretical studies suggest a mechanism involving Lewis acid promoted insertio...
Persistent confusion and controversy surrounding gene patents

The development of patent-specific educational resources and prompt resolution of patentability rules unsettled by recent US Supreme Court decisions are urgently needed in the genomics industry.
Crystal growth, structure, and properties, of a new oxovanadium(IV) phosphate material, [H2en]4[V7P8O35(OH)6(H2O)]·3H2O prepared via a mild one step hydrothermal route

Abstract One new oxovanadium(IV) phosphate material, [H2en]4[V7P8O35(OH)6(H2O)]·3H2O was prepared utilizing a one step, mild hydrothermal route involving ethylenediamine as the reducing agent. The compound was structurally characterized by single crystal and powder X-ray diffraction methods and found to crystallize in the monoclinic space group C2/c. The temperature dependence of the magnetic susceptibility of was measured and found to be paramagnetic down to 2 K. The compound was further characterized by IR and UV–Vis spectroscopies.
QCM viscometer for bioremediation monitoring

A quartz crystal microbalance (QCM) has been used to monitor the polymer production of a bacterial population in liquid medium. The increasing amount of produced polymer corresponds to an increase in the viscosity of the liquid, which is directly measurable as the fluid contacts the surface of the quartz crystal in the sensor system. This procedure is being developed as a novel method for measuring microbial polymer production and growth of an environmental isolate obtained from a river sediment contaminated with petroleum hydrocarbons. This measurement technique may be used to monitor growth characteristics of unknown anaerobic bacteria when used in conjunction with other currently employed microbiological test methods such as spectrophotometry to measure turbidity. In the presence of glucose, a novel, strictly anaerobic bacterial isolate, designated strain JEL-1, produces a viscous, as yet unidentified polymer. In defined minimal media containing amino acids and glucose under a nitrogen gas atmosphere, copious quantities of this polymer are produced. This research investigates the corresponding increase in quantity of the polymer produced by JEL-1 as well as the polymer production rate in a controlled liquid medium.
New principles for auxetic periodic design.

We show that, for any given dimension $d\geq 2$, the range of distinct possible designs for periodic frameworks with auxetic capabilities is infinite. We rely on a purely geometric approach to auxetic trajectories developed within our general theory of deformations of periodic frameworks.
The Effect of Vietnam-Era Conscription and Genetic Potential for Educational Attainment on Schooling Outcomes

This study examines whether draft lottery estimates of the causal effects of Vietnam-era military service on schooling vary by an individual's genetic propensity toward educational attainment. To capture the complex genetic architecture that underlies the bio-developmental pathways, behavioral traits and evoked environments associated with educational attainment, we construct polygenic scores (PGS) for respondents in the Health and Retirement Study (HRS) that aggregate thousands of individual loci across the human genome and weight them by effect sizes derived from a recent genome-wide association study (GWAS) of years of education. Our findings suggest veterans with below average PGSs for educational attainment may have completed fewer years of schooling than comparable non-veterans. On the other hand, we do not find any difference in the educational attainment of veterans and non-veterans with above average PGSs. Results indicate that public policies and exogenous environments may induce heterogeneous treatment effects by genetic disposition.
Kinetic corrections from analytic non-Maxwellian distribution functions in magnetized plasmas

In magnetized plasma physics, almost all developed analytic theories assume a Maxwellian distribution function (MDF) and in some cases small deviations are described using the perturbation theory. The deviations with respect to the Maxwellian equilibrium, called kinetic effects, are required to be taken into account especially for fusion reactor plasmas. Generally, because the perturbation theory is not consistent with observed steady-state non-Maxwellians, these kinetic effects are numerically evaluated by very central processing unit (CPU)-expensive codes, avoiding the analytic complexity of velocity phase space integrals. We develop here a new method based on analytic non-Maxwellian distribution functions constructed from non-orthogonal basis sets in order to (i) use as few parameters as possible, (ii) increase the efficiency to model numerical and experimental non-Maxwellians, (iii) help to understand unsolved problems such as diagnostics discrepancies from the physical interpretation of the parameters, and (iv) obtain analytic corrections due to kinetic effects given by a small number of terms and removing the numerical error of the evaluation of velocity phase space integrals. This work does not attempt to derive new physical effects even if it could be possible to discover one from the better understandings of some unsolved problems, but here we focus on the analytic prediction of kinetic corrections from analytic non-Maxwellians. As applications, examples of analytic kinetic corrections are shown for the secondary electron emission, the Langmuir probe characteristic curve, and the entropy. This is done by using three analytic representations of the distribution function: the Kappa distribution function, the bi-modal or a new interpreted non-Maxwellian distribution function (INMDF). The existence of INMDFs is proved by new understandings of the experimental discrepancy of the measured electron temperature between two diagnostics in JET. As main results, it is shown that (i) the empirical formula for the secondary electron emission is not consistent with a MDF due to the presence of super-thermal particles, (ii) the super-thermal particles can replace a diffusion parameter in the Langmuir probe current formula, and (iii) the entropy can explicitly decrease in presence of sources only for the introduced INMDF without violating the second law of thermodynamics. Moreover, the first order entropy of an infinite number of super-thermal tails stays the same as the entropy of a MDF. The latter demystifies the Maxwell's demon by statistically describing non-isolated systems.
Benchmarking of de novo assembly algorithms for Nanopore data reveals optimal performance of OLC approaches

Improved DNA sequencing methods have transformed the field of genomics over the last decade. This has become possible due to the development of inexpensive short read sequencing technologies which have now resulted in three generations of sequencing platforms. More recently, a new fourth generation of Nanopore based single molecule sequencing technology, was developed based on MinION® sequencer which is portable, inexpensive and fast. It is capable of generating reads of length greater than 100 kb. Though it has many specific advantages, the two major limitations of the MinION reads are high error rates and the need for the development of downstream pipelines. The algorithms for error correction have already emerged, while development of pipelines is still at nascent stage. In this study, we benchmarked available assembler algorithms to find an appropriate framework that can efficiently assemble Nanopore sequenced reads. To address this, we employed genome-scale Nanopore sequenced datasets available for E. coli and yeast genomes respectively. In order to comprehensively evaluate multiple algorithmic frameworks, we included assemblers based on de Bruijn graphs (Velvet and ABySS), Overlap Layout Consensus (OLC) (Celera) and Greedy extension (SSAKE) approaches. We analyzed the quality, accuracy of the assemblies as well as the computational performance of each of the assemblers included in our benchmark. Our analysis unveiled that OLC-based algorithm, Celera, could generate a high quality assembly with ten times higher N50 & mean contig values as well as one-fifth the number of total number of contigs compared to other tools. Celera was also found to exhibit an average genome coverage of 12 % in E. coli dataset and 70 % in Yeast dataset as well as relatively lesser run times. In contrast, de Bruijn graph based assemblers Velvet and ABySS generated the assemblies of moderate quality, in less time when there is no limitation on the memory allocation, while greedy extension based algorithm SSAKE generated an assembly of very poor quality but with genome coverage of 90 % on yeast dataset. OLC can be considered as a favorable algorithmic framework for the development of assembler tools for Nanopore-based data, followed by de Bruijn based algorithms as they consume relatively less or similar run times as OLC-based algorithms for generating assembly, irrespective of the memory allocated for the task. However, few improvements must be made to the existing de Bruijn implementations in order to generate an assembly with reasonable quality. Our findings should help in stimulating the development of novel assemblers for handling Nanopore sequence data.
Generating and analyzing spatial social networks

In this paper, we propose a class of models for generating spatial versions of three classic networks: Erdos-Renyi (ER), Watts-Strogatz (WS), and Barabasi-Albert (BA). We assume that nodes have geographical coordinates, are uniformly distributed over an m × m Cartesian space, and long-distance connections are penalized. Our computational results show higher clustering coefficient, assortativity, and transitivity in all three spatial networks, and imperfect power law degree distribution in the BA network. Furthermore, we analyze a special case with geographically clustered coordinates, resembling real human communities, in which points are clustered over k centers. Comparison between the uniformly and geographically clustered versions of the proposed spatial networks show an increase in values of the clustering coefficient, assortativity, and transitivity, and a lognormal degree distribution for spatially clustered ER, taller degree distribution and higher average path length for spatially clustered WS, and higher clustering coefficient and transitivity for the spatially clustered BA networks.
How African American Adolescents Manage Depression: Being With Others

BACKGROUND: African American (AA) adolescents with depression face serious negative outcomes. Despite racial/ethnic disparities in treatment utilization, few studies have explored how AA adolescents manage their depression. OBJECTIVE: To describe common ways AA adolescents manage depressive symptoms through relationships with people in their lives. DESIGN: Qualitative descriptive methods were used to analyze the narratives of 22 AA young adults who had been depressed as adolescents and 5 AA adolescents in treatment for depression. RESULTS: A typology describing the varied ways AA adolescents manage their depressive symptoms through interactions with other people was constructed and labeled Being With Others. The five categories in the typology are keeping others at bay, striking out at others, seeking help from others, joining in with others, and having others reach out. CONCLUSIONS: Clinicians might use the Being With Others typology to guide discussions related to detecting, assessing, and treating AA a...
Using Real-Time Fear Appeals to Improve Social Media Security

Social media sites has been become major targets for cyber-security attacks due to their large user base. Many studies investigated the vulnerabilities and privacy issues of social networking sites and made recommendations on how to mitigate security risks. However, social media users' awareness of vulnerabilities doesn't always be turned into the actions complying with security recommendations. In this paper, we explore the relationship between social media users' perception of security risks and their actual behaviors on the sites. Built on protection motivation theory (PMT), we propose to develop a real time fear appeals system that can warn users about the security risks and stimulate the users' risk-mitigating behaviors on social media sites. The research plan is presented.
Rethinking Financial Reporting: Standards, Norms and Institutions

Since the passage of the US federal securities laws more than eight decades ago, much regulatory effort has been devoted to improving financial reporting in business, government and not-for-profit organizations. Yet, evidence on improvements or abatement of misreporting by error or intent remains scarce. In the context of this experience, it may be useful to explore what we might mean by better financial reporting, and how we might define and implement processes to move in that direction. A broad agreement on the way ahead seems necessary to make progress.
Amphetamine enhances endurance by increasing heat dissipation

Athletes use amphetamines to improve their performance through largely unknown mechanisms. Considering that body temperature is one of the major determinants of exhaustion during exercise, we investigated the influence of amphetamine on the thermoregulation. To explore this, we measured core body temperature and oxygen consumption of control and amphetamine-trea ted rats running on a treadmill with an incrementally increasing load (both speed and incline). Experimental results showed that rats treated with amphetamine (2 mg/kg) were able to run significantly longer than control rats. Due to a progressively increasing workload, which was matched by oxygen consumption, the control group exhibited a steady increase in the body temperature. The administration of amphetamine slowed down the temperature rise (thus decreasing core body temperature) in the beginning of the run without affecting oxygen consumption. In contrast, a lower dose of amphetamine (1 mg/kg) had no effect on measured parameters. Using a mathematical model describing temperature dynamics in two compartments (the core and the muscles), we were able to infer what physiological parameters were affected by amphetamine. Modeling revealed that amphetamine administration increases heat dissipation in the core. Furthermore, the model predicted that the muscle temperature at the end of the run in the amphetamine-treated group was significantly higher than in the control group. Therefore, we conclude that amphetamine may mask or delay fatigue by slowing down exercise-induced core body temperature growth by increasing heat dissipation. However, this affects the integrity of thermoregulatory system and may result in potentially dangerous overheating of the muscles.
Don't Be Greedy: Leveraging Community Structure to Find High Quality Seed Sets for Influence Maximization

We consider the problem of maximizing the spread of influence in a social network by choosing a fixed number of initial seeds — a central problem in the study of network cascades. The majority of existing work on this problem, formally referred to as the influence maximization problem, is designed for submodular cascades. Despite the empirical evidence that many cascades are non-submodular, little work has been done focusing on non-submodular influence maximization.
In situ pre-growth calibration using reflectance as a control strategy for MOCVD fabrication of device structures

In situ normal incidence reflectance, combined with a virtual interface model, is being used routinely on a commercial metal organic chemical vapor deposition reactor to measure growth rates of compound semiconductor films. The technique serves as a pre-growth calibration tool analogous to the use of reflection high-energy electron diffraction in molecular beam epitaxy as well as a real-time monitor throughout the run. An application of the method to the growth of a vertical cavity surface emitting laser (VCSEL) device structure is presented. All necessary calibration information can be obtained using a single run lasting less than 1 h. Working VCSEL devices are obtained on the first try after calibration. Repeated runs have yielded ±0.3% reproducibility of the Fabry-Perot cavity wavelength over the course of more than 100 runs.
Indium-Mediated Stereoselective Allylation.

ConspectusStereoselective indium-mediated organic reactions have enjoyed tremendous growth in the last 25 years. This is in part due to the insensitivity of allylindium to moisture, affording facile and practical reaction conditions coupled with outstanding functional group tolerance and minimal side reactions. Despite the plethora of articles about allylindium, there is much yet to be discovered and exploited for efficient and sustainable synthesis.In this Account, we describe indium-mediated synthetic methods for the preparation of chiral amines with the aim to present a balance of practical method development, novel asymmetric chemistry, and mechanistic understanding that impact multiple chemical and materials science disciplines. In 2005, we demonstrated the indium-mediated allylation of chiral hydrazones with complete diastereoselectivity (>99:1) and quantitative yields. Further, we revealed the first example of enantioselective indium-mediated allylation of hydrazones using catalytic (R)-3,3′-bis(tr...
Higher-harmonic collective modes in a trapped gas from second-order hydrodynamics

Utilizing a second-order hydrodynamics formalism, the dispersion relations for the frequencies and damping rates of collective oscillations as well as spatial structure of these modes up to the decapole oscillation in both two- and three- dimensional gas geometries are calculated. In addition to higher-order modes, the formalism also gives rise to purely damped "non-hydrodynamic" modes. We calculate the amplitude of the various modes for both symmetric and asymmetric trap quenches, finding excellent agreement with an exact quantum mechanical calculation. We find that higher-order hydrodynamic modes are more sensitive to the value of shear viscosity, which may be of interest for the precision extraction of transport coefficients in Fermi gas systems.
Late effects of total-body roentgen irradiation. Longevity and incidence of nephrosclerosis as influenced by partial body shielding

Two hundred forty-two female Wistar rats were observed throughout their life span following 1,000 r hypoxic total-body or partial-body irradiation. Hypoxic radiation with superimposed anesthesia resulted in 67 percent 30 day mortality, compared to 9 percent mortality without anesthesia. Selection of the colony by acute postirradiation deaths did not influence the magnitude of late radiation sequelae as measured by lifeshortening. Growth retardation during the second postirradiation year was well correlated with lifeshortening. Life- shortening was observed after partialbody irradiation to and extent approximately proportional to the weight of radiated tissue. Nephrosclerosis was not observed unless the upper abdomen was included within the radiation field. Other than nephrosclerosis, a similar incidence of disease was observed at death in control and irradiated rats whether partial-body or total-body irradiated. (auth)
Riemannian SVRG: fast stochastic optimization on riemannian manifolds

We study optimization of finite sums of geodesically smooth functions on Riemannian manifolds. Although variance reduction techniques for optimizing finite-sums have witnessed tremendous attention in the recent years, existing work is limited to vector space problems. We introduce Riemannian SVRG (RSVRG), a new variance reduced Riemannian optimization method. We analyze RSVRG for both geodesically convex and nonconvex (smooth) functions. Our analysis reveals that RSVRG inherits advantages of the usual SVRG method, but with factors depending on curvature of the manifold that influence its convergence. To our knowledge, RSVRG is the first provably fast stochastic Riemannian method. Moreover, our paper presents the first non-asymptotic complexity analysis (novel even for the batch setting) for nonconvex Riemannian optimization. Our results have several implications; for instance, they offer a Riemannian perspective on variance reduced PCA, which promises a short, transparent convergence analysis.
Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast.

Abstract Ribosome profiling quantitatively captures ribosome locations during translation. The resulting profiles of ribosome locations are widely used to study translational speed. However, an accurate estimation of the ribosome location depends on identifying the A-site from ribosome profiling reads, a problem that was previously unsolved. Here, we propose a novel method to estimate the ribosome A-site positions from high-coverage ribosome profiling reads. Our model allows more reads to be used, accurately explains the 3-nt periodicity of ribosome profiling reads from various lengths, and recovers consistent ribosome positions across different lengths. Our recovered ribosome positions are correctly highly skewed toward a single frame within a codon. They retain subcodon resolution and enable detection of off-frame translational events, such as frameshifts. Our method improves the correlation with other estimates of codon decoding time. Furthermore, the refined profiles show that yeast wobble-pairing cod...
Design of Stable Canals and Channels in Erodible Material

Major factors which must be integrated into design of irrigation canal; factors causing change in stream regimen; methods by which proper size and shape of channel can be computed; practical consideration and field experience of channel stability problems; basic data needed for adequate design of channel.
Deterministic Discrepancy Minimization via the Multiplicative Weight Update Method

A well-known theorem of Spencer shows that any set system with n sets over n elements admits a coloring of discrepancy \(O(\sqrt{n})\). While the original proof was non-constructive, recent progress brought polynomial time algorithms by Bansal, Lovett and Meka, and Rothvoss. All those algorithms are randomized, even though Bansal’s algorithm admitted a complicated derandomization.
Development of a prototype blood fractionation cartridge for plasma analysis by paper spray mass spectrometry

Abstract Drug monitoring of biofluids is often time consuming and prohibitively expensive. Analysis of dried blood spots offers advantages, such as reduced sample volume, but depends on extensive sample preparation and the presence of a trained lab technician. Paper spray mass spectrometry allows rapid analysis of small molecules from blood spots with minimal sample preparation, however, plasma is often the preferred matrix for bioanalysis. Plasma spots can be analyzed by paper spray MS, but a centrifugation step to isolate the plasma is required. We demonstrate here the development of a paper spray cartridge containing a plasma fractionation membrane to perform automatic on-cartridge plasma fractionation from whole blood samples. Three commercially available blood fractionation membranes were evaluated based on: 1) accuracy of drug concentration determination in plasma, and 2) extent of cell lysis and/or penetration. The accuracy of drug concentration determination was quantitatively determined using high performance liquid chromatography–mass spectrometry (HPLC–MS). While the fractionation membranes were capable of yielding plasma samples with low levels of cell lysis, the membranes did exhibit drug binding to varying degrees, as indicated by a decrease in the drug concentration relative to plasma obtained by centrifugation. Using the membrane exhibiting the lowest binding, we developed a composite paper spray cartridge incorporating the selected fractionation membrane. Quantitative analysis of the plasma samples by paper spray MS yielded results similar to those found with HPLC–MS, but without the need for offline extraction or chromatography.
Response surface methodology: a modeling tool for integrated circuit designers

An approach to design is described which allows the designer to statistically analyze a circuit's output characteristics. The results of this analysis give the designer the ability to reduce the sensitivity and to optimize these output characteristics with respect to process, package, and environmental variations. In addition, the authors demonstrate the means by which to establish output specifications before time and money are invested in fabricating devices in silicon. Finally, examples of the successful application of this technique to the design and development of an ECL (emitter-coupled logic) family are discussed. The methods for applying the results from this statistical technique to manufacturing and testing are also shown. >