cssi/SciSciGPT-SciSciNet huggingface dataset:
In silico scaling and prioritization of chemical disposition and chemical toxicity of 15,145 organic chemicals

Abstract This report describes the development and beta-test of methods that prioritize and scale in silico predictions of chemical disposition {(CD) intestinal absorption, membrane permeability, distribution, sequestration, toxicokinetics} and chemical toxicity {(CT) genetic, carcinogenicity, developmental, teratology}. It reports > 4.5 million data records for 15,145 organic chemicals that are ingredients in 32 different purpose groups of foods, drugs, and cosmetics, and 3682 colorants assigned to 36 chemical classes. Prioritization and scaling were facilitated by using: reference databases with known activities; data pre-processing; and prioritization P-metrics and P-indices to accentuate prediction strength of evidence and discriminate negative, indeterminate, and positive predictions. CD is computed based upon molecular descriptor properties of 1860 reference pharmaceuticals. CT is based upon predicted toxicities of 11,810 reference bioavailable test chemicals predicted with 3 software programs, 130 QSAR or expert system models. Results reveal major differences in toxicological activities: flavors and fragrances had very low predicted CD/CT activities, conversely, many colorants had high predicted genetic and carcinogenic activities. Contrasting CD/CT activities of flavors and hair dyes are presented. Furthermore, colorant chemical classes had different toxicological profiles, and a few classes having safer profiles were identified. Prediction data are also evaluated for DNA-reactivity as specified in ICH M7, persistent organic chemicals, and an alternative testing scheme is suggested to incorporate this methodology.
Predictive ability of bedside nasal endoscopy to diagnose invasive fungal sinusitis in a pediatric population.

Abstract Introduction Invasive fungal sinusitis (IFS) is a rare but deadly clinical entity that occurs in immunocompromised patients. Diagnosis in children typically requires operative biopsies under general anesthesia, which has associated risks. Findings on bedside nasal endoscopy (BNE) can be used with history, exam, and imaging to determine the need for surgery, however, the accuracy of this tool has not been established among pediatric patients. Methods Patients who underwent BNE for evaluation of IFS from 2008 to 2016 at the Children's Hospital of Philadelphia were identified using Current Procedural Terminology (CPT) codes. Retrospective chart analysis was performed and included underlying diagnoses, presenting signs and symptoms, imaging findings, endoscopic findings and outcomes. Results Nineteen patients were identified who underwent evaluation for IFS using BNE during the period studied. Eight patients had exam findings that were concerning for IFS, including debris or crusting, darkened or pale mucosa, or copious, thick and/or purulent secretions. Immediate operative biopsies and debridement revealed IFS in six of eight patients. Eleven patients had exam findings deemed not concerning for IFS including mucosal edema, mucous without purulence, or normal findings. Six of eleven patients underwent operative biopsy despite negative endoscopy, and five were observed clinically. None of the 11 patients with negative bedside endoscopy developed IFS. Conclusions All patients with IFS had concerning exam findings on endoscopy and were treated with immediate biopsies and debridement. No patient with normal or non-concerning findings on BNE progressed to have invasive fungal sinusitis. While suspicion for IFS in immunocompromised children must remain high, BNE is feasible and useful in its assessment.
More unaffected first-degree relatives of essential tremor cases have mild cognitive deficits than age-matched controls.

Abstract Background In numerous case-control studies, essential tremor (ET) has been associated with cognitive impairment. ET is often familial. However, cognitive impairment has not been studied in family members of ET cases. Endophenotypes are measurable clinical characteristics that may be present in individuals with increased risk for disease; as such, they may be present before disease onset. We administered a global cognitive screen to first-degree relatives of ET cases (FD-ET) and age-matched controls (Co). Methods We administered the Montreal Cognitive Assessment (MoCA) to 156 FD-ET and 73 Co, none of whom were diagnosed with ET or reported tremor. MoCA Results FD-ET and Co were similar with respect to age (60.1 ± 8.3 vs. 60.9 ± 7.4 years) and numerous demographic factors. FD-ET and Co also had similar MoCA scores; however, 34 of 156 (21.8%) FD-ET had a MoCA score Conclusion More FD-ET had low MoCA scores when compared with Co. These data provide additional support for the scientific notions that (1) cognitive difficulties are a disease-associated feature of ET and (2) there may be a pre-tremor phase of illness in ET.
The Alternative Healthy Eating Index and Physical Function Impairment in Men

Physical function is increasingly recognized as integral to healthy aging, in particular as a core component of mobility and independent living in older adults. Thus, it is important to identify strategies for the prevention of physical function decline. Longitudinal cohort study. A total of 12,658 men from the Health Professionals Follow-Up Study were followed from 2008–2012. We examined the association between the Alternative Healthy Eating Index-2010 (AHEI), a measure of diet quality combining 11 dietary components (vegetables, fruits, nuts and legumes, red and processed meats, sugar-sweetened beverages and fruit juices, alcohol, whole grains, omega-3 fatty acids, polyunsaturated fatty acids, trans fatty acids, sodium), and impairment in physical function, as measured by the SF-36. Multivariable logistic regression models were used to estimate the odds ratios (OR) and 95% confidence intervals (CI) of impairment in physical function. In the multivariable-adjusted model, each 10-point increase in total AHEI score was associated with a 10% lower odds of impairment in physical function (OR=0.90, 95% CI: 0.86,0.95), and in the categorical analysis, men with AHEI scores in the top quintile had a 26% lower odds (OR=0.74, 95% CI:0.63,0.86) compared with men in the bottom quintile. For individual AHEI components, higher intake of vegetables (p-trend=0.01), nuts and legumes (p-trend<0.01), polyunsaturated fatty acids (p-trend<0.01) and lower intake of red and processed meats (p-trend=0.03) and sugar-sweetened beverages (p-trend=0.01) were significantly associated with lower odds of physical impairment. For specific foods, higher consumption of lettuce, broccoli, blueberries, peanuts, walnuts and other nuts were associated with lower odds of impairment. In this large cohort of older men, better overall diet quality was significantly associated with a lower odds of impairment in physical function. Given the value of physical function to healthy aging and quality of life, this may represent a particularly compelling public health rationale for older men to improve their diet.
Long-Term Donor-Site Morbidity After Free, Nonvascularized Toe Phalanx Transfer for Congenital Differences of the Hand.

Purpose Toe phalanx transplantation is a well-established technique for addressing bony deficiency in the reconstruction of hypoplastic digits in patients with congenital differences of the hand. Prior studies have commented on varying degrees of donor-site morbidity, although assessment of morbidity with validated outcome scores is lacking. This study seeks to evaluate donor-site morbidity after toe phalanx harvest using validated outcome measures. Methods We identified all children who underwent free, nonvascularized toe phalanx transfer to the hand at our institution from 2001 to 2011. We administered the Oxford Ankle Foot Questionnaire for Children (OXAFQ-C) and the Foot and Ankle Ability Measure (FAAM) to all patients, scaling results according to published scoring instructions. Results Thirty-six patients with 83 toe phalanx transfers were able to be contacted, with a mean follow-up of 5.3 years (range, 18 months–11.2 years). The results of the OXAFQ-C showed mean scores of 99.96% (Physical), 100% (School and Play), and 96.01% (Emotional). The FAAM mean scores were 99.08% (Sports) and 99.17% (Activities of Daily Living). There were no lower extremity complications during the study period. Conclusions In contrast to varying degrees of donor-site morbidity reported in the current literature, this study demonstrates that toe phalanx harvest causes almost no measurable lower extremity morbidity or dysfunction over the mid- to long-term. Type of study/level of evidence Therapeutic IV.
High Salt Activates CD11c+ Antigen-Presenting Cells via SGK (Serum Glucocorticoid Kinase) 1 to Promote Renal Inflammation and Salt-Sensitive Hypertension

Salt-sensing mechanisms in hypertension involving the kidney, vasculature, and central nervous system have been well studied; however, recent studies suggest that immune cells can sense sodium (Na+). Antigen-presenting cells (APCs) including dendritic cells critically modulate inflammation by activating T cells and producing cytokines. We recently found that Na+ enters dendritic cells through amiloride-sensitive channels including the α and γ subunits of the epithelial sodium channel (ENaC) and mediates nicotinamide adenine dinucleotide phosphate oxidase-dependent formation of immunogenic IsoLG (isolevuglandin)-protein adducts leading to inflammation and hypertension. Here, we describe a novel pathway in which the salt-sensing kinase SGK1 (serum/glucocorticoid kinase 1) in APCs mediates salt-induced expression and assembly of ENaC-α and ENaC-γ and promotes salt-sensitive hypertension by activation of the nicotinamide adenine dinucleotide phosphate oxidase and formation of IsoLG-protein adducts. Mice lacking SGK1 in CD11c+ cells were protected from renal inflammation, endothelial dysfunction, and developed blunted hypertension during the high salt feeding phase of the N-Nitro-L-arginine methyl ester hydrochloride/high salt model of salt-sensitive hypertension. CD11c+ APCs treated with high salt exhibited increased expression of ENaC-γ which coimmunoprecipitated with ENaC-α. This was associated with increased activation and expression of various nicotinamide adenine dinucleotide phosphate oxidase subunits. Genetic deletion or pharmacological inhibition of SGK1 in CD11c+ cells prevented the high salt-induced expression of ENaC and nicotinamide adenine dinucleotide phosphate oxidase. These studies indicate that expression of SGK1 in CD11c+ APCs contributes to the pathogenesis of salt-sensitive hypertension.
Lactating adenoma arising from a tubular adenoma in a pediatric patient

Abstract We are reporting a rare case of tubular adenoma of the breast in a pediatric patient progressing to a lactating adenoma during pregnancy. The patient first noticed the mass at 14 years of age, and the size did not change considerably until pregnancy. The patient became pregnant at 16 years of age, and the breast tumor size increased to 20 x 20 cm in size. Magnetic Resonance Imaging (MRI) revealed an enhancing right breast mass. Initial ultrasonography (US) showed a large, complex, mixed cystic and solid mass with microlobulated margins. A follow-up US a year later depicted significantly increased heterogenous mass size. Initial US-core needle biopsy revealed a single layer of epithelial cells with variable stoma and chronic inflammation. A lactating adenoma was declared on repeat US core needle biopsy. No calcifications were noted, but due to overwhelming size, the patient was carefully monitored through pregnancy and post-partum. After delivery, the mass gradually decreased in size over the course of a year to 6 x 5 cm.
Complete genome sequence of Vibrio natriegens phage Phriendly.

ABSTRACT Vibrio natriegens is a fast-growing marine bacterium of interest for biotechnology applications. Here, we describe the isolation and genome annotation of V. natriegens podophage Phriendly. Among the 72 predicted coding genes and 1 tRNA, Phriendly’s 50,218-bp genome has low sequence identity to known phages.
Machine Learning-based Primary User Emulation Attack Detection In Cognitive Radio Networks using Pattern Described Link-Signature (PDLS)

A machine learning (ML) framework is proposed for primary user emulation attack (PUEA) detection in Cognitive Radio Networks (CRN). The ML framework is based on various classification models that exploit features extracted using the proposed Pattern Described Link-Signature method (PDLS) to distinguish between legitimate and malicious users. PDLS defines Link-signature from the channel impulse response (CIR) of the wireless link in the multipath environment. Previous works define Link-signature as the amplitude (or power) value of CIR while PDLS, on the other hand, defines it as a pattern that describes the structure of 52 sub-CIR (i.e., CIR contains 52 sub-CIR) in Orthogonal Frequency Division Multiplexing (OFDM) based transceivers. The proposed scheme is tested by developing a Software-Defined Radio (SDR) testbed to capture real wireless channel measurements. The testbed is based on IEEE 802.11a/g/p standard transceiver which comprises OFDM physical layer. Experimental results show that the proposed approach can distinguish between legitimate and malicious users effectively.
Financial Strategy for a Deflationary Era

Today's deflationary environment makes financial considerations more challenging, and perhaps more counter-intuitive than ever: * Less debt is now "optimal" * Extend duration, while rates are low * Build liquidity to insure your equity * Issue equity, despite low share prices * Dividends versus buybacks
Skin and Soft Tissue Coverage—Looking Ahead

The future of soft-tissue coverage and reconstruction of the hand will evolve as a combination of technologic and biochemical advances, improved surgical methods, and physician imagination.
Differences in resting cerebellar and prefrontal cortical blood flow in spinal cord injury-related neuropathic pain: A brief report

Context: Little is understood about differences in resting neural activity among those with spinal cord injury (SCI)-related neuropathic pain. The purpose of this pilot study was to determine resti...
Improving the Speed and Quality of GAN by Adversarial Training

Generative adversarial networks (GAN) have shown remarkable results in image generation tasks. High fidelity class-conditional GAN methods often rely on stabilization techniques by constraining the global Lipschitz continuity. Such regularization leads to less expressive models and slower convergence speed; other techniques, such as the large batch training, require unconventional computing power and are not widely accessible. In this paper, we develop an efficient algorithm, namely FastGAN (Free AdverSarial Training), to improve the speed and quality of GAN training based on the adversarial training technique. We benchmark our method on CIFAR10, a subset of ImageNet, and the full ImageNet datasets. We choose strong baselines such as SNGAN and SAGAN; the results demonstrate that our training algorithm can achieve better generation quality (in terms of the Inception score and Frechet Inception distance) with less overall training time. Most notably, our training algorithm brings ImageNet training to the broader public by requiring 2-4 GPUs.
Abstract A21: TRIM29 promotes invasion and migration of bladder cancer cells by regulating myosin-intermediate filament network and focal adhesion

Development of invasive progression in human bladder cancer is a key determinant of patient outcomes. Therefore, understanding the drivers of bladder cancer invasive progression is critical to improving patient care. We have previously shown that TRIM29 (also known as ataxia-telangiectasia group D complementing gene, ATDC) is highly expressed in muscle-invasive bladder cancer and plays an important role in driving tumor formation and invasion in vitro and in vivo. TRIM29 is upregulated by TP63 in basal subtype tumors, but the mechanism by which TRIM29 promotes tumor invasion was unknown. To elucidate the mechanism by which TRIM29 drives bladder cancer invasion, we developed a 3-D bladder cancer spheroid invasion assay that allows observation of the invasive process of cancer spheroids in a real-time fashion and observation of protein expression using confocal microscopy. Using this system, we confirmed that TRIM29 is required for bladder cancer stromal invasion. To determine if TRIM29 is specifically required for cell migration, which is an important ability contributing to invasive behavior, scratch assays were performed and we found TRIM29 is required for migration. Cancer cell migration requires modulation of cell adhesion and actin/myosin activation. To examine the role of TRIM29 in cell adhesion and motility, gene knockout or knockdowns of TRIM29 were generated in human bladder cancer cell lines (UM-UC5, UC9, UC13, UC14). Interestingly, TRIM29 KO/KD downregulates the expression of keratin 14 (KRT14), a member of type I keratin family that constitutes intermediate filament (IF) network, as well as myosin IIA (MYH9), a non-muscle motor protein that is essential for cell adhesion and migration. Using immunofluorescent confocal microscopy, we found that TRIM29 also modulates formation of focal adhesion plaques in bladder cancer during cell migration. Taken together, these findings suggest a novel mechanism by which TRIM29 regulates bladder cancer cell motility and invasion. Citation Format: Yin Wang, Erica R. Gumkowski, Phillip L. Palmbos. TRIM29 promotes invasion and migration of bladder cancer cells by regulating myosin-intermediate filament network and focal adhesion [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2019 May 18-21; Denver, CO. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(15_Suppl):Abstract nr A21.
An apparatus for studying electrical breakdown in liquid helium at 0.4 K and testing electrode materials for the neutron electric dipole moment experiment at the Spallation Neutron Source.

We have constructed an apparatus to study DC electrical breakdown in liquid helium at temperatures as low as 0.4 K and at pressures between the saturated vapor pressure and ∼600 Torr. The apparatus can house a set of electrodes that are 12 cm in diameter with a gap of 1–2 cm between them, and a potential up to ±50 kV can be applied to each electrode. Initial results demonstrated that it is possible to apply fields exceeding 100 kV/cm in a 1 cm gap between two electropolished stainless steel electrodes 12 cm in diameter for a wide range of pressures at 0.4 K. We also measured the current between two electrodes. Our initial results, I 5 × 1018 Ω cm. This lower bound is 5 times larger than the bound previously measured. We report the design, construction, and operational experience of the apparatus, as well as initial results.
Agricultural Chemicals in Ground Water: Suggestions for The Environmental Protection Agency Strategy

Ground water, a hidden resource whose volume is over 50 times that of the nation's surface water, was once thought to remain forever pure. People had little reason not to believe that the soil would naturally purify water returning to an aquifer. It was not until the late 1970s when the Love Canal and Times Beach incidences redirected public opinion and touched off a nationwide concern for the protection of ground water.In August 1984, the Environmental Protection Agency (EPA) issued a Ground Water Protection Strategy to "provide a common reference for responsible institutions as they work toward the shared goal of preserving, for current and future generations, clean ground water for drinking and other uses, while protecting the public health of citizens who may be exposed to the effects of past contamination."1 More specifically, "EPA will increase efforts to protect ground water from pesticide and nitrate contamination."In response, the EPA's Office of Pesticide Protection reviewed existing information...
Traversing the vertical pedicle flap for the treatment of severely buried penis in children

Objective To assess the effect of traversing the vertical pedicle flap (TVPF) for the treatment of severely buried penis in children. METHODS Totally 43 children with severely buried penis underwentTVPF (n = 21)or modifiedShiraki surgery (control, n = 22) in our hospitalfrom February to December 2014. Wecompared the operation time, intra-operation blood loss, foreskin swelling time, and parents' satisfaction with penile appearance between the two groups. RESULTS No statistically significant differences were observed between the TVPFand control groups in the operation time (［45.0 ±6.8］ vs ［42.0 ±5.3］ min, P>0.05) or intra-operation blood loss(［5.0 ±1.2］ vs ［6.0 ±0.8］ ml, P>0.05). The average foreskin swelling time was markedly shorter in the TVPFgroup than in the control (［9.0 ±2.3］ vs ［15.0 ±4.8］ d, P<0.05)and the parents' satisfaction with penile appearancewas higher in the former than in the latter (95.23vs31.81 %, P<0.05). The elastic bandages were removedfor all the patientsat 3 days postoperatively, and 3 to 6-month follow-up revealed no penile retraction or relapse. CONCLUSIONS The method of traversing the vertical pedicle flap is a feasible surgical option for the treatment of severely buried penis in children, which can make a rational use of the foreskin,remove the tight ring, and achieve a satisfactory appearance of the penis.
Postoperative inpatient utilization of opioid and opioid-sparing analgesics in the United States hospitals, 2007-2017.

Purpose To evaluate recent trends in inpatient postoperative utilization of opioid and non-opioid analgesics in US hospitals. Methods Using Premier Research database (October 2007-September 2017), we identified adults who were hospitalized for inpatient surgical procedures (N = 6 068 133). For each month, we calculated proportion of patients admitted that month who were administered (1) opioids, (2) acetaminophen, (3) non-steroidal anti-inflammatory drugs (NSADs), and (4) gabapentinoids (gabapentin or pregabalin) during the postoperative period, defined as inpatient postoperative days 1-7, unless discharged earlier. For patients administered opioids, we estimated total and average daily postoperative opioid dose in morphine milligram equivalents (MMEs). Monthly measures were standardized to the distribution of surgeries and the length of postoperative stay within each surgery during the last year of available data. Results Overall, 90.8% of patients were administered opioids postoperatively; mean total postoperative dose was 304 MMEs (median 130). Both the frequency and the amount of opioids administered remained stable over 2007-2017. Postoperative use of acetaminophen increased from mean standardized monthly prevalence of 78% in 2007-2008 to 85% in 2017, while the use of NSAIDs remained stable at a standardized mean of 37%. The use of gabapentinoids increased from below 10% in 2007-2008 to the mean standardized monthly prevalence of 23% in 2017. Conclusion Despite growing awareness of risks associated with postoperative opioid use, we observed no change in postoperative utilization of opioids in US hospitals. Increasing the use of non-opioid pain management approaches could constitute an important target in our efforts to curtail US opioid epidemic.
Scrambling for Contact: The Determinants of Inter-INGO Cooperation in Non-Western Countries

Even before the devastating hurricane and earthquake of 2010, Haiti had been dubbed the “republic of NGOs” (Kristoff and Panarelli 2010). Non-governmental organizations, most of them international (hereafter INGOs), were carrying out the majority of social service provision within the state, providing everything from vaccinations and basic health care to education and sanitation.1 While no formal recording procedures existed, estimates of the numbers of INGOs within Haiti were in the tens of thousands. After the hurricane, as could be expected, there was tremendous chaos in the ballooning INGO community. With little oversight and millions of donor aid dollars, many INGOs were accused of less than ideal practices, including allegations of fraud and money laundering; INGOs were lambasted as being “predators, not humanitarians” (Lendman 2010). In the few years since the devastation, Haiti remains in serious trouble: poverty in several areas has increased since 2010, there has been a cholera epidemic, and homelessness is widespread. This unfortunate situation seems to fit well in many regards with Cooley and Ron (2002)’s idea of the “NGO scramble.” Issues with the “market based structures” of aid to INGOs create “self-interested action, inter-INGO competition, and poor project implementation” (14). Cooley and Ron (2002) contend that these issues lessen the overall effect of the “normative agendas, moral character, or nominal goals” that are supposed to separate non-profit organizations from their for-profit counterparts (6).
An ESR Study of the Oxidation and Reduction of Bisulfite (Hydrated Sulfur Dioxide) in Biological Systems

Sulfur dioxide is recognized as a major air pollutant, particularly near large cities (Rall, 1974), while the ionized forms, bisulfite and sulfite, are found as preservatives in food and wine. In the lung, sulfur dioxide is hydrated rapidly according to the following equation, $$ {H_2}O + S{O_2} \rightleftharpoons HSO_3^ - + {H^ + }$$ with the equilibrium constant 1.07 × 102 mole/liter. The bisulfite anion is a weak acid which dissociates according to the reaction, $$HSO_3^ - + {H_2}O \rightleftharpoons {H_3}{O^ + } + SO_3^{ - 2}$$ with an equilibrium constant of 1.07 × 107 mole/liter. At pH values above 7 the equilibrium lies to the right and sulfite predominates, although there is always an equilibrium between sulfite and bisulfite. In this paper the terminology (bi)sulfite will be used when it cannot be determined which species is involved in a given reaction.
Bilevel Network Interdiction Models: Formulations and Solutions

The bilevel network-interdiction problem (BNI) models the effective use of limited resources, by an “interdictor,” to attack a network that an “enemy” may use to the interdictor's disadvantage. BNI is a two-person, zero-sum, sequential-play (Stackelberg) game with two stages: in the first stage, the interdictor attacks components of his enemy's network, that is, nodes and or/arcs; and in the second stage the enemy observes the damage caused by the attack and operates the damaged network so as to optimize a measure of functionality such as throughput, output or cost. For example, using a limited number of aerial sorties to attack and destroy production and distribution assets, an interdictor may wish to minimize the maximum “flow” of munitions that his enemy can produce and move to a battlefront. This article models interdictions with binary variables and simple constraints; solution of an optimization model, often a linear program, represents optimal network operation by the enemy. Simple models can be converted mixed-integer programs, but solution methods based on decomposition may be preferred for efficiency and generality. Keywords: interdict; multicommodity; system interdiction; network interdiction; minimax theorem
Use of a High‐Fidelity UAS Simulation for Design, Testing, Training, and Mission Planning for Operation in Complex Environments

Today, both military and civilian forces operate Unmanned Air Systems (UAS) in mountainous, desert, littoral, and urban areas. The environmental features of these natural and man-made environments (e.g., wind effects coupled with terrain features) can make low-level flight of small air vehicles extremely challenging. Modeling and simulation (M&S) tools can provide design engineers and analysts with a high-fidelity representation of UAS flight in these complex environments where wind gusts and thermally and/or geometrically influenced local vortices are naturally present. An open-architecture modeling toolset, with modular components representing this and other challenges in these types of terrains, such as communications, air vehicle aerodynamic characteristics, autopilots, sensors, and autonomy algorithms, can provide a capability to evaluate performance enhancing technologies (e.g., development of new airframes specifically designed for operations in these chaotic regimes), to conduct realistic operator training, and to perform more accurate mission planning. Keywords: unmanned air systems; mission planning; complex terrain; modeling and simulation tools; aerodynamic modeling
Computer-aided tutorials and tests for use in distance learning

Compared to the traditional on-campus students, remote students in distance education courses find it more difficult to develop problem-solving skills. In this paper, we propose the use of computer-aided tutorials and tests (CATTs) as convenient tools for remote students to practice and improve problem-solving and test taking skills at their own pace. Example of CATTs developed with Authorware software for use in distance education is presented.
Phylogenetic Profiles as a Unified Framework for Measuring Protein Structure, Function and Evolution

The sequence of amino acids in a protein is believed to determine its native state structure, which in turn is related to the functionality of the protein. In addition, information pertaining to evolutionary relationships is contained in homologous sequences. One powerful method for inferring these sequence attributes is through comparison of a query sequence with reference sequences that contain significant homology and whose structure, function, and/or evolutionary relationships are already known. In spite of decades of concerted work, there is no simple framework for deducing structure, function, and evolutionary (SF&E) relationships directly from sequence information alone, especially when the pair-wise identity is less than a threshold figure ~25% [1,2]. However, recent research has shown that sequence identity as low as 8% is sufficient to yield common structure/function relationships and sequence identities as large as 88% may yet result in distinct structure and function [3,4]. Starting with a basic premise that protein sequence encodes information about SF&E, one might ask how one could tease out these measures in an unbiased manner. Here we present a unified framework for inferring SF&E from sequence information using a knowledge-based approach which generates phylogenetic profiles in an unbiased manner. We illustrate the power of phylogenetic profiles generated using the Gestalt Domain Detection Algorithm Basic Local Alignment Tool (GDDA-BLAST) to derive structural domains, functional annotation, and evolutionary relationships for a host of ion-channels and human proteins of unknown function. These data are in excellent accord with published data and new experiments. Our results suggest that there is a wealth of previously unexplored information in protein sequence.
Small Fiber Neuropathy in Sarcoidosis: The Cleveland Clinic Experience (P7.093)

OBJECTIVE: Review the characteristics of patients at the Cleveland Clinic with sarcoidosis and small fiber neuropathy and compare treatment responses to to IVIG, antiTNF or both. BACKGROUND: Small fiber neuropathy, seen in up to 40% of sarcoidosis patients, is often refractory to immunosuppressive therapies. Anecdotal reports have shown benefit with IVIG or anti-tumor necrosis factor therapy (antiTNF), but larger studies are lacking. We review characteristics of 86 patients with sarcoidosis-associated small fiber neuropathy (SSFN) and their response to IVIG and/or antiTNF. DESIGN/METHODS: This was a retrospective review of 86 patients. Data collected included autonomic vs. somatic symptoms, distribution, therapy administered, and qualitative response. RESULTS: 87 SSFN patients (56 women, 31 men) were included in the study. Ages ranged from 23 to 82 years (mean 50). SSFN was diagnosed in 64 patients by intraepidermal nerve fiber density on skin biopsy, 18 by quantitative sudomotor axon reflex testing, and 5 clinically. 83 patients had somatic symptoms characterized by burning paresthesias and numbness that were length-dependent in 42 patients. Four patients had isolated dysautonomia manifested as either gastrointestinal dysfunction (n=2) or orthostasis (n=2). 57/87 patients received IVIG: 44 reported improvement, 8 had worsening of symptoms and 5 reported their symtpoms were unchanged. 14/87 patients received antiTNF: 7 reported improvement of symptoms, 4 had worsening of symptoms and 3 reported no change. 16/87 patients received IVIG and antiTNF concurrently: 11 reported an improvement of symptoms with both therapies, 2 had worsening of symptoms and 3 had no change. CONCLUSIONS: In our series, painful polyneuropathy was the most common presentation of SSFN and was non-length dependent in nearly half of the cases. IVIG appeared beneficial in treating somatic and autonomic symptoms. About 60% patients responded favorably to antiTNF with or without IVIG. Prospective studies are needed. Study Supported by: NA Disclosure: Dr. Ahmed has nothing to disclose. Dr. Tavee has nothing to disclose. Dr. Culver has nothing to disclose. Dr. Parambil has nothing to disclose.
Visual imagery for subsea teleprogramming

The objective of this work is to allow subsea teleoperative tasks to be performed efficiently even when all communication between human operator and remote robot is via an acoustic link. This paper describes the integration of remote site cameras into the teleprogramming system. Images from these cameras may be used for calibrating and maintaining the world model as well as for aiding the operator in diagnosing and recovering from unexpected events. The constrained communications channel forces the adoption of an intelligent approach to image transmission. The system automatically selects windowing and subsampling parameters while varying frame rates and task execution speeds to match that which the system can support given available bandwidth and computational constraints. Examples are presented from tests in which an operator in Philadelphia controlled a robot manipulator mounted on an underwater vehicle submerged off the Massachusetts coast.
Computer Vision and Computer Graphics Analysis of Paintings and Drawings: An Introduction to the Literature

In the past few years, a number of scholars trained in computer vision, pattern recognition, image processing, computer graphics, and art history have developed rigorous computer methods for addressing an increasing number of problems in the history of art. In some cases, these computer methods are more accurate than even highly trained connoisseurs, art historians and artists. Computer graphics models of artists' studios and subjects allow scholars to explore ``what if'' scenarios and determine artists' studio praxis. Rigorous computer ray-tracing software sheds light on claims that some artists employed optical tools. Computer methods will not replace tradition art historical methods of connoisseurship but enhance and extend them. As such, for these computer methods to be useful to the art community, they must continue to be refined through application to a variety of significant art historical problems.
Toward a Dyke Discourse

SUMMARY This essay argues the need for a dyke discourse that is a parallel project to queer theory but considers female subjectivity first and foremost and pays specific attention to desire and sexual practice as a mode of identity formation. The primary subject is the stonebutch -a queer masculine female, not a woman/not a man -and her partnered identity, the straight-appearing femme. Together, they fall out of the “woman-loving-woman” definition of lesbian, and problematize feminism's evacuation of female gender difference and assimiliationist strategies.
PEPTIDES AND OTHER NITROGEN SOURCES FOR GROWTH OF BACTEROIDES RUMINICOLA

Pittman, K. A. (Agricultural Research Service, Beltsville, Md.), and M. P. Bryant. Peptides and other nitrogen sources for growth of Bacteroides ruminicola. J. Bacteriol. 88:401–410. 1964.—Representative strains of Bacteroides ruminicola were found to utilize peptide nitrogen or ammonia nitrogen, but not to utilize significant amounts of free amino acid nitrogen or the nitrogen from a variety of other low molecular weight compounds for growth. All strains grew well in a defined medium containing glucose, minerals, B-vitamins, heme, volatile fatty acids, methionine, and cysteine, with ammonia as the main nitrogen source. Methionine and cysteine were required by some strains. The only compounds found to replace ammonia as the main nitrogen source were a few proteins; tryptic digests of protein; peptide-rich fractions of Sephadex G-25 fractionated tryptic digests of casein; and the octapeptides, oxytocin and vasopressin. Most of the nitrogen present in these compounds was utilized. However, the organism did not utilize nitrogen from any of 12 dipeptides, triglycylglycine, glutathione, or mixtures of free amino acids. Possible reasons for the inability of B. ruminicola to utilize low molecular weight nitrogen compounds are discussed.
Relation of Combined Non-High-Density Lipoprotein Cholesterol and Apolipoprotein B With Atherosclerosis in Adults With Type 1 Diabetes Mellitus.

Apolipoprotein B (apoB) and non–high-density lipoprotein cholesterol (non-HDL-C) are cardiovascular disease risk markers, although data in adults with type 1 diabetes mellitus (DM) are limited. We hypothesized that elevated apoB and non-HDL-C would be associated with greater odds of coronary artery calcification progression (CACp), a measure of coronary atherosclerosis, than either category alone in adults with type 1 DM. We grouped subjects with type 1 DM (n = 652) into 4 groups: elevated apoB (≥90 mg/dl) and elevated non-HDL-C (≥130 mg/dl), elevated non-HDL-C alone, elevated apoB alone, and normal apoB and non-HDL-C. We used logistic regression to examine the associations between the groups and CACp for a period of 6 years. We performed sensitivity analyses with elevated apoB and non-HDL-C redefined as at or more than the cohort means (91.4 and 119.0 mg/dl, respectively). Subjects with elevated apoB and non-HDL-C had greater odds of CACp compared with those with normal apoB and non-HDL-C (odds ratio 1.90, 95% confidence interval 1.15 to 3.15) and compared with subjects with elevated apoB alone (odds ratio 2.86, 95% confidence interval 1.43 to 5.74) adjusting for age, gender, duration, hemoglobin A1c, and statins. Similar results were obtained with elevated apoB and non-HDL-C defined as at or more than the cohort means. In conclusion, elevated apoB and non-HDL-C carry a greater risk of atherosclerosis than elevated apoB in the absence of elevated non-HDL-C in adults with type 1 DM. These data suggest that apoB and non-HDL-C should be viewed as complementary rather than competitive indexes of cardiovascular disease risk in type 1 DM.
SEMIPARAMETRIC METHODS IN ECONOMETRICS: by by Joel L. Horowitz, Springer, 1998

Semiparametric and nonparametric estimation have attracted a great deal of attention from statisticians and theoretical econometricians in the past decade. Various new models have been proposed, and new methods for estimating those models have been suggested. These new models and methods are scattered in various academic journals and are not easily accessible to other researchers. Moreover, the new methods are technical, not easily understood by nonexperts such as graduate students and applied econometricians. Horowitz has two goals in his book Semiparametric Methods in Econometrics. First, he wants to provide a central place for those who want to check out the semiparametric literature. Second, he wants to present technical materials in a nontechnical way so that graduate students and applied econometricians who often do not have expertise in this area can comprehend the new methods. In my view, Horowitz has achieved both goals.
The Promoter of the Yeast INO4 Regulatory Gene: a Model of the Simplest Yeast Promoter

In Saccharomyces cerevisiae, the phospholipid biosynthetic genes are transcriptionally regulated in response to inositol and choline. This regulation requires the transcriptional activator proteins Ino4p and Ino2p, which form a heterodimer that binds to the UAS(INO) element. We have previously shown that the promoters of the INO4 and INO2 genes are among the weakest promoters characterized in yeast. Because little is known about the promoters of weakly expressed yeast genes, we report here the analysis of the constitutive INO4 promoter. Promoter deletion constructs scanning 1,000 bp upstream of the INO4 gene identified a small region (-58 to -46) that is absolutely required for expression. S1 nuclease mapping shows that this region contains the transcription start sites for the INO4 gene. An additional element (-114 to -86) modestly enhances INO4 promoter activity (fivefold). Thus, the region required for INO4 transcription is limited to 68 bp. These studies also found that INO4 gene expression is not autoregulated by Ino2p and Ino4p, despite the presence of a putative UAS(INO) element in the INO4 promoter. We further report that the INO4 steady-state transcript levels and Ino4p levels are regulated twofold in response to inositol and choline, suggesting a posttranscriptional mechanism of regulation.
1 GHz NMR spectroscopy: innovation in magnet technology

The present period is one of rapid development and major extension of the technology for high resolution and solid state NMR spectrometer magnets. Programs which have already been initiated have as their objective proton frequencies of 1 GHz and greater, eventually requiring HTS superconductors. These magnets will contain inner coils containing HTS conductors, surrounded by a set of relatively large coils fabricated with metallic superconductors. These coils represent a major extension of the adiabatically stable magnet technology that has evolved to address the performance issues posed by this type of magnet. The developments which are desirable for these large magnets are identified to include tough epoxy, interface to and thermal performance of external reinforcement, and high strength-high current density metallic superconductor.
Extension of positive functionals on certain ordered spaces

An ordered linear spaceL is said to satisfy extension property (E1) if for every directed subspaceM ofL and positive linear functional ϕ onM, ϕ can be extended toL.
Allergen skin-test reactivity in a community population sample: correlation with age, histamine skin reactions, and total serum immunoglobulin E

Abstract Allergen skin reactivity to 14 common local antigens was studied in a community population sample. Differences in the prevalence of positive reactions were related to both the specific antigen itself and the age of the subjects. For most allergens, peak prevalence occurred in the 20- to 34-yr age group, falling thereafter with increasing age. The frequency distribution of reactions revealed a bimodal curve, peaks occurring among nonreactors and those with eight positive reactions out of the 14 tests that were applied. The major contributor to this age-skin test relationship was the level of total serum IgE that was highest in young people and decreased progressively with age. Histamine skin reactions, which were smallest in younger subjects compared with all three older age groups, also contributed to the age-related prevalence of allergen skin-test reactions.
Initial Experience with a Sutureless, Screw-in Electrode for Cardiac Pacing

Abstract This report is based on our initial experience with a new sutureless, corkscrew electrode for cardiac pacing. The electrode may be inserted quickly and securely under direct vision through a small anterior mediastinal or transxiphoid incision. This technique, which was employed in 26 patients between July, 1971, and December, 1972, was developed in an attempt to gain the advantages of both the pervenous and epicardial approaches, i.e., secure placement of the electrode in the myocardium with a minor, well-tolerated procedure that can be performed under local anesthesia. Results to date are very promising and indicate that the technique may very well become the method of choice in the future.
An electron microscope study of the uptake, transport, and storage of colloidal materials by the cells of the vertebrate nephron

Trypan blue and colloidal thorium dioxide were used to study the uptake, transport, and storage of colloidal particles by the tubular epithelium of frog and rat kidneys. Colloidal particles apparently enter the proximal tubular cells by passing between the microvilli of the brush border, first appearing within small, apical vesicles. The absorbed materials appear to be conveyed to the mid-region of the cells by larger, smooth-walled vesicles, and are segregated or stored within membrane-limited bodies or cytosomes. The cytosomes are limited by single membranes, have a characteristic internal structure and are considered to represent lysosomes. These observations suggest a mechanism by which native colloidal materials, such as proteins, could be taken up and stored by the tubular cells in vivo ; a similar mechanism may be responsible for the formation of so-called “hyaline droplets.” Evidence is also provided for the concept that lysosomes play an important role in the cellular storage of reabsorbed materials.
Complicating the Case for Teacher Education: Asking Different Questions

Abstract The purpose of this case study was to analyze the way the Professional Development School (PDS) model was institutionalized at a large research university in the mid-west. Data was gathered through interviews with key players (Professors, Administrators and Master teachers), document analysis and critical discourse analysis of the surrounding texts. Texts included research produced through the PDS, foundational literature such as Holmes Group documents and scholarly literature about PDS. This article presents the themes and foundational concepts that emerged from the data and suggests a number of interesting conclusions. Overall, it is clear that PDS is a very complicated reform model and that there is a tendency to valorize institutional efforts and results. Also, the origin of the reform model indicates a top-down implementation that involves an exclusivist gendered model of professionalization and suggests that only ‘good teachers’ were invited and that failure occurred but was not well docume...
Addressing data veracity in big data applications

Big data applications such as in smart electric grids, transportation, and remote environment monitoring involve geographically dispersed sensors that periodically send back information to central nodes. In many cases, data from sensors is not available at central nodes at a frequency that is required for real-time modeling and decision-making. This may be due to physical limitations of the transmission networks, or due to consumers limiting frequent transmission of data from sensors located at their premises for security and privacy concerns. Such scenarios lead to partial data problem and raise the issue of data veracity in big data applications. We describe a novel solution to the problem of making short term predictions (up to a few hours ahead) in absence of real-time data from sensors in Smart Grid. A key implication of our work is that by using real-time data from only a small subset of influential sensors, we are able to make predictions for all sensors. We thus reduce the communication complexity involved in transmitting sensory data in Smart Grids. We use real-world electricity consumption data from smart meters to empirically demonstrate the usefulness of our method. Our dataset consists of data collected at 15-min intervals from 170 smart meters in the USC Microgrid for 7 years, totaling 41,697,600 data points.
A constitutive equation for collagen fibers

Abstract A constitutive equation for collagen fibers is developed in the form of the ‘quasi-linear’ viscoelasticity law suggested by Y. C. Fung. This mathematical model is used to predict the experimental responses of tests of collagen fiber bundles extracted from the tails of mature rats. All experimental tests were conducted with the specimens immersed in a constant temperature saline bath. From relaxation tests, two material constants were obtained and used to predict the results of constant strain rate tests, hysteresis loops, and sinusoidal tests.