cssi/SciSciGPT-SciSciNet huggingface dataset:
CHAPTER 5 – Quaternary Structure of Proteins

The chapter begins by describing the principles that help predict the quaternary structure of an oligomeric protein. It also discusses the association of protein subunits, and helical or continuous protein polymers. Because protein-protein recognition results in a stereochemically constant interaction between protomers, two types of polymers of globular proteins are most often observed: rodlike and closed forms. The rodlike aggregates have helical symmetry. The quaternary structure of closed aggregates with relation to oligomeric enzymes is described in detail in the chapter. Closed form aggregates are also symmetrical, most often using forms of cyclic symmetry. The biological implications of quaternary structure are listed in the chapter along with the details of surface accessibility, or calculating the surface area lost from a protein molecule when the oligomer is formed. The chapter concludes with information on generating coordinates for other subunits. A dimeric protein composed of two identical subunits is nearly always found with two fold rotational symmetry. This symmetrical association optimizes the thermodynamic stabilization occurring between complementary surfaces of the protein subunits.
Video Scene Understanding Using Multi-scale Analysis

We propose a novel method for automatically discovering key motion patterns happening in a scene by observing the scene for an extended period. Our method does not rely on object detection and tracking, and uses low level features, the direction of pixel wise optical flow. We first divide the video into clips and estimate a sequence of flow-fields. Each moving pixel is quantized based on its location and motion direction. This is essentially a bag of words representation of clips. Once a bag of words representation is obtained, we proceed to the screening stage, using a measure called the ‘conditional entropy’. After obtaining useful words we apply Diffusion maps. Diffusion maps framework embeds the manifold points into a lower dimensional space while preserving the intrinsic local geometric structure. Finally, these useful words in lower dimensional space are clustered to discover key motion patterns. Diffusion map embedding involves diffusion time parameter which gives us ability to detect key motion patterns at different scales using multi-scale analysis. In addition, clips which are represented in terms of frequency of motion patterns can also be clustered to determine multiple dominant motion patterns which occur simultaneously, providing us further understanding of the scene. We have tested our approach on two challenging datasets and obtained interesting and promising results.
Analysis of EBSD Grain Size Measurements Using Microstructure Simulations and a Customizable Pattern Matching Library for Grain Perimeter Estimation

Grain size data from electron backscatter diffraction (EBSD) maps are often reported as the mean of the circle equivalent diameters of the measured grain areas. Circle equivalent diameters are not directly comparable to the lineal intercept measurements more historically common for grain size characterization in analog optical microscopy. While the value of mean lineal intercept is the same in 2D and 3D for a given probe direction, the mean 2D circle equivalent section diameter is not directly related to any 3D property. Estimation of mean lineal intercept from circle equivalent diameter is usually carried out by again assuming feature circularity, despite the obvious corners that are inherent to grains from the requirements of space filling. A direct conversion between section areas and lineal intercepts can be performed if the grain perimeters are known. In the present work, a novel pattern matching library approach is investigated for measurement of grain perimeters using simulated 2D EBSD maps. The results are compared to alternative approaches for perimeter measurement and assessed with respect to spatial resolution, grain size distribution parameters, and relevant ASTM and ISO measurement standards. The benefits and drawbacks of each approach are discussed. Empirical estimators for conversion between lineal intercept, circle equivalent diameter, and ASTM grain size number are presented.
Biogenic sulfide control by nitrate and (per)chlorate - A monitoring and modeling investigation

Biosouring is commonly encountered during secondary oil recovery when seawater or another high sulfate water source is utilized for flooding; as a result, effective souring control is of great interest to the oil industry. Here we describe a laboratory study to evaluate the relative effectiveness of souring interventions through the injection of nitrate, chlorate and perchlorate, collectively (per)chlorate, solutions and whether in-situ galvanic potential measurements can be used for convenient and quantitative tracking of sulfide dynamics. Nitrate has typically been the chemical of choice for souring treatments, while the efficacy of (per)chlorate as a new candidate inhibitor has only been explored recently. (Per)chlorate is known to inhibit oil reservoir souring via mechanisms such as toxicity, bio-competitive exclusion and sulfur redox cycling. Two sets of experiments under different matrix and inoculation conditions were conducted to evaluate treatment efficiency under variable baseline physical and biogeochemical conditions. Our data demonstrated the sensitivity of the galvanic potential signals to sulfide concentrations where the sulfide-galvanic potential correlation is similar to the theoretical predictions based on the Nernst equation, demonstrating the feasibility of using galvanic potential as a quick and economical method for quantifying in situ sulfide concentrations for tracking reservoir souring processes and subsequent intervention effectiveness. Our results show that all three chemicals were effective at suppressing sulfidogenesis. A reactive transport model for perchlorate treatment was developed to simulate the reaction processes and explore the interactions between the underlying competing mechanisms of this inhibitor. A baseline simulation captured the temporal patterns of the effluent chemical species. Subsequent simulations in which individual inhibition mechanisms were systematically removed elucidated the relative role that each inhibition mechanism played at the different phases of the experiment. The simulation results complement the experimental findings. Our study supports the potential advantages of souring control with (per)chlorate treatments, and the application of galvanic signal as an economic, in-situ monitoring approach for tracking souring dynamics and treatment efficacy.
Design, manufacturing, and opto-mechanical considerations for multimodal micro-endoscope featuring optical coherence microscopy, multiphoton microscopy, and visible navigation

Complex endoscopes which utilize optics with less than 1.5 mm diameter have an elevated risk of failure. Therefore, to ensure functionality and minimize risk proper design, optomechanical analysis and modelling must be performed while taking into consideration current manufacturing capabilities. Our endoscope is designed to perform Optical Coherence and Multiphoton Microscopy (OCM and MPM) which are powerful endoscopic imaging techniques used to characterize tissue. Separately each imaging technique has limitations when used by itself; however, this design combines these two modalities into a single optical system to work in synergy achieving both high sensitivity and specificity for diagnosis at the point of care. The optical design features two optical paths with different numerical apertures (NA) through a single lens system with a scanning optical fiber. The dual path is achieved using dichroic coatings embedded in a triplet that functions in a telescope like fashion. A high NA ~0.44 path is designed to perform OCM and MPM while a low NA ~.18 path is designed for the visible spectrum to allow navigation of the endoscope to areas of interest. We present the optical design of the endoscope, optomechanical considerations, manufacturability, stress and temperature effects. All these factors may be a source of problems in such small optics utilizing rare materials such as ZnS MS lenses. While very tight tolerances were the driving factor for the manufacturability of this system, temperature and stress must also be evaluated to obtain a better idea of the durability of the endoscope at the point of care. While it is challenging to evaluate the real performance of multimodality endoscopes, the models ensure that the system is designed for the expected imaging techniques, providing acceptable imaging across the entire field of view. Finally, we will give insight on what lessons were learned during the design, analysis, lens manufacturing, and assembling processes of the endoscope to provide a baseline of parameters to take into consideration when designing such complex small optical systems.
Boiling water reactor dynamics identification by the dynamic data system methodology

A simplified model describing the complicated boiling water reactor (BWR) kinetics is developed by combining two different approaches: the analytical and the experimental, the latter based on the dynamic data system methodology. This model is capable of adequately representing the BWR main dynamics, which can be, in turn, conveniently used to predict its kinetics. Although the system exhibits some highly nonlinear characteristics, it is approximated by a linear model. By using Peach Bottom-2 real operating data without perturbation, the dynamics of the BWR are experimentally identified, and the results are found to be in close agreement with those obtained by the General Electric Company.
Young Adult Outcome of Children with “Situational” Hyperactivity: A Prospective, Controlled Follow-Up Study

To examine the importance of symptom pervasiveness in ADHD, we conducted a prospective, 12-year follow-up study of boys (ages 6-12) considered hyperactive at school and home (Pervasive ADHD), boys considered hyperactive by teachers but not parents (School Only ADHD), boys considered hyperactive by parents but not teachers (Home Only ADHD), and nonhyperactive comparisons. Follow-up was completed on 82-94% participants. Clinicians interviewed participants and their parents, blind to childhood status. At follow-up, antisocial disorder was significantly more prevalent among Pervasive and School Only ADHD (29% for both) than Home Only ADHD (0%) and comparisons (8%). In a similar manner, severity of behavioral problems distinguished groups (Pervasive, School > Home, comparisons), as did educational attainment and academic performance (poorest for Pervasive and School). These findings stress the validity of teacher reports in the diagnosis of ADHD.
Theory of mind and social competence among school-age Latino children

The present study examined relations between Theory of Mind (ToM) understanding and social competence among school-age Latino children. Participants included 62 children ages 6–12 years. Picture vo...
Prototyping Mina Loy's Alphabet

An important branch of digital humanities involves prototyping the past. This entails approaching material forms of knowledge as sites within which epistemological and ontological problems may be e...
Effects of liquid smoke infusion on osmotic dehydration kinetics and microstructural characteristics of apple cubes

Abstract The influence of the addition of Refined Liquid Smoke (RLS) (1% w/w) to a sugar-based Osmotic Solution (OS) (42 °Brix) on the osmotic dehydration (OD) kinetics and microstructure of apple cubes was evaluated. Cubes of 10 mm were cut from peeled apples and subjected to OD at the incubation temperature of 50 °C and over a range of OD duration (5–240 min). Influence of addition of RLS was evaluated for selected OD kinetic variables: solid gain (SG), water loss (WL), dry matter (DM), soluble solid content (SSC), and moisture content. Results showed that addition of RLS significantly increased SG, DM, and SSC in apple cubes compared to pure sugar solution-based OD. As a result of RLS addition, the sugar concentration in apple cubes increased from 9.90 °Brix to 33.8 °Brix whereas it was 31.02 °Brix for the pure sugar solution-based OD. Further kinetic analysis showed that the effective diffusion coefficient for SG was same (4.40 × 10−10 m2/s) irrespective of the addition of RLS; however, the effective diffusion coefficients for WL were different (2.94 × 10−10 m2/s for pure sugar-based OD and 4.40 × 10−10 m2/s for RLS-added OD). Microstructural visualization of the dried apples revealed that the addition of the RLS might have prevented the collapse of cell wall up to the first hour of OD.
Unexpected Loss of Sensitivity to the nAChR Antagonist Activity of Mecamylamine and DHβE in Nicotine-Tolerant C57BL/6J Mice

There has always been interest in developing nAChR antagonists as smoking cessation aids, to add to nAChR agonists (e.g., nicotine replacement) already used for that indication. Previous studies have demonstrated that daily nicotine treatment confers tolerance to some of the effects of nicotine, as well as cross-tolerance to other nAChR agonists. The current study assessed the extent to which antagonism of nicotine varies as a function of daily nicotine treatment. The rate-decreasing and hypothermic effects of nicotine, as well as antagonism of those effects, were examined in C57BL/6J mice before, during treatment with, and after discontinuation of three daily injections of 1.78 mg/kg nicotine. The nonselective nAChR antagonist mecamylamine and the β2 nAChR antagonist DHβE were studied in combination with nicotine. The ED50 values of nicotine to produce rate-decreasing and hypothermic effects were, respectively, 0.44 and 0.82 mg/kg prior, 1.6 and 3.2 mg/kg during, and 0.74 and 1.1 mg/kg after discontinuation of daily nicotine treatment. Prior to daily nicotine treatment, mecamylamine decreased response rate and rectal temperature; however, during daily nicotine, mecamylamine (up to 5.6 mg/kg) only decreased rectal temperature. DHβE (up to 5.6 mg/kg) when studied prior to daily nicotine decreased rectal temperature, but that decrease was abolished during chronic nicotine treatment. Mecamylamine and DHβE antagonized the rate-decreasing and hypothermic effects of nicotine before and after daily nicotine; however, during daily nicotine, mecamylamine and DHβE antagonized only the hypothermic effects of nicotine. The differential antagonism of rate-decreasing and hypothermic effects implicates differential involvement of nAChR subtypes. The decreased capacity of mecamylamine and DHβE to antagonize nicotine during chronic nicotine treatment may indicate that their effectiveness as smoking cessations might vary as a function of nicotine tolerance and dependence.
INTEGRATING ENVIRONMENTAL HEALTH EQUITY CONSIDERATIONS IN RISK BASED DECISION MAKING: CHALLENGES AND OPPORUNITIES

Background The United States (US) presidential Executive Order No. 12898 mandates each Federal agency to make achieving Environmental Justice (EJ) part of its mission by identifying and addressing,...
A cross-linguistic comparison on the use of acoustic cues for ambiguity resolution

In producing structurally ambiguous sentences, speakers often rely on prosodic acoustic cues (duration, pitch, and intensity) to enhance communication. This study compared speakers of two typologically different languages in their use of these cues for ambiguity resolution. Ten English and 10 Korean speakers completed a production task in their native language. Stimulus sentences included a relative clause which could modify either the first or the second noun (e.g., the boss of the clerk who was dishonest). The participants produced each sentence twice, being directed each time to convey one or the other of the two possible meanings. English speakers used both prosodic boundary cues, by inserting pause between words, and word prominence, by producing greater pitch movement and intensity on the heads of prosodic phrases. Korean speakers, on the other hand, used pre-boundary word lengthening and pause to mark prosodic phrase boundaries but did not use pitch or intensity to manipulate word prominence. These results suggest that the prosodic typology of languages (e.g., head-prominence vs. edge-prominence) influences the interface between syntax and phonology.In producing structurally ambiguous sentences, speakers often rely on prosodic acoustic cues (duration, pitch, and intensity) to enhance communication. This study compared speakers of two typologically different languages in their use of these cues for ambiguity resolution. Ten English and 10 Korean speakers completed a production task in their native language. Stimulus sentences included a relative clause which could modify either the first or the second noun (e.g., the boss of the clerk who was dishonest). The participants produced each sentence twice, being directed each time to convey one or the other of the two possible meanings. English speakers used both prosodic boundary cues, by inserting pause between words, and word prominence, by producing greater pitch movement and intensity on the heads of prosodic phrases. Korean speakers, on the other hand, used pre-boundary word lengthening and pause to mark prosodic phrase boundaries but did not use pitch or intensity to manipulate word prominence. These...
The Role of Palliative Care in the Elderly Surgical ICU Patient

Management of geriatric trauma patients is a multidisciplinary effort. The purpose of this paper is to review recent literature and further elucidate the role of palliative care in the geriatric trauma patient population. Recognition of the resources provided by palliative care continues to increase. Adoption of early consultations may improve both patient and family experiences especially in end-of-life situations. Early identification of at risk patients allows for proper utilization of consultative resources. Palliative care has several defined roles in the elderly trauma population which include end-of-life decision-making, spiritual support, family support, and symptom management. Integration of palliative care into the multidisciplinary team caring for geriatric trauma patients should be undertaken.
Stormwater ponds in the southeastern U.S. coastal plain: hydrogeology, contaminant fate, and the need for a social-ecological framework.

In lowland coastal regions of the southeastern United States, stormwater ponds are being built as the “green infrastructure” best management practice of choice for addressing the hydrologic changes associated with rapid urban and suburban development. In addition to dampening storm flows, stormwater ponds may provide pollution control and other ecosystem services. However, ponds are not native to this landscape. This review summarizes what is known about the effectiveness of these engineered ponds, which take many shapes and forms, in the context of hydrology, contaminant fate, and management. Research needs are identified and include evaluating pond performance and redesign options more comprehensively and applying a social-ecological framework for the future of stormwater pond management.
Vulnerable Populations Exposed to Lead-Contaminated Drinking Water within Houston Ship Channel Communities

Recent events have drawn increased attention to potential lead exposures from contaminated drinking water. Further, homes with older infrastructure are at greatest risk due to the presence of the disinfectant chemical chloramine, which can leach lead from older pipes. There is a growing need to determine the extent of lead leaching especially within vulnerable communities and homes with children. This pilot study collected survey data and performed lead analysis on drinking water in the small community of Manchester in Houston, TX. Manchester is characterized by industrial sites, flooding, and a low socioeconomic population. Surveys and water analyses were completed on randomly selected homes (N = 13) and documented perceptions of participants on their drinking water regarding presence and concentration of lead. Lead was discovered in 30.8% of homes ranging from 0.6 to 2.4 (µg/L), all below the US Environmental Protection Agency action level of 15 ppb, but above the water standard goals. These findings further suggest that contaminated water is a broad issue requiring concerted efforts to ensure the health of US residents.
Rho-family G-proteins are required for the recovery of traumatized hair bundle mechanoreceptors in the sea anemone, Nematostella vectensis.

Immersing anemones in calcium-free seawater disorganizes hair bundle mechanoreceptors on tentacles of sea anemones while causing a loss of vibration sensitivity. Remarkably, anemone hair bundles recover after being returned to calcium-containing seawater. Reorganization of actin in stereocilia likely follows during the recovery of normal morphology of hair bundles after such immersion. Previous studies have reported that Rho G-proteins are located in the stereocilia of hair bundles in sea anemones where they participate in polymerizing actin in stereocilia upon activation of specific chemoreceptors. We here find that immersing anemones in calcium-free seawater significantly reduces the abundance of hair bundles. A partial recovery of abundance of hair bundles occurs within 3 h post-immersion, but a full recovery of abundance does not occur even 6 h after specimens are returned to calcium-containing seawater. Anemones recovering from immersion in calcium-free seawater feature hair bundles that are significantly wider at their tips than in controls. The hair bundles subsequently narrow at their tips, becoming comparable to those of untreated controls within 6 h. Stereocilia of hair bundles are significantly longer in experimental animals than in controls at 2 h of recovery before shortening to lengths comparable to untreated controls at 6 h. In the presence of Rho inhibitors, the recovery in abundance of hair bundles through 6 h is delayed or inhibited. Likewise, in the presence of Rho inhibitors, stereocilia fail to significantly elongate within 2 h of recovery. These data suggest that Rho G-proteins participate in the normal recovery of abundance and recovery of normal morphology of experimentally damaged hair bundle mechanoreceptors.
Epilepsy Surgery in Children Under Three Years of Age.

Investigators from the University Medical Centre Schleswig-Holstein, Epilepsy Centre Kork, University of Freiburg, University Children’s Hospital Heidelberg, Goethe University, and University Children’s Hospital Zurich investigated seizure occurrence and cognitive development following epilepsy surgery by retrospectively studying 48 children under the age of three.
Finite-horizon semi-Markov game for time-sensitive attack response and probabilistic risk assessment in nuclear power plants

Abstract Cybersecurity has drawn increasing attention in the nuclear industry. To improve the cyber-security posture, it is important to develop effective methods for cyber-attack response and cyber-security risk assessment. In this research, we develop a finite-horizon semi-Markov general-sum game between the defender (i.e., plant operator) and the attacker to obtain the time-sensitive attack response strategy and the real-time risk assessment in nuclear power plants. We propose methods for identifying system states of concern to reduce the state space and for determining state transition probabilities by integrating probabilistic risk assessment techniques. After a proper discretization of the developed continuous-time model, we use dynamic programming to derive the time-varying and state-dependent strategy of the defender based on the solution concept of the mixed-strategy Nash equilibrium. For risk assessment, three risk metrics are considered, and an exact analytical algorithm and a Monte Carlo simulation-based algorithm for obtaining the metrics are developed. Both players’ strategies and the risk metrics are illustrated using a digital feedwater control system used in pressurized water reactors. The results show that the proposed method can support plant operators in timely cyber-attack response and effective risk assessment, reduce the risk, and improve the resilience of nuclear power plants to malicious cyber-attacks.
Pervasive Small RNAs in Cardiometabolic Research: Great Potential Accompanied by Biological and Technical Barriers

Advances in small RNA sequencing have revealed the enormous diversity of small noncoding RNA (sRNA) classes in mammalian cells. At this point, most investigators in diabetes are aware of the success of microRNA (miRNA) research and appreciate the importance of posttranscriptional gene regulation in glycemic control. Nevertheless, miRNAs are just one of multiple classes of sRNAs and likely represent only a minor fraction of sRNA sequences in a given cell. Despite the widespread appreciation of sRNAs, very little research into non-miRNA sRNA function has been completed, likely due to some major barriers that present unique challenges for study. To emphasize the importance of sRNA research in cardiometabolic diseases, we highlight the success of miRNAs and competitive endogenous RNAs in cholesterol and glucose metabolism. Moreover, we argue that sequencing studies have demonstrated that miRNAs are just the tip of the iceberg for sRNAs. We are likely standing at the precipice of immense discovery for novel sRNA-mediated gene regulation in cardiometabolic diseases. To realize this potential, we must first address critical barriers with an open mind and refrain from viewing non-miRNA sRNA function through the lens of miRNAs, as they likely have their own set of distinct regulatory factors and functional mechanisms.
The effectiveness of cryotherapy in the management of sports injuries

Cryotherapy is widely applied and accepted as a beneficial treatment for soft-tissue injury and postoperative management. It is the one of the most effective interventions for pain management and swelling in acute sports injuries. However, the most efficient Cryotherapeutic agent remains unknown. This paper analyzes different methods of application of cryotherapy in sports injury rehabilitation based on recent scientific evidences. This information will assist health-care practitioners who are involved in sports injury and postoperative management.
Fathers' Experiences of Being Present at an Unplanned Out-of-Hospital Birth: A Qualitative Study.

Purpose The purpose of this study was to investigate fathers' experiences of being present at an unplanned birth outside a maternity facility. Materials and methods This was a qualitative interview study with 12 fathers from six of Norway's eleven counties. All had been present at an unplanned out-of-hospital birth in 2015-2020. Data were analyzed using systematic text condensation. Results The data analysis resulted in four themes. The first theme described the fathers' stress and worry and how they managed to keep a cool head and think rationally in a totally unprepared situation. The second theme described the fathers' need for help and the reassuring feeling provided by contact with health professionals. The third theme described how the birth increased the father's attachment to his partner and baby, while the fourth theme described fathers' feelings of exclusion and their reactions following the birth. Conclusion Fathers' perceived lack of expertise and their fear of complications led to stress, worry and anxiety, but support from health personnel provided reassurance and control. Many fathers experienced mastery, pride and joy after the birth, but when arriving at hospital, they felt rejected and wished that maternity care staff had approached them to talk about the experience.
Aerococcus-related infections and their significance: A 9-year retrospective study

Introduction: Aerococcus spp. is a Gram-positive, catalase- and oxidase-negative, microaerophilic, nonmotile bacteria species rarely associated with human infections such as arthritis, bacteremia, endocarditis, and meningitis. The bacteria are also often confused with streptococci species or treated as a contaminant. Patients and Methodology: We conducted a retrospective, observational cohort study on all patients with Aerococcus spp. isolates in blood samples from July 2010 to June 2019. All categorical data were presented as counts and proportions, whereas continuous data were presented as median and interquartile ranges. Results: A total of 20 Aerococcus spp. isolates were identified over the study period of 9 years. Of these, Aerococcus urinae was isolated in 10 (50%), Aerococcus viridans in 6 (30%), and Aerococcus spp. (not speciated) in 4 (20%). The median age was 74.3 years (12 males and 8 females). The two most frequent presentations were fever (15 of 20) and altered mentation (6 of 15). Most of the patients (11 of 15) had at least one predisposing comorbidity related to the urinary tract system (8 with recurrent urinary tract infection, 7 with urinary incontinence, 3 with an indwelling catheter, 2 with renal stones, and 1 each with benign prostatic hyperplasia and a recent cystoscopy). The median white blood cell count was 18,426 cells/mL, median hemoglobin 10.96 g/dL, median platelet count 191,000 cells/μL, median blood urea nitrogen 28.6 mg/dL, and median creatinine 1.54 mg/dL. The urinary tract was the most likely source of bacteremia (10 of 20) based on either imaging findings (5 cases), positive urine culture for Aerococcus spp. (4 cases), or instrumentation history (1 case). In the rest, the cause of bacteremia could not be found. Endocarditis was suspected in 9 out of 20 patients. Transthoracic echocardiography/transesophageal echocardiography (TEE) confirmed 3 cases (2 aortic valves, 1 mitral valve and pacemaker). Interestingly, one case had septic emboli causing a right frontal stroke with a normal TEE and normal Doppler study for deep venous thrombosis. Blood cultures were positive in 35% (7 of 20) with polymicrobial growth, 3 with coagulase-negative staphylococci, 2 with Enterococcus faecalis, and the other 2 each with Diphtheroids spp. and Proteus mirabilis. Of the 20 cases, 9 and 10 required intensive care unit level care and vasopressor support, respectively. Most of the patients were treated for 5–14 days except the 3 cases with infective endocarditis (IE). The median hospital stay duration was 6.55 days with 2 fatalities (2 out of 20 patients). Conclusion: Old age and underlying urologic conditions are the best-known risk factors for Aerococcus spp. infection. Recent advances in diagnostic technology have led to an increase in detection of Aerococcus spp.-related infections. The rare occurrence of Aerococcus spp. in human infections and resultant lack of randomized control trials have resulted in a significant degree of clinical uncertainty in the management of Aerococcus spp. IE.
Assessing and Maximizing Cultivated Diversity with Plate-Wash PCR and High Throughput Sequencing

Molecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed the great plate count anomaly by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Molecular methods indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments were not detected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete, albeit more complex, understanding of which organisms were present compared to what was eventually cultivated. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against a multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools.
Regulations Implementing the Food Safety Modernization Act

The FDA has been charged by the 2010 Food Safety Modernization Act (FSMA) with improving food safety in the United States. The four large regulations analyzed in this paper do not appear able to accomplish that mission. Part of the reason for this failure is that Congress has narrowly prescribed some of the reforms that must be in these regulations. In addition to those requirements, however, the FDA is proposing even more expansionist regulations. There are two problems with these regulations and the expansions proposed in the FSMA: either they do not address an actual food safety risk in the areas they cover, or, where there is a significant risk, analysis shows that they will not effectively reduce that risk. Either way, the costs of these rules exceed the benefits, in some cases by a great deal.
Opportunities and Challenges in Artificial Intelligence from a Business Perspective

The main insight of this article is that we should promote competing architectures for AI (both hardware and software) to ensure proper check and balance system. As AI develops, the competing architectures will ensure that no one node in the system becomes strong enough to impose its will on the entire system, much like in the US government. Most of the AI systems are designed to function like human brain and are centralized in nature. However, competing systems that are distributed networks relying on collective wisdom of different nodes rather than delegating the task of analysis and decision making to a central node are being developed by companies like Prowler. These systems, much like the US Congress (the Senate and the House of Representatives) are composed of individuals representing different constituencies, none very powerful individually, but as a body are powerful enough to counterbalance the presidency. The main threat of AI, as voiced by the likes of Elon Musk and Steven Hawkins is the possibility that a machine equipped with AI takes actions detrimental to human race and thwarts the decision making power of mankind. Even though this risk is very low at the moment, it is likely to increase as general purpose AI continues to reach new heights. Many have recognized the existence of the threat but have taken refuge in sentences like “nothing like this is possible in the near future.” However, I contend that we should encourage competing and drastically different hardware technologies and systems architecture today to ensure that as and when AI reaches its potential it continues to serve mankind and that there are adequate safeguards in place that can make takeover of the system by a runaway algorithm or a rogue person less likely.
Reduced Smooth Muscle Contractile Capacity Facilitates Maladaptive Arterial Remodeling.

Albeit seldom considered explicitly, the vasoactive state of a central artery can contribute significantly to the in vivo values of flow-induced wall shear stress and pressure-induced wall stress, which in turn are strong determinants of wall growth and remodeling. In this technical brief, we test the hypothesis that diminished vasoactive capacity compromises effective mechano-adaptations of central arteries. Toward this end, we use consistent methods to re-interpret previously published data on carotid artery remodeling in a common mouse model of induced hypertension and a separate model of connective tissue disease that results in Marfan syndrome. Animals have identical backgrounds and in both cases, the data are consistent with the hypothesis considered. In particular, individual carotid arteries with strong (normal) vasoactive capacity tend to maintain wall thickness and in vivo axial stress closer to homeostatic, thus resulting in passive circumferential wall stress and energy storage closer to normal values. We conclude, therefore, that effective vasoactivity helps to control the biomechanical state in which cells and matrix turnover, thus helping to delineate mechano-adaptive from maladaptive remodeling. Future analyses of experimental data and computational models of growth and remodeling should account for this strong coupling between smooth muscle contractile capacity and central arterial remodeling.
A Fully Integrated O-band Coherent Optical Receiver Operating up to 80 Gb/s

This paper presents an O-band QPSK coherent receiver, consisting of a dual-polarization silicon photonic receiver and a dual-channel electronic integrated circuit with receiver chain and Costas loop. Measurements are performed at 56 Gb/s and 80 Gb/s, and the receiver performance is characterized in terms of error vector magnitude (EVM) and estimated bit-error ratio (BER).
The Global Real Estate Crash: Evidence from an International Database

The past decade has been a period of globalization in the world’s investment markets. Access to international investment has broadened dramatically as barriers to cross-border investment have lifted. During the 1980’s many equity and debt markets around the world performed well, and none more so than those in emerging markets. Willingness by U.S. investors to diversify beyond their borders was based, in part, upon the availability of statistical information about the risk and return characteristics of these markets, as well as upon the increasing use of optimization models to manage portfolio risk and return.
Efficient Private Information Retrieval Over Unsynchronized Databases

Web search histories can reveal detailed and sensitive information about people. Private information retrieval (PIR) tackles this potential privacy violation by allowing users to retrieve the $w$ th record of a database without revealing $w$ to the server. However, most known PIR schemes are either very inefficient (and therefore unlikely to gain traction in a practical sense) or reliant on some restrictive assumptions. In this paper, we consider an efficient class of schemes called multi-server PIR. Multi-server PIR assumes that the client communicates with multiple, non-colluding servers, each possessing an identical copy of the database. Significant prior work has gone towards relaxing the anti-collusion assumption, but the literature does not address the assumption that servers store perfectly-synchronized databases. This seems implausible, especially if servers are not meant to collude. We propose the first multi-server PIR scheme to return the desired record even when servers' databases are not perfectly synchronized. Our scheme asymptotically has the same computational and communication complexity as state-of-the-art PIR schemes for synchronized databases; this comes at the expense of probabilistic success and two rounds of communication (most existing schemes require only one). Additionally, this approach efficiently processes multiple concurrent PIR queries.
Measurements of Temperature Induced Deformations in Composite Cylindrical Shells

Teas were conducted measuring the deformations of composite open cylindrical shells subjected to temperature changes. The cylindrical shells were made of 16 plies of Fiberite T300/934 unidirectional graphite-epoxy tape arranged as cither [02/902]2, or [902/02)2,. The measured deformations were compared to the results of a higher order shell theory. It is shown that terms representing extensional strain in the thickness direction must be considered for the analysis to represent the data accurately.
Interaction of PRP4 with Krüppel-Like Factor 13 Regulates CCL5 Transcription

Activation of resting T lymphocytes initiates differentiation into mature effector cells over 3–7 days. The chemokine CCL5 (RANTES) and its major transcriptional regulator, Kruppel-like factor 13 (KLF13), are expressed late (3–5 days) after activation in T lymphocytes. Using yeast two-hybrid screening of a human thymus cDNA library, PRP4, a serine/threonine protein kinase, was identified as a KLF13-binding protein. Specific interaction of KLF13 and PRP4 was confirmed by reciprocal coimmunoprecipitation. PRP4 is expressed in PHA-stimulated human T lymphocytes from days 1 and 7 with a peak at day 3. Using an in vitro kinase assay, it was found that PRP4 phosphorylates KLF13. Furthermore, although phosphorylation of KLF13 by PRP4 results in lower binding affinity to the A/B site of the CCL5 promoter, coexpression of PRP4 and KLF13 increases nuclear localization of KLF13 and CCL5 transcription. Finally, knock-down of PRP4 by small interfering RNA markedly decreases CCL5 expression in T lymphocytes. Thus, PRP4-mediated phosphorylation of KLF13 plays a role in the regulation of CCL5 expression in T lymphocytes.
Émigré: Metalevel Architecture and Migratory Work

Migratory work extends traditional mobile work with an innate awareness of, and adaptability to, both technical and social surroundings. We are designing a technical framework, Emigre, that is based on the use of architectural meta-level representations to support rapid development and semi-automated run-time adaptation of migratory work applications.
Did you say susi or shushi? Measuring the emergence of robust fricative contrasts in English- and Japanese-acquiring children

While the English fricatives /s/ and /S/ can be welldifferentiated by the centroid frequency of the frication noise alone, the Japanese fricatives /s/ and /C/ cannot be. Measures of perceived spectral peak frequency and shape developed for stop bursts were adapted to describe sibilant fricative contrasts in Englishand Japanese-speaking adults and children. These measures captured both the cross-language differences and more subtle inter-individual differences related to languagespecific marking of gender. They could also be used in deriving a measure of robustness of contrast that captured cross-language differences in fricative development.
Seeing the light: The effects of particles, dissolved materials, and temperature on in situ measurements of DOM fluorescence in rivers and streams

Field-deployable sensors designed to continuously measure the fluorescence of colored dissolved organic matter (FDOM) in situ are of growing interest. However, the ability to make FDOM measurements that are comparable across sites and over time requires a clear understanding of how instrument characteristics and environmental conditions affect the measurements. In particular, the effects of water temperature and light attenuation by both colored dissolved material and suspended particles may be significant in settings such as rivers and streams. Using natural standard reference materials, we characterized the performance of four commerciallyavailable FDOM sensors under controlled laboratory conditions over ranges of temperature, dissolved organic matter (DOM) concentrations, and turbidity that spanned typical environmental ranges. We also examined field data from several major rivers to assess how often attenuation artifacts or temperature effects might be important. We found that raw (uncorrected) FDOM values were strongly affected by the light attenuation that results from dissolved substances and suspended particles as well as by water temperature. Observed effects of light attenuation and temperature agreed well with theory. Our results show that correction of measured FDOM values to account for these effects is necessary and feasible over much of the range of temperature, DOM concentration, and turbidity commonly encountered in surface waters. In most cases, collecting high-quality FDOM measurements that are comparable through time and between sites will require concurrent measurements of temperature and turbidity, and periodic discrete sample collection for laboratory measurement of DOM.
Application of Reference Guidelines in Chat Reference Interactions

Abstract Virtual reference guidelines have existed in one form or another for a number of years. However, relatively few studies have been conducted to evaluate whether they have actually been implemented in the field. Perhaps the best-known guidelines are the Reference and User Services Association Guidelines for Behavioral Performance of Reference and Information Service Providers. This article details a field study of chat reference transactions recorded from a random sample of virtual reference services in academic libraries, public libraries, and regional library consortia in the United States. The authors examined the transactions and evaluated the reference interview for adherence to the guidelines. Initial findings indicate librarians often fail to incorporate the guidelines into chat reference interactions. It is the authors' hope that this study will result in a heightened awareness of the factors that can facilitate or impede positive reference transactions online.
Increased release of [3H]acetylcholine in vitro from the mouse hippocampus by a convulsant barbiturate.

Abstract The effects of the convulsant barbiturate, 5-(2-cyclohexylidene-ethyl)-5-ethyl barbituric acid (CHEB), on the spontaneous release of [3H]acetylcholine (ACh) from mouse hippocampal slices in an in vitro superfusion system have been evaluated. The pattern of the release of [3H]ACh by a single treatment with CHEB or an elevated potassium concentration was similar, with the peak release occurring in the same fraction. A maximally effective concentration of CHEB (500 μM) caused a 177% stimulation of spontaneous release of [3H]ACh, while 50 mM KCl increased the release by 2100% above the baseline. The stimulation of the spontaneous release of [3H]ACh by CHEB was concentration-dependent with an EC50 of 180 μM. The pattern of release of [3H]ACh induced by multiple treatment with CHEB and elevated potassium appeared to differ, suggesting that different pools of [3H]ACh in the cholinergic neurons might be affected by these treatments. The action of CHEB on the sponaneous release of [3H]ACh was unique among some other convulsant drugs that were studied. Another convulsant barbiturate, S(+)-1-methyl-5-phenyl-5-propyl barbituric acid [S(+)-MPPB], pentylenetetrazol and a convulsant benzodiazepine 1,3-dihydro-5-methyl-2H-1,4-benzodiazepine-2-one (Ro-5-3663) did not affect the spontaneous release of [3H]ACh. The relationship between the stimulation of release of ACh and the convulsant action of the barbiturates is discussed.
The relationship of severity of agoraphobia to associated psychopathology

Abstract The relationships of avoidance behavior and panic frequency with other measures of psychopathology in a large sample of agoraphobic outpatients are examined and implications for research and treatment discussed.
Lies, damned lies, and political campaigns

Abstract Despite a pervasive presence in politics, lying has not traditionally played a role in formal models of elections. In this paper we develop a model that allows candidates in the campaign stage to misrepresent their policy intentions if elected to office, and in which the willingness to lie varies across candidates. We find that candidates more willing to lie are favored, but that this advantage is limited by the electoral mechanism and to such an extent that more honest candidates win a significant fraction of elections. Most notably, the possibility that some candidates lie more than others affects the behavior of all candidates, changing the nature of political campaigns in an empirically consistent manner. This effect also implies that misleading conclusions will be drawn if homogeneous candidate honesty is assumed.
Picosecond CARS Spectral Imaging with Principal Component Analysis

We demonstrate the utility of picosecond spectral coherent anti-Stokes Raman scattering imaging with principal component analysis to rapidly map lipophilic components in cardiovascular tissues, facilitating the interrogation of atherosclerosis.