cssi/SciSciGPT-SciSciNet huggingface dataset:
Exploring How Deep Neural Networks Form Phonemic Categories

Deep neural networks (DNNs) have become the dominant technique for acoustic-phonetic modeling due to their markedly improved performance over other models. Despite this, little is understood about the computation they implement in creating phonemic categories from highly variable acoustic signals. In this paper, we analyzed a DNN trained for phoneme recognition and characterized its representational properties, both at the single node and population level in each layer. At the single node level, we found strong selectivity to distinct phonetic features in all layers. Node selectivity to specific manners and places of articulation appeared from the first hidden layer and became more explicit in deeper layers. Furthermore, we found that nodes with similar phonetic feature selectivity were differentially activated to different exemplars of these features. Thus, each node becomes tuned to a particular acoustic manifestation of the same feature, providing an effective representational basis for the formation of invariant phonemic categories. This study reveals that phonetic features organize the activations in different layers of a DNN, a result that mirrors the recent findings of feature encoding in the human auditory system. These insights may provide better understanding of the limitations of current models, leading to new strategies to improve their performance. Index Terms: Deep neural networks, deep learning, automatic speech recognition.
The Design and Analysis of (MASH)-ARROW for Liquid Core Optical Waveguiding

A Multi- and Single- layer Hybridized Anti-Resonant Reflection Optical Waveguide (MASH)-ARROW, is proposed to introduce a novel mechanism for 2D planar liquid core waveguiding and analyzed with finite element method for optofluidic sensing applications.
A Primer on Quantitized Data Analysis and Permutation Testing

Quantitization refers to transforming qualitative data into numerical format. Approaches to quantitization include dichotomizing qualitative themes and counting qualitative codes. Statistical analysis of themes and code counts has the potential to produce valuable information for mixed methods researchers. Examples of quantitized statistical analysis are presented along with ways in which the results can provide useful insights. With regard to analyzing code counts, due to limitations associated with traditional parametric and nonparametric tests of significance, permutation testing is offered as a rigorous alternative. A detailed example of permutation testing using readily available resampling software is provided.
Acetone–Heptane as a Solvent System for Combining Chromatography on Silica Gel with Solvent Recycling

Solvents used in chromatographic purification of intermediates and products are a major source of waste and expense in synthetic research and synthetic processes. The ethyl acetate–hexane mixtures most commonly used for flash chromatography on silica gel are not readily separable by distillation due to their similar boiling points and azeotrope formation. Potential solvents for chromatography that are more amenable to separation and recovery by distillation were thus explored. Acetone–heptane mixtures were found to be convenient and sufficiently separable for routine use and recovery for organic separations. The greater eluotropic strength and especially the transparent short-wavelength UV window of acetone provide additional advantages over the commonly used ethyl acetate. The recycling of solvents from chromatography can greatly reduce the volume of waste generated by synthetic laboratories while also reducing operating costs.
Tunable Protein and Bacterial Cell Adsorption on Colloidally Templated Superhydrophobic Polythiophene Films

A facile approach for enabling or inhibiting the adsorption of protein and adhesion of bacterial cells on a potential-induced reversibly wettable polythiophene film is described. The superhydrophobic polymeric surface was first prepared by a two-step process that combines the layering of polystyrene (PS) latex particles via a Langmuir–Blodgett (LB)-like technique followed by cyclic voltammetric (CV)–electrodeposition of polythiophene from a terthiophene ester monomer. The polythiophene conducting polymer coating enabled control of the wettability of the surface by simply changing its redox property via potential switching. The influence of morphology on this switching behavior is also described. The wettability in return controls the adsorption of protein and adhesion of bacterial cells. For instance, the undoped polythiophene film, which is superhydrophobic, inhibits the adhesion of fibrinogen proteins and Escherichia coli (E. coli) cells. On the other hand, the doped film, which is hydrophilic, leads to...
AGGRESSIVE 3RD-BODY WEAR CHALLENGE TO VITAMIN E CROSS-LINKED POLYETHYLENE: A HIP SIMULATOR MODEL TO TEN MILLION CYCLES DURATION

Introduction Over 40-years the dominant form of implant fixation has been bone cement (PMMA). However the presence of circulating PMMA debris represents a 3rd-body wear mechanism for metal-on-polyethylene (MPE). Wear studies using PMMA slurries represent tests of clinical relevance (Table 1). Cup designs now use many varieties of highly-crosslinked polyethylene (HXPE) of improved wear resistance. However there appears to be no adverse wear studies of vitamin-E blended cups.1–4 The addition of vitamin E as an anti-oxidant is the currently preferred method to preserve mechanical properties and ageing resistance of HXPE. Therefore the present study examined the response of vitamin-E blended liners to PMMA abrasion combined with CoCr and ceramic heads. The hip simulator wear study was run in two phases to compare wear with, (i) clean lubricants and (ii) PMMA slurries. Methods The vitamin-e blended polyethylene liners (HXe+) were provided by DJO Surgical (Austin, TX) with 40mm CoCr and ceramic femoral heads (Biolox-delta). Polyethylene liners were run in standard “Inverted” test. (Table 1) All cups were run in ‘clean’ serum lubricant for 6-million load cycles (6Mc)5 and in a debris slurry (PMMA: 5mg/ml concentration) for 2Mc.4 A commercial bone cement powder was used as “abrasive” (Biomet, Warsaw, IN). PMMA slurries were added at test intervals 6, 6.5, 7 and 7.5Mc.4 Wear was assessed gravimetrically and characterized by linear regression. Bearing roughness was analyzed by interferometry and SEM. Results The acetabular cups showed low wear-rates to 6Mc duration with both ceramic and CoCr heads (Fig. 1). The debris slurries created much higher wear-rates, whereas control liners continued as before (Table 2). Discussion This is the 1st study of vitamin-E blended polyethylene under 3rd-body wear conditions. With clean lubricant conditions, CPE combination wore approximately 50% less than MPE combination. Under abrasive lubricant conditions, CPE and MPE combinations wore at approximately same rate but more than an order of magnitude greater than the clean test phase. This was typical of such PMMA abrasion tests (Table 1). However there are no guidelines as to optimal choice of particulate type, morphology, dosage, frequency of injection or duration of test intervals (Table 1). The production of particulates in vivo is an unpredictable phenomenon and consequently laboratory simulation is fraught with uncertainties.6 On completion of the abrasive challenge (6–8Mc duration), our study will continue under clean conditions to 10Mc to define the important recovery phase of the vitamin-E blended polyethylene.3
How Does Knowledge Evolve?: Evidence from Solid-State Lighting

In this paper, we study knowledge evolution of an emerging industry. We use the phenomenon of the emergence of solid-state lighting industry to examine the technical development, the first step of ...
Improved pulse-echo imaging performance for flexure-mode pMUT arrays

Piezoelectric micromachined ultrasound transducers (pMUTs) are potential candidates for catheter-based ultrasound phased arrays. pMUTs consist of lead zirconate titanate (PZT) thin film membranes formed on silicon substrates and are operated in flexure mode by driving the PZT film above its coercive field to induce flextensional motion. The fundamental operation of pMUT devices has been demonstrated; however, pulse-echo imaging has been limited to date. The objective of this work was to optimize transducer design for improved pulse-echo imaging performance. Flexure mode operation was optimized by (1) increasing transmit voltage above the PZT coercive field to induce ferroelectric domain switching, and (2) using partial cycle transmit pulses to increase the polarization in the PZT thin film and increase receive signal. As a result, pulse-echo images of tissue were obtained. 1-D arrays operating at 5 MHz were capable of resolving targets in a commercial tissue phantom as well as human anatomy. Real-time 3-D imaging was also demonstrated using 2-D arrays at 5 and 12.5 MHz. These results suggest that pMUTs have sufficient performance for application in ultrasound imaging with frequency range suitable for catheter-based phased-array transducers.
The Dualism of Modern Just War Theory

Conventional modern just war theory is fundamentally incoherent. On the one hand, the theory contains a theory of public war wherein ethical responsibility for the justice of war belongs uniquely to political sovereigns while subjects, including soldiers, are obligated to serve in war upon the sovereign’s command. On the other hand, the theory contains a theory of discrimination which presupposes that participants in war, including soldiers, are responsible for the justice of the wars they fight. Moreover, these two components are derived from two inconsistent visions of political justice. The theory of public war, it turns out, is derived from a theory of justice that places the value of political society conceived of as a supra-individual communal entity above the value of the private individual. The theory of discrimination, however, is derived from a theory of justice that places the value of the private individual above that of political society. This inconsistency is revealed by analyzing the theories of Vitoria, Grotius, and Walzer. Appreciating this problem also helps situate the recent revisionist critiques of conventional just war theory.
Abstract 101: Mesenchymal Stem Cells Attenuate Experimental Abdominal Aortic Aneurysm Formation via Inhibition of IL-17

Objective: The immunomodulatory effects of mesenchymal stem cells (MSCs) remain to be defined in abdominal aortic aneurysm (AAA) formation. This study investigates the role of MSCs in the attenuation of AAA via inhibition of IL-17 using an in vivo elastase-perfusion murine model and by in vitro studies. Methods: AAAs were induced in 8- to 12-week old C57BL/6 (WT) mice using an elastase-perfusion (or heat inactivated elastase as control) AAA mouse model. The abdominal aorta was perfused for 5 minutes with 0.4 U/mL type 1 porcine pancreatic elastase. WT mice were also treated with MSCs (1x10 6 cells; intravenously) administered on day 1. On day 14 following perfusion, the abdominal aorta was measured by video micrometry and expressed as percentage increase over baseline aortic diameter. Cytokine analysis of aortic tissue was performed by multiplex-bead based ELISA. In vitro experiments evaluated cell proliferation and IL-17 production in mixed lymphocyte reactions with or without MSC treatment. Groups were compared using ANOVA followed by Bonferroni post hoc test. Results: A significant increase in aortic diameter was observed on day 14 in elastase-perfused WT mice compared to controls, which was significantly attenuated in the elastase-perfused WT mice treated with MSCs (141.1±16.2% vs 51.2±4.15% vs. 82.1±9.2%, respectively; p In vitro experiments demonstrated that activation of mononuclear cells (MNCs) by anti-human CD3 and CD28 resulted in significant cell proliferation compared to unstimulated MNCs, and was significantly suppressed by MSCs co-cultured with MNCs (18,323.2+882.2 vs. 1475.7+182.0 vs. 646.5+29.1 cpm, respectively; p Conclusions: Mesenchymal stem cells attenuate AAA formation likely via mitigation of lymphocyte-produced IL-17 thereby offering a novel therapeutic strategy for treatment of aortic aneurysms.
WeBuild: Automatically Distributing Assembly Tasks Among Collocated Workers to Improve Coordination

Physical construction and assembly tasks are often carried out by groups of collocated workers, and they can be difficult to coordinate. Group members must spend time deciding how to split up the task, how to assign subtasks to each other, and in what order subtasks should be completed. Informed by an observational study examining group coordination challenges, we built a task distribution system called WeBuild. Our custom algorithm dynamically assigns subtasks to workers in a group, taking into account factors such as the dependencies between subtasks and the skills of each group member. Each worker views personalized step-by-step instructions on a mobile phone, while a dashboard visualizes the entire process. An initial study found that WeBuild reduced the start-up time needed to coordinate and begin a task, and provides direction for future research to build on toward improving group efficiency and coordination for complex tasks.
Real-time OPF based on quasi-Newton methods

Optimal power flow is a central problem in the operation of power systems. So far the majority of the literature deals with offline algorithms for traditional applications, but the proliferation of distributed energy resources and smart appliances in power networks motivates real-time and scalable algorithms. We introduce a real-time OPF algorithm based on quasi-Newton methods that can track the optimal operation when the state of the network is changing. Theory and simulations show that the proposed algorithm has guaranteed tracking performance and is computationally efficient.
Vicious-Circle Behavior in the Shuttlebox

A series of experiments was conducted on vicious-circle phenomena with rats in a shuttlebox. After an avoidance criterion was reached, shock in the middle third of the box prolonged responding relative to regular extinction for the majority of rats but resulted in inhibition for a minority. Continuous versus discontinuous shock and a 13.5-sec. versus a 37.5-sec. intertrial interval had no significant effects on the phenomenon.
Understanding the Emotional Labor Process: Does Individual Differences Make a Difference?

The emotional labor literature suffers from a lack of consensus in regards to what emotional labor is and what are its outcomes. This paper expands upon the work of Van Dijk & Brown (2006) who argu...
Shared additive genetic variation for alcohol dependence among subjects of African and European ancestry.

Alcohol dependence (AD) affects individuals from all racial/ethnic groups, and previous research suggests that there is considerable variation in AD risk between and among various ancestrally defined groups in the United States. Although the reasons for these differences are likely due in part to contributions of complex sociocultural factors, limited research has attempted to examine whether similar genetic variation plays a role across ancestral groups. Using a pooled sample of individuals of African and European ancestry (AA/EA) obtained through data shared within the Database for Genotypes and Phenotypes, we estimated the extent to which additive genetic similarity for AD between AA and EAs using common single nucleotide polymorphisms overlapped across the two populations. AD was represented as a factor score by using Diagnostic and Statistical Manual dependence criteria, and genetic data were imputed by using the 1000 Genomes Reference Panel. Analyses revealed a significant single nucleotide polymorphism-based heritability of 17 percent (SE = 5) in EAs and 24 percent (SE = 15) in AAs. Further, a significant genetic correlation of 0.77 (SE = 0.46) suggests that the allelic architecture influencing the AD factor for EAs and AAs is largely similar across the two populations. Analyses indicated that investigating the genetic underpinnings of alcohol dependence in different ethnic groups may serve to highlight core etiological factors common to both groups and unique etiological factors specific to each ethnic group.
Recruitment through Rule Breaking: Establishing Social Ties with Gang Members

Many contemporary violence prevention programs direct concentrated law enforcement, social service, or educational attention toward individuals engaged in violence, and yet, this population is ofte...
What Are the Goals of Lipid Testing

Lipids can be measured for immediate diagnostic purposes in which a dyslipidemia is in the differential diagnosis of the patient's presenting complaint. For example, a fasting lipid profile (specifically including triglycerides) would be appropriate in a patient presenting with acute pancreatitis of unclear origin (supposing that alcohol exposure, cholelithiasis, and trauma were excluded). Lipid screening for general cardiovascular risk assessment at frequencies accepted by clinical societies and payers alike remains the most common reason for measurements such as “the lipid profile (1).” Rarely, lipids are measured in search of hypolipidemia (e.g., possible causes of abetalipoprotienemia or hypobetalipoproteinemia). ### How can lipid testing be classified? The traditional lipid assessment is the “lipid profile,” sometimes referred to as a “lipoprotein profile.” We can group lipid testing into (1) standard tests, (2) supplemental standard tests (3 …
Risk factors for opioid overdose among hospitalized patients

WHAT IS KNOWN AND OBJECTIVE Hospitalized patients are at risk for opioid overdose. Little is known about the risk factors for these events. METHOD Opioid overdose cases were identified by naloxone orders in computerized order entry system from a single institution. For each case, two controls were randomly selected. Data were collected on factors including age, gender, weight, opioid dose, route of administration, concomitant CNS depressants, renal function and comorbid conditions. RESULTS AND DISCUSSION Between 2010 and 2013, we identified 44 cases of opioid overdose (OD), none of which were fatal, and matched these to 88 controls (no OD). Patients with a history of substance use disorder were excluded from the study. Factors associated with opioid overdose included age of 65 or older (40.9% OD vs 29.5% no OD, P = .026), being in an ICU (MICU/CICU 27.3% OD vs. 3.4% no OD, P < .001; SICU 18.1% OD vs 5.7% no OD, P = .031) and renal impairment (eGFR ≤60, 50.0% OD vs 28.4% no OD, P = .034). Total 24-hour opioid dose was lower in OD group, but the difference was not statistically significant (71.9 vs 107.2 mg morphine equivalent, P = .116). OD cases were more likely to have received concomitant CNS depressants, but the difference was statistically significant only for those who received 3 or more (15.9% OD vs 0% no OD, P = <.001). Heart disease was the only comorbidity significantly associated with an increased risk of opioid overdose (43.2% vs 20.5%, P = .025). Patient's BMI, duration of opioid use, route of administration and history of COPD and/or psychiatry were not associated with opioid overdoses. WHAT IS NEW AND CONCLUSION Among hospitalized patients, risk factors of opioid overdose include age of 65 or greater, being in an ICU, renal impairment and concomitant administration of CNS depressant medications. These findings may help with the development and implementation of measures to prevent overdose.
On-demand release of Candida albicans biofilms from urinary catheters by mechanical surface deformation.

Candida albicans is a leading cause of catheter-associated urinary tract infections and elimination of these biofilm-based infections without antifungal agents would constitute a significant medical advance. A novel urinary catheter prototype that utilizes on-demand surface deformation is effective at eliminating bacterial biofilms and here the broader applicability of this prototype to remove fungal biofilms has been demonstrated. C. albicans biofilms were debonded from prototypes by selectively inflating four additional intralumens surrounding the main lumen of the catheters to provide the necessary surface strain to remove the adhered biofilm. Deformable catheters eliminated significantly more biofilm than the controls (>90% eliminated vs 10% control; p < 0.001). Mechanical testing revealed that fungal biofilms have an elastic modulus of 45 ± 6.7 kPa with a fracture energy of 0.4-2 J m-2. This study underscores the potential of mechanical disruption as a materials design strategy to combat fungal device-associated infections.
Global Differences in Atherosclerosis

Cardiovascular disease causes one third of the deaths in the world. Eighty percent of these deaths are in developing countries. In developed countries death from infectious diseases has diminished as death from cardiovascular disease has increased. The proportion of cardiovascular deaths due to coronary heart disease and stroke varies between countries. The risk factors for cardiovascular diseases are known. Deaths can be largely accounted for by nine risk factors. These risk factors are common across the world regardless of geography, ethnicity, and gender. The origins of many risk factors relate to social, economic, fiscal, and political circumstances. Global institutions allocate insufficient funds to the prevention of cardiovascular disease. Informing the public and patients will put pressure on politicians to respond to the increasing global attrition of cardiovascular disease.
Searching for Mutually Unbiased Observables

We call two non-degenerate observables “mutually unbiased” if every eigenstate of one of them is a state of complete ignorance relative to the other one. For example, for a spin-1/2 particle, the spin components in the x, y, and z directions are all unbiased with respect to each other, since a knowledge of any of these components entails a complete lack of knowledge about the others. It turns out that if, for a given system, there exist a sufficient number of mutually unbiased observables, then measurements of these observables can be used to determine as efficiently as possible the state of an ensemble of such systems. For a system with a finite number N of orthogonal states, the number of mutually unbiased observables one needs is N+1. We have shown that precisely N+1 such observables can indeed be found if N is a power of a prime. We do not know whether this number can be found if N is not a power of a prime.
Tree-Based Forecasting Methods

The past two chapters have provided the necessary technical background for a consideration of statistical procedures that can be especially effective in criminal justice forecasting. The joint probability distribution model, data partitioning, and asymmetric costs should now be familiar. These features combine to make tree-based methods of recursive partitioning the fundamental building blocks for the machine learning procedures discussed. The main focus is random forests. Stochastic gradient boosting and Bayesian trees are discussed briefly as worthy competitors to random forests. Although neural nets and deep learning are not tree-based, they are also considered. Current claims about remarkable performance need to be dispassionately addressed, especially in comparison to tree-based methods.
Josephson Transmission Line Oscillators

In this paper, the term “Josephson transmission line” (or JTL) will refer to a wave structure composed of two superconducting metal strips separated by an insulating barrier that is thin enough (− 25A) to permit transverse (Josephson type) tunneling of electrons in the superconducting state [1]. JTL’s as long as 35 cm have been fabricated by a process employing rf sputtering of the metal layers and photoresist definition of all patterns [2,3]. A diagram of the basic structure to be considered is shown in Fig. 1 where a TEM wave is assumed to propagate in the x-direction. The dependent variables of this wave can be viewed as the transverse voltage v(x,t) across the insulating barrier and the logitudinal current i(x,t) flowing parallel to the insulating barrier in the x-direction.
Refinements on Estimating Fixed Base Modes on a Slip Table

In prior work by the author and others [1–3], a new method was demonstrated to extract fixed base modes from a modal test performed on a test article mounted on a vibration slip table. This paper addresses uncertainty that was apparent in frequency and damping estimates in previous work [3]. After reviewing the method based on substructure coupling, additional testing indicates that some of the frequency error was due to different size attachment bolts in the seismic mass truth test and the slip table test. In the previous work, the largest errors in prediction of the truth data were associated with damping. A procedure to subtract significant low frequency slip table damping is implemented and the resulting corrected damping estimate presented.
Presence of Phenolic Compounds in Sewage, Effluent and Sludge from Municipal Sewage Treatment Plants

A total of 25 municipal sewage treatment plants were sampled, 10 of which were resampled, to determine the quantity of phenolics in the sewage, final effluent and the anaerobically digested sludge using capillary GC/MS/DS/techniques. The study noted in decreasing order of frequency in raw sewage: phenol, pentachloro-phenol, dimethyl phenol, 3-methyl, 4-chlorophenol, 2,4,6-trichloro-phenol, 2,4-dichlorophenol, 2-nitrophenol, 2-chlorophenol, 2,4-dinitro-6-methylphenol and 2,4-dinitrophenol. The maximum concentration of phenol in sewage and sludge was 2800 ppb and 4460 respectively, while similar values for pentachlorophenol were 58 and 1200 ppb. Statistically calculated concentration reductions for phenol and dimethyl phenol were generally greater than noted for tri- and pentachlorophenol. Low decreases or increases were noted for monochlorophenol and especially for dichlorophenol as a result of the chloronation of the final effluent.
Hyperuricemia induced by ethambutol.

Ethambutol is commonly used to treat infections in man caused by Mycobacterium tuberculosis (Fig. 1). We have found that ethambutol also produces a substantial increase in the serum urate concentration in many patients receiving this agent (Postlethwaite, et al., 1972).
Automated Abdominal Segmentation of CT Scans for Body Composition Analysis Using Deep Learning

Purpose To develop and evaluate a fully automated algorithm for segmenting the abdomen from CT to quantify body composition. Materials and Methods For this retrospective study, a convolutional neural network based on the U-Net architecture was trained to perform abdominal segmentation on a data set of 2430 two-dimensional CT examinations and was tested on 270 CT examinations. It was further tested on a separate data set of 2369 patients with hepatocellular carcinoma (HCC). CT examinations were performed between 1997 and 2015. The mean age of patients was 67 years; for male patients, it was 67 years (range, 29-94 years), and for female patients, it was 66 years (range, 31-97 years). Differences in segmentation performance were assessed by using two-way analysis of variance with Bonferroni correction. Results Compared with reference segmentation, the model for this study achieved Dice scores (mean ± standard deviation) of 0.98 ± 0.03, 0.96 ± 0.02, and 0.97 ± 0.01 in the test set, and 0.94 ± 0.05, 0.92 ± 0.04, and 0.98 ± 0.02 in the HCC data set, for the subcutaneous, muscle, and visceral adipose tissue compartments, respectively. Performance met or exceeded that of expert manual segmentation. Conclusion Model performance met or exceeded the accuracy of expert manual segmentation of CT examinations for both the test data set and the hepatocellular carcinoma data set. The model generalized well to multiple levels of the abdomen and may be capable of fully automated quantification of body composition metrics in three-dimensional CT examinations. © RSNA, 2018 Online supplemental material is available for this article. See also the editorial by Chang in this issue.
Periocular Asymmetry in Infants with Deformational Posterior Plagiocephaly.

Purpose To analyze the clinical significance of the periorbital features associated with the facial asymmetry that is common in deformational posterior plagiocephaly (DPP). Patients and methods We identified 32 patients with DPP, photographed their faces and tops of their head, and performed a complete eye examination. Four examiners analyzed the patient's periorbital features on the photographs. Results Median age was 6.5 months (range 3-12 months). Pseudoptosis was identified in 30 patients and pseudo-brow ptosis in 19. Pseudoptosis was marked in 17 patients. Five patients were misdiagnosed with congenital blepharoptosis and received regular follow-ups for amblyopia checks until the diagnosis of pseudoptosis was established. All patients had normal levator function and symmetric eyelid crease. One patient with pseudoptosis and physiologic anisocoria was diagnosed with pseudo-Horner syndrome after a negative 10% cocaine test. None of the patients developed meridional or occlusion amblyopia. Conclusion DPP is the most frequent form of skull deformation in infants. Its main features are occipital flatness and facial asymmetry. Infants with DPP may present with pseudoptosis and pseudo-brow ptosis on the contralateral side of the occipital flatness. The pseudoptosis in DPP is non-amblyogenic, therefore, ophthalmologic intervention and regular follow-ups are not necessary unless other abnormalities co-exist.
Analysis of gst::egfp mRNA Levels by RT-qPCR: Part I

Abstract Total RNA that you purified in the last session will be converted to complementary DNA (cDNA) by a reverse transcription reaction. Then, cDNA will be used as a template for quantitative (real-time) PCR. You will amplify cDNA with primers specific to egfp (your test gene) and 23S rRNA (your reference gene).
Unbundling the knowledge economy

Instructors, researchers, and students often see universities as obviously unique institutions, not cut off from ‘the real world’ but certainly different from it. This is not the case with the grou...
Profile Hidden Markov Models Are Not Identifiable

Profile Hidden Markov Models (HMMs) are graphical models that can be used to produce finite length sequences from a distribution. In fact, although they were only introduced for bioinformatics 25 years ago (by Haussler et al., Hawaii International Conference on Systems Science, 1993), they are arguably the most commonly used statistical model in bioinformatics, with multiple applications, including protein structure and function prediction, classifications of novel proteins into existing protein families and superfamilies, metagenomics, and multiple sequence alignment. The standard use of profile HMMs in bioinformatics has two steps: first a profile HMM is built for a collection of molecular sequences (which may not be in a multiple sequence alignment), and then the profile HMM is used in some subsequent analysis of new molecular sequences. The construction of the profile thus is itself a statistical estimation problem, since any given set of sequences might potentially fit more than one model well. Hence, a basic question about profile HMMs is whether they are statistically identifiable , which means that no two profile HMMs can produce the same distribution on finite length sequences. Indeed, statistical identifiability is a fundamental aspect of any statistical model, and yet it is not known whether profile HMMs are statistically identifiable. In this paper, we report on preliminary results towards characterizing the statistical identifiability of profile HMMs in one of the standard forms used in bioinformatics.
A Systematic Review of Pica and Geophagy in Japan and Korea

Pica, the craved and purposive consumption of non-food substances, is a globally widespread behavior that has critical connections to public health. Although there is a rich literature describing these behaviors from nearly every culture around the world, there is a dearth of English language literature reporting these behaviors in Japan and Korea. Here, we systematically reviewed the medical evidence of pica in Korean and Japanese language journals to confirm their presence in these cultures and to characterize culturally-specific factors associated with these behaviors. We used Ichusi-Web and KoreaMed with a broad variety of recombined search terms including “pica,” “geophagy,” “amylophagy,” and “trichobezoar” in Korean and Japanese characters. Our results confirm that pica is present in both of these cultures, with particularly frequent reports of trichobezoar (the consumption of human hair).
Quantitative Analysis of Embedded Software Using Game-Theoretic Learning

Abstract : The analysis of quantitative properties, such as timing and power, is central to the design of reliable real-time embedded software and systems. However, the verification of such properties on a program is made difficult by their heavy dependence on the program's environment, such as the processor it runs on. Modeling the environment by hand can be tedious, error-prone, and time consuming. In this paper, we present a new, game-theoretic approach to analyzing quantitative properties that is based on performing systematic measurements to automatically learn a model of the environment. We model the estimation problem as a game between our algorithm (player) and the environment of the program (adversary) where the player seeks to accurately predict program properties while the adversary sets environment parameters to thwart the player. We present both theoretical and experimental evidence for the utility of our game-theoretic approach. On the theoretical side, we show that we can predict the program property for all execution paths with probability greater than 1 - delta by only making a number of measurements that is polynomial in ln(1/delta) and the program size. Experimental results for execution time analysis demonstrate that our approach is efficient, effective, and highly portable.
Bystanders in bullying: Introduction to the special issue

Bullying is a problem in most, if not all, contemporary schools around the world and is associated with socioemotional, academic, and physical difficulties for not only the victims of bullying, but also the youth who engage in bullying (Beran et al., 2008; Hawker & Boulton, 2000) and bystanders (Janosz et al., 2008; Juvonen et al., 2003). As the actions of bystanders contribute to the deterrence or maintenance of bullying (Salmivalli, 2010), it is critical to understand those factors that lead bystanders' to either protect the victim or facilitate the bullying. To this end, the articles in this special issue provide novel insights into bystanders of bullying, building upon emerging themes in the literature. This introduction summarizes the contributions of each article, focusing on three themes: (a) the process-oriented nature of the decision to defend victims or reinforce the aggressors, (b) the need to differentiate qualitatively different forms of defending, and (c) the role of classroom and societal norms in bystanders' behaviors. This introduction concludes with a call for a next generation of studies that integrates the lines of research presented in this special issue.
Adapting a Federal Disaster Medical Assistance Team to Operate during a Pandemic.

After Hurricane Laura struck the southeast coast of Louisiana in August 2020, the National Disaster Medical System (NDMS), a component of the U.S. Department of Health and Human Services (HHS) Office of the Assistant Secretary for Preparedness and Response (ASPR), deployed several 35-person Disaster Medical Assistance Teams (DMATs) in response to requests for medical support at three hospital locations that had been severely damaged in the storm. This was the first natural disaster medical deployment for NDMS during the COVID-19 pandemic. This article describes the modifications to the standard operating procedures that were made at one site to reduce the risk of infection to our patients and NDMS responders, including changes to the physical layout of the tenting, and alterations to the triage and treatment process.
Pseudocapillaria tomentosa, Mycoplasma spp., and intestinal lesions in experimentally infected zebrafish Danio rerio

Abstract Intestinal neoplasms and preneoplastic lesions are common in zebrafish research facilities. Previous studies have demonstrated that the neoplasms are caused by a transmissible agent, and two candidate agents have been implicated: a Mycoplasma sp. related to M. penetrans and the intestinal parasitic nematode, Pseudocapillaria tomentosa, and both agents are common in zebrafish facilities. To elucidate the role of these two agents in the occurrence and severity of the neoplasm and other intestinal lesions, we conducted two experimental inoculation studies. Exposed fish were examined at various time points over an 8 mo. period for intestinal histpathologic changes and the burden of Mycoplasma and nematodes. Fish exposed to a Mycoplasma isolate from zebrafish were associated with preneoplastic lesions. Fish exposed to the nematode alone or with the Mycoplasma isolate developed severe lesions and neoplasms. Both inflammation and neoplasm scores were associated with an increase in Mycoplasma burden. These results support the conclusions that P. tomentosa is a strong promoter of intestinal neoplasms in zebrafish, and that Mycoplasma alone can also cause intestinal lesions and accelerate cancer development in the context of nematode infection.
Rapid High-Fidelity Spin-State Readout in Si / Si - Ge Quantum Dots via rf Reflectometry

Silicon spin qubits show great promise as a scalable qubit platform for fault-tolerant quantum computing. However, fast high-fidelity readout of charge and spin states, which is required for quantum error correction, has remained elusive. Radio-frequency reflectometry enables rapid high-fidelity readout of $\mathrm{Ga}\mathrm{As}$ spin qubits, but the large capacitances between accumulation gates and the underlying two-dimensional electron gas in accumulation-mode $\mathrm{Si}$ quantum-dot devices, as well as the relatively low two-dimensional electron gas mobilities, have made radio-frequency reflectometry challenging in these platforms. In this work, we implement radio-frequency reflectometry in a $\mathrm{Si}$/$\mathrm{Si}\text{\ensuremath{-}}\mathrm{Ge}$ quantum-dot device with overlapping gates by making minor device-level changes that eliminate these challenges. We demonstrate charge-state readout with a fidelity above $99.9\mathrm{%}$ in an integration time of $300\phantom{\rule{0.2em}{0ex}}\mathrm{ns}$. We measure the singlet and triplet states of a double quantum dot via both conventional Pauli spin blockade and a charge latching mechanism, and we achieve maximum fidelities of $82.9$ and $99.0\mathrm{%}$ in $2.08$- and $1.6$-$\ensuremath{\mu}\mathrm{s}$ integration times, respectively. We also use radio-frequency reflectometry to perform single-shot readout of single-spin states via spin-selective tunneling in microsecond-scale integration times.
El relato disciplinar consagrado en torno a la sociología universitaria en dictadura y la “producción de ausencias”: estudiar sociología en Antofagasta, 1972-1984

This article presents the academic institutionalization of sociology at the former Universidad del Norte (Antofagasta, Chile, 1972-1984)- now Universidad Catolica del Norte, which until now has been absent from the discourse and historicization of Chilean sociology. In this case, the need to critically analyze the construction of the disciplinary narrative consecrated about sociology in Chile during the eighties is posed to make certain absences visible regarding the discipline’s institutionalization and restructuring. We warn that the difficulty in recording regional sociologies’ experiences is attributable to the civil-military dictatorship’s impact on the field’s domain and operations. The research articulates the focus of recent history and social studies of science.
Pandemic-Specific Factors Related to Generalized Anxiety Disorder during the Initial COVID-19 Protocols in the United States.

Little is known about the psychological stress and secondary impacts emerging among the general U.S. population as a result of the ongoing COVID-19 pandemic. The purpose for the current study is to...
Comparing the use of individual and composite terms to evaluate adverse drug event disproportionality: a focus on glucagon-like peptide-1 receptor agonists and diabetic retinopathy

Background: The SUSTAIN-6 trial showed significantly higher rates of retinopathy complications in the semaglutide group compared to placebo. Observational studies have not consistently corroborated...
A systematic review of neurocognitive dysfunction with overactive bladder medications

The aim of this study is to report cognitive dysfunction with commonly used antimuscarinic overactive bladder medications in patients suffering from overactive bladder disorder with and without baseline neurologic conditions. We conducted an Ovid MEDLINE, Embase, and PsycINFO search from January 1998 to December 2018 using PRISMA guidelines. Eighteen studies met the inclusion criteria, including 5 randomized controlled trials and 13 observational studies. Cognitive decline was reported with oxybutynin use (5 of 8 studies) and tolterodine use (4 of 7 studies) among patients with and without baseline cognitive impairment. Oxybutynin use was linked to functional, mental, and behavioral decline among patients with Alzheimer’s disease (2 studies). No cognitive decline was detected among patients with and without baseline cognitive impairment taking trospium (6 studies), darifenacin (3 studies), imidafenacin (2 studies), and fesoterodine (1 study). Solifenacin was not associated with cognitive decline (2 studies) but was linked to an increased risk of dementia among patients with diabetes (1 study). In this review, cognitive decline was reported with oxybutynin and tolterodine use and should be used with caution in adults over 65 years of age. Solifenacin, fesoterodine, and imidafenacin showed mixed results related to central nervous system effect. Trospium and darifenacin were not associated with cognitive decline among patients with and without baseline cognitive impairment.
Finite Element Analysis as an Iterative Design Tool for Students in an Introductory Biomechanics Course.

Insufficient engineering analysis is a common weakness of student capstone design projects. Efforts made earlier in a curriculum to introduce analysis techniques should improve student confidence in applying these important skills toward design. To address student shortcomings in design, we implemented a new design project assignment for second-year undergraduate biomedical engineering students. The project involves the iterative design of a fracture fixation plate and is part of a broader effort to integrate relevant hands-on projects throughout our curriculum. Students are tasked with (1) using computer-aided design (CAD) software to make design changes to a fixation plate, (2) creating and executing finite element models to assess performance after each change, (3) iterating through three design changes, and (4) performing mechanical testing of the final device to verify model results. Quantitative and qualitative methods were used to assess student knowledge, confidence, and achievement in design. Students exhibited design knowledge gains and cognizance of prior coursework knowledge integration into their designs. Further, students self-reported confidence gains in approaching design, working with hardware and software, and communicating results. Finally, student self-assessments exceeded instructor assessment of student design reports, indicating that students have significant room for growth as they progress through the curriculum. Beyond the gains observed in design knowledge, confidence, and achievement, the fracture fixation project described here builds student experience with CAD, finite element analysis, 3D printing, mechanical testing, and design communication. These skills contribute to the growing toolbox that students ultimately bring to capstone design.
High-Sensitivity C-Reactive Protein Modifies the Cardiovascular Risk of Lipoprotein(a): Multi-Ethnic Study of Atherosclerosis

Abstract Background Little is known about the relationship between lipoprotein (a) [Lp(a)] and high-sensitivity C-reactive protein (hsCRP) and their joint association with atherosclerotic cardiovascular disease (ASCVD). Objectives The purpose of this study was to assess whether Lp(a)-associated ASCVD risk is modified by hsCRP in the context of primary prevention. Methods The current study included 4,679 participants from the MESA (Multi-Ethnic Study of Atherosclerosis) Apolipoprotein ancillary data set. Cox proportional hazards models and Kaplan-Meier curves were used to assess the association among Lp(a), hsCRP, and time to cardiovascular disease (CVD) events. Results During a mean follow-up of 13.6 years, 684 CVD events occurred. A significant interaction was observed between Lp(a) and hsCRP (P = 0.04). With hsCRP 100 mg/dL. However, with hsCRP ≥2 mg/L, a significant CVD risk was observed with Lp(a) of 50-99.9 mg/dL (HR: 1.36; 95% CI: 1.02-1.81) and Lp(a) ≥100 mg/dL (HR: 2.09; 95% CI: 1.40-3.13). Isolated elevations of either Lp(a) or hsCRP were not associated with increased CVD risk. In contrast, the combination of elevated Lp(a) (≥50 mg/dL) and hsCRP (≥2 mg/L) was independently associated with significant CVD risk (HR: 1.62; 95% CI: 1.25-2.10) and all-cause mortality (HR: 1.39; 95% CI: 1.12-1.72). Conclusions Lp(a)-associated ASCVD risk is observed only with concomitant elevation of hsCRP. Individuals with concomitant presence of elevated Lp(a) and systemic inflammation have greater ASCVD risk and all-cause mortality, and thus may merit closer surveillance and more aggressive ASCVD risk management.
An Examination of Nationwide Trends in Accelerated Partial Breast Irradiation - The Replacement of Breast Brachytherapy with Intraoperative Radiotherapy and External Beam Radiation.

PURPOSE To examine recent modality utilization trends in accelerated partial breast irradiation (APBI) in the National Cancer Database (NCDB) based on the American Society for Radiation Oncology (ASTRO) guidelines. MATERIALS AND METHODS A total of 58,194 patients treated with APBI were identified. Patients were segregated by APBI modality (brachytherapy, external beam radiotherapy [EBRT], and intraoperative radiotherapy ([IORT]). These patients were then further classified by suitability to receive APBI based on ASTRO guidelines. Temporal trends in utilization were evaluated using linear regression. Logistic regression was applied to study factors contributing to APBI modality choice and treatment within the ASTRO suitability groups. RESULTS Patients treated with brachytherapy, EBRT, and IORT comprised 70.5%, 17.5%, and 12.0% of patients treated with APBI. From 2008 to 2017, total APBI cases remained relatively stable (-54.1 cases/year, p=0.161) while brachytherapy cases decreased by 258.7 cases/year (p<0.001). EBRT and IORT increased by 51.5 cases/year (p=0.019) and 153.1 cases/year (p<0.001), respectively. 40.0% of patients treated with APBI were classified as "suitable", which increased from 2010-2017 from 35.3% to 45.3% (slope= 1.51%/year, r2=0.61, p=0.022). In comparison, 36.0% (36.1% in 2010 to 33.1% in 2017) of patients were classified as "cautionary" (slope= -0.33%/year, r2=0.63, p=0.019) and 23.9% (28.6% in 2010 to 21.6% in 2017) of patients were classified as "unsuitable" (slope= -1.18%/year, r2=0.67, p=0.012). CONCLUSIONS While overall APBI utilization has remained stable since 2008, this has been accompanied by a decline in brachytherapy and a rise in IORT. The causes of these trends should be the topic of future research.