cssi/SciSciGPT-SciSciNet huggingface dataset:
Financing higher student performance standards: the case of New York State

Many states have made performance standards the centerpiece of educational reform. Unfortunately, school aid systems have not kept up. Most aid systems ensure minimum spending per pupil instead of minimum student performance; that is, they fail to recognize that the cost of achieving a performance standard varies across school districts. This paper derives an educational cost index and incorporates it into an aid formula designed to bring all districts up to a performance standard. A district’s performance can be moved toward a standard through a property tax rate increase, an efficiency increase, or increased state aid. In New York State, boosting efficiency to the current “bestpractice” level would not bring large city districts even up to a minimal performance standard. In fact, these districts cannot achieve such a standard without large increases in state aid and local tax rates, accompanied by reforms that improve the productivity of teachers and administrators. © 2000 Elsevier Science Ltd. All rights reserved.
Semi-analytical solution for flow in leaky unconfined aquifer–aquitard systems

This study presents a semi-analytical solution for the problem of leakage in an unconfined aquifer bounded below by an aquitard of finite or semi-infinite extent. The homogeneous anisotropic unconfined aquifer of infinite radial extent is pumped continuously at a constant rate from a well of infinitesimal radius. The aquitard is also homogeneous, anisotropic and of infinite radial extent. Flow in both the aquifer and the aquitard is allowed to occur both vertically and horizontally. Exact solutions to the governing equations given in this work are developed in the double Laplace-Hankel transform space for drawdown response in the unconfined aquifer and the underlying aquitard. The inverse transforms of the solutions are obtained numerically. The theoretical results show that leakage can cause significant departure, at both early and late times, from the solution with no leakage. The solution presented here can be used in least-squares routines for estimation of hydraulic parameters for two-layered unconfined aquifer-aquitard systems.
Fine structure of the rostral pars distalis of the adenohypophysis of the killifish, Fundulus heteroclitus, in fresh and salt water

A fine structural study has confirmed earlier light microscopic observations indicating that prolactin cells are the only endocrine cells present in the main body of the rostral pars distalis of the adenohypophysis of Fundulus heteroclitus, a killifish common in New England coastal waters. Some ACTH cells occurred in thin plaques applied to the neurohypophysial trunk in the posterior part of the region. In freshwater-adapted specimens the volume occupied by the prolactin cell mass was larger than in saltwater-adapted specimens and contained larger prolactin cells. A paucity of contact specializations between the parenchymal cells may facilitate their spatial rearrangement as the prolactin cell population varies with changes in ambient salinity. Many fine neurohypophysial processes penetrated deeply into the rostral pars distalis and contained Type B (aminergic) nerve fibers believed to modulate prolactin secretion. These fibers ended mainly on the basement membrane that separates the neurohypophysial processes from the parenchyma. Synaptic contacts on prolactin cells were not observed but no prolactin cell appeared to be more than five cell widths from such a nerve terminal. The results emphasize the usefulness of the rostral pars distalis of this easily obtained and maintained teleost for studies of prolactin cell function.
P-sim: a simulator for peer-to-peer networks

In the past few years, there has been intense interest in designing and studying peer-to-peer networks. Many initial measurement studies on current deployed peer-to-peer networks attempted to understand their performance. However, the large size and complex nature of these networks make it difficult to analyze their properties. Simulation of these peer-to-peer networks enables a methodical evaluation and analysis of their performance. However, to our knowledge, there is no tool for simulating different peer-to-peer network protocols for a comparative study. We present p-sim: a tool that can simulate peer-to-peer networks on top of representative Internet topologies, p-sim has several capabilities to provide an accurate model of real-world peer-to-peer networks, p-sim can scale to thousands of nodes and is extensible to simulate new peer-to-peer network protocols. In this paper, we discuss the capabilities of p-sim, its user-interface and two case-studies.
Objective Quantification of Arm Rigidity in MPTP-treated Primates

Rigidity is a cardinal symptom of Parkinson's disease and is frequently used as an outcome measure in clinical and non-human primate studies examining the effects of medication or surgical intervention. A limitation of current rigidity assessment methods is that they are inherently subjective. To better understand the physiological mechanisms of rigidity and how various therapeutic approaches work, a more objective and quantitative method is needed. In this study, an automated arm rigidity testing (ART) system was developed to objectively quantify rigidity while the primate's limb was moved between two user-specified angles. Recordings of normal force versus elbow-angle were categorized according to area and slope. These quantitative measures of rigidity were investigated in three rhesus macaque monkeys treated with 1-methyl 4-phenyl 1,2,3,6-tetrahydropyridine and compared with clinical assessment methods. The ART system incorporates electromyographical recordings that can detect and differentiate active from actual resistance. The ART system detected significant changes in rigidity measures following administration of apomorphine or deep brain stimulation of the globus pallidus internus. The most sensitive measures were total area, extension slope, and flexion slope. The ART system provides precise and reliable measures of rigidity that are objective and quantitative.
Helicobacter pylori is associated with lower androgen activity among men in NHANES III

Chen et al ,1 using a nationally representative sample of the US population from the National Health and Nutrition Examination Survey III (NHANES III), intriguingly suggest infection with Helicobacter (H) pylori may have positive health effects in addition to a causal role in gastric cancer. H pylori has a long history of coexistence with humans. Research on the human microbiome has also highlighted the symbiotic relation of gut microorganisms with their hosts. Animal biology suggests immune defence trades-off against reproductive success such that infections suppresses androgens.2 Correspondingly, changing the gut microbial environment in mice changes mice testosterone levels.3 The same mechanisms may also apply to humans, particularly at older ages when the immune system is less effective. H pylori could modulate androgen production and thereby affect health because androgens, and similarly endocrine disruptors, may play a role in chronic diseases. Two androgen biomarkers (serum testosterone and androstanediol glucuronide (3-α-diol-G) (AAG)) were assayed for a male subsample (12+ years) from NHANES III who …
A study of mesoscale gravity waves over the North Atlantic with satellite observations and a mesoscale model

Satellite microwave data are used to study gravity wave properties and variabilities over the northeastern United States and the North Atlantic in the December-January periods. The gravity waves in this region, found in many winters, can reach the stratopause with growing amplitude. The Advanced Microwave Sounding Unit-A (AMSU-A) observations show that the wave occurrences are correlated well with the intensity and location of the tropospheric baroclinic jet front systems. To further investigate the cause(s) and properties of the North Atlantic gravity waves, we focus on a series of wave events during 19-21 January 2003 and compare AMSU-A observations to simulations from a mesoscale model (MM5). The simulated gravity waves compare qualitatively well with the satellite observations in terms of wave structures, timing, and overall morphology. Excitation mechanisms of these large-amplitude waves in the troposphere are complex and subject to further investigations.
Photoemission Spectroscopy of Single Crystal HTSC Materials: A Fermi Liquid Electronic Structure

Photoemission spectra from HTSC materials ( primarily 123 -type ), cleaved and measured at 20K, reveal a rich DOS structure which compares favorably with a calculated band structure, except for a residual 0.5 eV shift which may reflect some correlation effects. Band dispersion is observed throughout the valence bands, with clear evidence for a 0.2 eV wide band dispersing through EF. The orbital character at EF is a mix of Cu-3d and O-2p. There is unambiguous evidence for a large BCS-like gap (2Δ≥ 4kTc).
A search algorithm and data structure for an efficient information system

This paper describes a system for information storage, retrieval, and updating, with special attention to the search algorithm and data structure demanded for maximum program efficieny. The program efficiency is especially warranted when a natural language or a symbolic language is involved in the searching process.The system is a basic framework for an efficient information system. It can be implemented for text processing and document retrieval; numerical data retrieval; and for handling of large files such as dictionaries, catalogs, and personnel records, as well as graphic informations. Currently, eight commands are implemented and operational in batch mode on a CDC 3600: STORE, RETRIEVE, ADD, DELETE, REPLACE, PRINT, COMPRESS and LIST. Further development will be on the use of teletype console, CRT terminal, and plotter under a time-sharing environment for producing immediate responses.The maximum program efficiency is obtained through a unique search algorithm and data structure. Instead of examining the recall ratio and the precision ratio at a higher level, this efficiency is measured in the most basic term of "average number of searches" required for looking up an item. In order to identify an item, at least one search is necessary even if it is found the first time. However, through the use of the hash-address of a key or keyword, in conjunction with an indirect-chaining list-structured table, and a large available space list, the average number of searches required for retrieving a certain item is 1.25 regardless of the size of the file in question. This is to be compared with 15.6 searches for the binary search technique in a 50,000-item file, and 5.8 searches for the letter-table method with no regard to file size.
LEARNING CONTEXT AND ITS EFFECTS ON SECOND LANGUAGE ACQUISITION: Introduction

Thirty years ago, Dell Hymes ( 1972 ) observed that knowing what goes on outside the school setting is necessary to understanding what goes on inside. He noted further that “the key to understanding language in context is to start not with language but with context … [and then to] systematically relate the two” (pp. xix–lvii). Recently, the importance of learning context has stirred debate within SLA circles, and two coexisting lines of research have contributed to the overall picture that researchers and pedagogues have on SLA. On the one hand, scholars such as Long ( 1997 ) contended that it is important to provide an understanding of the acquisition process in psycholinguistic terms relatively independent of external factors (e.g., sociolinguistic variables or the particular methodology employed in a classroom). Researchers such as Firth and Wagner ( 1997 ) contended that the best predictive models of SLA consider the interaction of social activity and psycholinguistic elements.
Combined Numerical and Experimental Investigation of a 15-cm Valveless Pulsejet

The pulsejet, due to its simplicity, may be an ideal micro propulsion system. In this paper, modern computational and experimental tools are used to investigate the operation of a 15-cm overall length valveless pulsejet. Gas dynamics, acoustics and chemical kinetics are studied to gain understanding of various physical phenomena affecting pulsejet operation, scalability, and efficiency. Pressure, temperature, thrust, and frequency are measured as a function of valveless inlet and exit lengths and different geometries. At this length scale, it is necessary to run the pulsejets on hydrogen fuel. Numerical simulations are performed utilizing CFX to model the 3-D compressible vicious flow in the pulsejet using the integrated Westbrook–Dryer single step combustion model. The turbulent flow and reaction rate are modeled with the k–ɛ model and the Eddy Dissipation Model (EDM), respectively. Simulation results provide physical insight into the pulsejet cycle; comparisons with experimental data are discussed.
LONG-TERM PATTERNS IN TROPICAL REFORESTATION: PLANT COMMUNITY COMPOSITION AND ABOVEGROUND BIOMASS ACCUMULATION

Primary tropical forests are renowned for their high biodiversity and carbon storage, and considerable research has documented both species and carbon losses with deforestation and agricultural land uses. Economic drivers are now leading to the abandonment of agricultural lands, and the area in secondary forests is increasing. We know little about how long it takes for these ecosystems to achieve the structural and compositional characteristics of primary forests. In this study, we examine changes in plant species composition and aboveground biomass during eight decades of tropical secondary succession in Puerto Rico, and compare these patterns with primary forests. Using a well-replicated chronosequence approach, we sampled primary forests and secondary forests established 10, 20, 30, 60, and 80 years ago on abandoned pastures. Tree species composition in all secondary forests was different from that of primary forests and could be divided into early (10-, 20-, and 30-year) vs. late (60- and 80-year) successional phases. The highest rates of aboveground biomass accumulation occurred in the first 20 years, with rates of C sequestration peaking at 6.7 6 0.5 Mg Cha � 1 � yr � 1 . Reforestation of pastures resulted in an accumulation of 125 Mg C/ha in aboveground standing live biomass over 80 years. The 80 year-old secondary forests had greater biomass than the primary forests, due to the replacement of woody species by palms in the primary forests. Our results show that these new ecosystems have different species composition, but similar species richness, and significant potential for carbon sequestration, compared to remnant primary forests.
Project selection for technology investment

Aerojet is a leading manufacturer of propulsion systems for military and space applications. Like all technology companies, Aerojet faces the challenge of allocating limited research and development (R&D) funds among competing technology projects with uncertain rewards. This paper describes the design and implementation of improvements to an annual process for selecting a portfolio of R&D project investments. These improvements streamline the process by which company experts provide their opinions on qualitative aspects of candidate R&D projects. A questionnaire was designed which gathers expert opinion regarding a technology's potential impact, strategic fit, technical risk, completion deadline, and appeal. Responses are complied by a scoring algorithm. The output of the algorithm is a prioritized list of technologies for next year's investment of R&D funds. In order to allow Aerojet to potentially make use of this method, this project implemented a prototype decision support system (DSS) within Microsoft access.
Insiders versus Outsiders: Preferential Trade Agreements, Trade Distortions, and Militarized Conflict

A growing literature examines the link between preferential trade agreements (PTAs) and peace among member states. However, despite the potentially competitive nature of these agreements, there has been little research examining whether and how PTAs could induce hostilities between members and nonmembers. In this article, I argue that dyadic conflict is more likely when one dyad member’s exclusive PTA with a third party results in lower exports for the dyad member that is excluded from the agreement. Importantly, I contend that trade creating as well as trade diverting PTAs can have this effect. I use a triadic extension of the gravity model of trade to estimate how an exclusive PTA influences the exports of nonmembers relative to PTA members. Using these estimates in statistical tests of dyadic militarized interstate dispute onset spanning 1961 to 2000, I find that PTA-induced trade distortions are associated with a higher likelihood of conflict between members and nonmembers.
“I swear!” Physician oaths and their current relevance

Most graduating medical students will take some sort of oath that is to inspire them to take their proper place in the comradeship of physicians and remind them of their obligations to their patients, society, and their profession. The nature of these oaths has changed over the years as society itself has changed. What may be considered moral, ethical, or legal at one time can appear quaint or outrageous in another time and place. Several classic and newer oaths can be compared and contrasted in what they are tasking the newly minted physician to do.
KRAS in Pancreatic Cancer

Pancreatic cancer is one of the most feared malignancies. The most common form of pancreatic cancer is adenocarcinoma arising from the ductal epithelium. KRAS is the most common oncogene that has been found to be mutated. However, targeting KRAS directly has been difficult. We do not know a lot about the relationship between KRAS and other signaling pathways. At the same time, little is known about the non KRAS mutated or wild type (WT) tumors. Most of the data that we have as far, as mutational status is concerned, has been obtained from the tumor itself and not from metastatic lesions. In this review, we discuss two abstracts (Abstracts #e15214 and #e15207) published in conjunction with the 2014 ASCO Annual Meeting. These discuss the relationship between KRAS and other signaling pathways and the differences between mutated KRAS and WT tumors. The studies found low rate of KRAS mutation in cells obtained from ascitic fluid. While the studies are small, these are novel findings that are worth exploring further. They increase our understanding of the biology of the disease and take us a step closer to treating this deadly malignancy. Image: KRAS mutation and concordance rates with primary tumor.
Welfare reducing trade and optimal trade policy

Abstract This paper shows that free trade reduces the welfare of a small country with unemployment unless the free trade price of the importable falls below the autarky equivalent price. A decline in the price of the importable from the autarky level not only improves the terms of trade but also reduces employment and production in the importable sector. A numerical example illustrates that the autarky equivalent price of the importable can be substantially lower than the autarky price. If an optimal tariff is used, however, restricted trade improves welfare above the autarky level.
Parties and Democratic Quality in Central and Eastern Europe: Identifying Causal Mechanisms between Non-Programmatic Parties and Participation

This paper assesses the relationship between non-programmatic parties (NPP) and participation following the - effect-of-the-causes - approach. Using the method of process-tracing it identifies the causal mechanisms linking non-programmatic parties and one of the dimensions of democratic quality - participation - in the Czech Republic, Poland and Ukraine. It shows that the effect of NPP discourse on participation is contingent on the type of non-programmatic party and saliency of the election. In the Polish case where NPPs manifested as populist parties, their confrontational rhetoric and policies contributed to higher voter mobilization. On the other hand, in the Czech and Ukrainian cases, different manifestation of NPP did not have a significant effect on participation.
Two and Three Versus One-Dimensional Problems

The one-dimensional Schrodinger equation for a particle in a potential V1 (x) is $$ \left\{ { - \frac{{\hbar ^2 }} {{2m}}\frac{{d^2 }} {{dx^2 }} + V_1 (x)} \right\}\psi _n (x) = E_n \psi _n (x), $$ (8.1) where $$ \int\limits_{ - \infty }^{ + \infty } {\left| {\psi _n (x)} \right|^2 dx = 1.} $$ .
Rectal suction biopsy to exclude the diagnosis of Hirschsprung disease.

ABSTRACTObjectives:Hirschsprung disease (HD) is defined as the absence of ganglion cells in the Meissner and Auerbach plexuses. Diagnosis depends on demonstrating the absence of ganglion cells in rectal biopsy specimens. Rectal suction biopsy is widely employed as the method of choice in obtaining s
Optimization Model and Algorithm for Solving Lot-Sizing Disassembly with Multi-resource Constraint

For the discarded products disassembly of environmentally conscious manufacturing research field,a method to optimize lot-sizing disassembly with multi-resource constraints was proposed.A mathematical model was established to minimize the time of disassembly,and the software of CPLEX was used to solve this model.Simulation results of several randomly generated problem instances validated the effectiveness of the proposed model,which indicated that the optimal disassembly quantity,the purchase quantity,and whether a component needs.to be disassembled could be solved.What's more,the external demand of each component could be satisfied at the same time.It could be concluded that there exists influence on the difficulty of solving the lot-sizing disassembly problem from the in-degree and out-degree of nodes and the percentage of common components.
Community involvement in health (CIH) as a conceptual base for gerontological health-care research

Community involvement in health (CIH) is a conceptual base for effective primary health care that involves every level of a community. CIH empowers people by facilitating the sharing of information and control, and thereby giving individuals, families and groups that make up a community, the ability and encouragement to be active, effective participants in managing their health. Elderly people are an integral part of a community: it is functional to view their needs and capacities within the context of the larger group. This article is based on research that used the perspectives of self-care and CIH to assess and implement solutions to problems identified by elderly residents of a black township. CIH is a flexible process that can make major contributions to care delivery and the health of people by creating a partnership between the health-care professional and the community. The process develops over time as people increase their ability to manage factors that affect their health. This study indicates that considerable time, effort and resources are needed to help the people of a community to become effectively involved in the improvement of their health status.
Evaluation of a media-based mammography program.

Reports indicate that only 15%-20% of women 50 years of age and older have had a mammogram. To promote screening mammography, the San Diego County Unit of the American Cancer Society sponsored a community-wide program that featured (1) discounted mammograms through participating clinics, (2) program promotion through television news, and (3) availability of a phone bank for obtaining referrals for mammography. Pre- and postintervention random sample phone surveys indicated that women’s intentions to obtain a mammogram increased significantly after the media campaign, particularly in those aware of the program. Women’s intentions after the media campaign predicted mammography compliance in the following year. A total of 3,102 women received mammograms directly through the program, with a “suspicious finding” rate of 4%. Participant satisfaction with the program was high.
Ovarian carcinoid. A light and electron microscopic study.

Electron microscopic study of a solid ovarian tumor occurring in an elderly patient confirmed the light microscopic diagnosis of a carcinoid. Teratoid elements were not demonstrable within the lesion; neither has an extragenital primary focus been detected at the time of operation or within the period of 2½ years that has elapsed subsequent to operation. It is emphasized that ovarian carcinoid tumors occurring in the absence of demonstrable teratomatous elements should not be regarded as metastatic; unless a primary focus elsewhere is known to exist or to have existed. Unnecessary anxiety, investigation, or even exploration may thus be averted.
The Effect of Budget Framing and Budget-Setting Process on Managerial Reporting

ABSTRACT Participative budgeting allows superiors to elicit private information from subordinates, which, in turn, should enable superiors to make better decisions. Self-interested subordinates, however, may bias their budget reports for personal gain, thereby reducing the value of their budget reports to superiors. One potential way to affect subordinates' budget reports is through the framing of the budget request. Another factor that may affect subordinates' budget reports is which party sets the budget. In our study, we examine three different budget frames (honest, fair, and preferred) and whether the subordinate or the superior sets the budget. We find that the framing of the budget does not result in differences in overall slack. Moreover, we find that subordinates' reports have more slack when superiors set the budget than when subordinates set the budget. Furthermore, many budgets are rejected by subordinates when superiors set the budget and, as a result, superiors' welfare is actually greater w...
Retention in Continuous Care and Sustained Viral Suppression

Objectives:To examine the relationship between retention in continuous care and sustained viral suppression.Methods:The authors retrospectively followed 653 persons who were virally suppressed and seeking care at an infectious disease clinic in Kentucky for an average of 6 years to determine the rates of retention in medical care (≥2 visits separated by ≥3 months within a 12-month period) and sustained viral suppression (<400 copies/mL). A generalized linear mixed model was used to determine an association between retention and suppression over time.Results:Approximately 61% of the study population were retained in continuous care and 75% had sustained viral suppression for all patient-years. Persons retained in care were 3 times the odds of sustaining viral suppression over time (P < .001).Conclusion:Retention is essential to achieving and maintaining viral suppression. Strategies should be set in place that emphasize increasing the rates of retention, which in turn may increase the rates of suppression.
A new approach for economic dispatch with disjoint feasible zones: Model and solution

The disjoint feasible zones make the economic dispatch problem non-convex. The existed solving schemes either rely on random searching, or use additional auxiliary variables, or involve high nonlinearity. In this paper, a new method is presented to overcome the main drawbacks in existed schemes. Due to its simple structure, the proposed approach also has the advantage to expedite the implementation.
Integrating Atlas and Graph Cut Methods for Left Ventricle Segmentation from Cardiac Cine MRI

Magnetic Resonance Imaging (MRI) has evolved as a clinical standard-of-care imaging modality for cardiac morphology, function assessment, and guidance of cardiac interventions. All these applications rely on accurate extraction of the myocardial tissue and blood pool from the imaging data. Here we propose a framework for left ventricle (LV) segmentation from cardiac cine MRI. First, we segment the LV blood pool using iterative graph cuts, and subsequently use this information to segment the myocardium. We formulate the segmentation procedure as an energy minimization problem in a graph subject to the shape prior obtained by label propagation from an average atlas using affine registration. The proposed framework has been validated on 30 patient cardiac cine MRI datasets available through the STACOM LV segmentation challenge and yielded fast, robust, and accurate segmentation results.
ShadowDB: a replicated database on a synthesized consensus core

This paper describes ShadowDB, a replicated version of the BerkeleyDB database. ShadowDB is a primary-backup based replication protocol where failure handling, the critical part of the protocol, is taken care of by a synthesized consensus service that is correct by construction. The service has been proven correct semiautomatically by the Nuprl proof assistant. We describe the design and process to prove the consensus protocol correct and present the database replication protocol. The performance of ShadowDB is good in the normal case and recovering from a failure only takes seconds. Our approach offers simplified means to diversify the code in a way that preserves correctness.
Safety of trastuzumab in women with HER2+ breast cancer.

e12522Background: Trastuzumab is widely used in management of HER2+ breast cancer patients. A known adverse effect of trastuzumab use is cardiac dysfunction, which can often be reversed with cessation of therapy. Our objectives were to 1) assess if trastuzumab can be safely administered to breast cancer patients with reduced cardiac function and 2) identify patient characteristics that predict susceptibility to trastuzumab-induced cardiac dysfunction. Methods: A retrospective analysis was performed on female patients seen at Mayo Clinic for HER2+ breast cancer and treated with trastuzumab for localized or metastatic disease between January 1, 2000 and August 31, 2015. Eligibility criteria included documentation of and results from at least one echocardiogram prior to and at least one after trastuzumab initiation. Left ventricular (LV) ejection fraction (EF) of 53% or more was considered normal. Any LVEF reduction of 10% or more was considered significant. Among patients with normal EF, age strata of < 45,...
Automatic extraction of 1D barcodes from video scans for drone-assisted inventory management in warehousing applications

The widespread use of barcodes has significantly contributed to accurate, efficient and economic inventory management in warehouses and distribution centres. However, its efficiency has always been...
Dynamic graphs, community detection, and Riemannian geometry

A community is a subset of a wider network where the members of that subset are more strongly connected to each other than they are to the rest of the network. In this paper, we consider the problem of identifying and tracking communities in graphs that change over time – dynamic community detection – and present a framework based on Riemannian geometry to aid in this task. Our framework currently supports several important operations such as interpolating between and averaging over graph snapshots. We compare these Riemannian methods with entry-wise linear interpolation and find that the Riemannian methods are generally better suited to dynamic community detection. Next steps with the Riemannian framework include producing a Riemannian least-squares regression method for working with noisy data and developing support methods, such as spectral sparsification, to improve the scalability of our current methods.
Promoting Vibrations and the Function of Enzymes. Emerging Theoretical and Experimental Convergence

A complete understanding of enzyme catalysis requires knowledge of both transition state features and the detailed motions of atoms that cause reactant molecules to form and traverse the transition state. The seeming intractability of the problem arises from the femtosecond lifetime of chemical transition states, preventing most experimental access. Computational chemistry is admirably suited to short time scale analysis but can be misled by inappropriate starting points or by biased assumptions. Kinetic isotope effects provide an experimental approach to transition state structure and a method for obtaining transition state analogues but, alone, do not inform how that transition state is reached. Enzyme structures with transition state analogues provide computational starting points near the transition state geometry. These well-conditioned starting points, combined with the unbiased computational method of transition path sampling, provide realistic atomistic motions involved in transition state formati...
Pharmaceutical Machine Learning: Virtual High-Throughput Screens Identifying Promising and Economical Small Molecule Inhibitors of Complement Factor C1s.

When excessively activated, C1 is insufficiently regulated, which results in tissue damage. Such tissue damage causes the complement system to become further activated to remove the resulting tissue damage, and a vicious cycle of activation/tissue damage occurs. Current Food and Drug Administration approved treatments include supplemental recombinant C1 inhibitor, but these are extremely costly and a more economical solution is desired. In our work, we have utilized an existing data set of 136 compounds that have been previously tested for activity against C1. Using these compounds and the activity data, we have created models using principal component analysis, genetic algorithm, and support vector machine approaches to characterize activity. The models were then utilized to virtually screen the 72 million compound PubChem repository. This first round of virtual high-throughput screening identified many economical and promising inhibitor candidates, a subset of which was tested to validate their biological activity. These results were used to retrain the models and rescreen PubChem in a second round vHTS. Hit rates for the first round vHTS were 57%, while hit rates for the second round vHTS were 50%. Additional structure–property analysis was performed on the active and inactive compounds to identify interesting scaffolds for further investigation.
The variable region gene assembly mechanism

Publisher Summary The mechanism responsible for generating diversity of antigen receptors is the assembly of the variable (V) region of each antigen receptor chain by the somatic recombination of variable (V), joining (J), and diversity (D) gene segments. This chapter reviews the current understanding of the mechanism of V (D) J recombination. The somatic recombination or V (D) J recombination occurs during early stages of lymphocyte differentiation, and is associated with the program of lymphocyte development. Because the V, D, and J segments that encode each antigen receptor V region can have several members, a significant level of diversity can be generated from the combinatorial assembly of these segments. Additional diversity of the antigen receptor can also be generated during the somatic recombination event. The junction of the assembled V-region gene segments encodes the third complementarity determining region (CDR3) of the immunoglobulin (Ig) V region that contacts the antigen and an analogous antigen contact region of the T-cell receptor. Thus, features of the recombination machinery that modify the joining segment ends during assembly can significantly contribute to increasing the diversity of the antigen receptor repertoires.
Kepler and the Incorporeality of Light

It is my purpose in this paper to explore Johannes Kepler’s ideas about the nature of light. It is my premise that we can succeed in this venture only if we go to the trouble of viewing Kepler’s theory against the background of the ancient and medieval optical tradition, which formed its immediate historical context. One reason for past failures is that we have inspected Kepler from the perspective of Newton or the present, rather than that of Aristotle or Plotinus or Roger Bacon. We have been so impressed with Kepler’s optical successes, in devising a new theory of vision, solving the ancient problem of the camera obscura, and formulating a geometrical theory of the telescope, that we have expended little effort in discovering whence they came or what they meant in the context of the optical tradition. Yet surely it was by grappling with the past — attempting to come to terms with the ideas of his predecessors, to separate the gold from the dross in ancient and medieval optical theory, to introduce clarity and precision, and to adjust existing theory to the teachings of sense, intellect, and philosophical presupposition — that Kepler fashioned his own theory. In short, Kepler’s achievement can be fully appreciated only if viewed within a disciplinary tradition. This will not strike historians as a novel thesis; the novelty will come if we put it into practice.
Fate and consequence of nutrients at an abandoned feedlot, Glacial Ridge National Wildlife Refuge, Minnesota, USA

Old, abandoned feedlots may serve as a source of nutrients that can degrade groundwater and downstream water quality. We characterized the distribution and concentration of nutrients at the Crookston Cattle Company feedlot (northwest Minnesota, USA), 15 years after it ended operations in 1999. Groundwater nitrate concentration decreased from 55 mg/L (as nitrogen) in 2003 to less than 5 mg/L since 2007. Results from stable isotope analysis, with δ15N and δ18O in groundwater nitrate ranging up to +44 and +30‰, respectively, suggest denitrification as the cause, rather than either nitrate transport from the site or dilution. Phosphorus, with soil B-horizon concentrations as much as 112 and averaging 24 mg/kg, is sequestered by carbonate-rich glacial sediments and, serendipitously, an iron-rich sand deposit formed millennia ago by wave action along the shore of glacial Lake Agassiz. Map analysis indicates roughly 20,000 kg of P in excess of background concentration remains in soil at the 15 ha site. Evidence suggests that the former feedlot has not affected water quality significantly in an agricultural ditch that drains the feedlot and its vicinity. Rather than originating from the feedlot, small increases of total phosphorus observed in the downstream ditch likely result from release of phosphorus from nearby recently restored wetlands. More consequential than elevated nutrient concentrations to the future reclamation of this and similar sites is the persistence of robust non-native species. Our results suggest that before development, feedlot sites should be evaluated for their phosphorus sequestration and denitrification potential, thus mitigating the potential for later off-site transport of nutrients.
On Matrix Pythagorean Triples

AbstractWe present a parametrization for the Pythagorean matrices, i.e., integer-valued matrices A, B, and C such that A2+B2=C2 .
Polynomials and Finite Fields

This chapter shows how to construct all fields with a finite number of elements: they all have \(p^{n}\) elements where p can be any prime number and n can be any number \(\ge 1\). For the construction we begin with the information on polynomials with coefficients in a field found in Chap. 6 and adapt to polynomials the results on unique factorization, ideals and cosets, and quotient rings obtained for \(\mathbb {Z}\) in Chaps. 3- 5. The outcome is that if m(x) is an irreducible polynomial in F[x], F a field, then the ring of cosets modulo the principal ideal generated by m(x) is also a field. Every finite field can be described in that way. The method also yields the complex numbers, when the field F is the field of real numbers and \(m(x) = x^{2} +1\). So complex numbers are cosets. They aren’t “imaginary” at all.
The Lack of Standardization of Allopathic and Osteopathic Medical School Grading Systems and Transcripts.

Objective The purpose of this study is to assess the variability in grading systems used by US allopathic and osteopathic medical schools across all 4 years of medical school coursework. Design Transcripts were reviewed from all participating allopathic and osteopathic medical schools for all 4 years of coursework for grading system type, the presence or absence of a key or guide, the inclusion of grade distribution within class year, inclusion of a class rank, and summary statements or evaluation systems used by the institution within the Medical Student Performance Evaluation to evaluate overall performance. Setting Loyola University Medical Center. Maywood, IL. Participants Transcripts were reviewed for 144 out of existing 147 allopathic medical schools (97.9%) and 37 out of 39 existing osteopathic medical schools (94.8%). Results For allopathic schools, grading system distribution for preclinical years was—41.6% Pass/Fail, 40.3% Honors, 13.2% Letter; while grading system distribution for clinical years was—78.5% Honors, 15.9% Letter. Only 35.4% of allopathic medical schools used the same system for all 4 years, while the remaining schools used a different system for preclinical and clinical years. For osteopathic medical schools, grading system distribution for preclinical years was—45.9% Letter, 32.4% Honors, and 13.5% Pass/Fail; while grading system distribution for clinical years was—59.5% Honors and 29.7% Letter (Table 4). Overall, 56.7% of osteopathic programs used the same system for all 4 years, while the remaining schools used a different system for the preclinical years than the clinical years. Variability also existed within each of these broader grading system categories (Table 1, Table 3). Conclusions Our results highlight the variability in grading systems used by medical schools both among programs and between preclinical and clinical years. From the residency program perspective, the lack of consistent, objective comparisons between school transcripts makes comparing applicants from different institutions difficult.
Aging and mixing as pseudo-chemical-reactions between, and on, particles: Perspectives on particle interaction and multi-modal ages in hillslopes and streams

Abstract The particle-tracking method was recently extended to allow inter-particle mass transfer and arbitrarily complex reactions by allowing each particle to represent any number of distinct chemical compounds. This methodology allows the tracking (and broadening due to mixing) of the age probability density function (PDF) on each particle. Aquifer heterogeneity leads to channeling and multi-modal age PDFs in stream samples. This observation supports the concept of age classes but clearly shows the more complicated interplay of dispersion, mixing, and travel times on the age distributions.
A Genome-Wide Approach Identifies Variations in the Aspartate Metabolism Pathway That Are Associated with Asparaginase Sensitivity

Asparaginase is an important drug for acute lymphoblastic leukemia (ALL). The basis for interindividual differences in asparaginase sensitivity remains unclear. To comprehensively identify genetic variants important in asparaginase sensitivity, we employed a genome-wide association approach using the HapMap lymphoblastoid cell lines from 87 individuals of European ancestry (CEU) and diagnostic ALL blasts from 42 newly diagnosed, genomically-determined white patients. In vitro sensitivity was based on IC 50 values measured following 48 hour exposures to native E. coli asparaginase (0.003–100 IU/ml) in CEU cell lines and 96 hour exposures (0.003–10 IU/ml) in patient samples using the methylthiazol tetrazolium assay. For CEU cell lines, single nucleotide polymorphism (SNP) genotypes were downloaded from the International HapMap database (www.hapmap.org) and gene expression data (Affymetrix GeneChip Human Exon 1.0 ST Array) were downloaded from http://www.ncbi.nlm.nih.gov/geo/query/acc. cgi?acc=GSE7761. For patients with ALL, we used the 500K SNP arrays to interrogate germline DNA and Affymetrix U133A GeneChip Array to assess gene expression in ALL blasts. We tested whether 2,390,203 SNP genotypes were associated with asparaginase IC 50 using a linear mixed effect model in CEU cell lines, setting a p value threshold of p 50 at the p ADSL gene) contributed to asparaginase sensitivity (p = 6.9 × 10 −4 and 9.1 × 10 − 4 , respectively) through their effects on ADSL gene expression. The top ranked KEGG pathway overrepresented by the 94 top-ranked genes (329 SNPs) was that of aspartate metabolism, which may be directly linked to the mechanism of action of asparaginase. The two most highly ranked genes ( ADSL and DARS ) in this pathway encompassed 7 SNPs (rs8135371, rs17001863, rs3768998, rs2278683, rs11893318, rs2322725, and rs7587285), all with p 50 among the CEU cell lines could be accounted for by these 7 SNPs (p = 5.9 × 10 −7 ). To examine the overall contribution of the aspartate metabolism pathway to asparaginase IC 50 , we compared all SNPs (935 in cell lines, 717 in patients) representing the aspartate pathway with those SNPs representing other pathways, using a random forest model. We found that the SNP genotypes in the aspartate pathway explained significantly more variation in asparaginase IC 50 in cell lines (11.4%, p = 6.9 × 10 −4 ) and in ALL patient samples (11.2%, p = 0.02) than other pathways. The expression of ADSL differed among ALL subtypes, with more sensitive subtypes (hyperdiploid and TEL-AML1 ALL) having lower ADSL expression than more resistant subtypes (T-ALL) (p = 1.1 × 10 −5 and 2.9 × 10 −9 , respectively). Genome-wide interrogation of CEU cell lines and primary ALL blasts revealed that inherited and acquired genomic interindividual variation in a plausible candidate pathway contribute to asparaginase sensitivity.
Rapid surveillance of COVID-19 in the United States using a prospective space-time scan statistic: Detecting and evaluating emerging clusters

Abstract Coronavirus disease 2019 (COVID-19) was first identified in Wuhan, China in December 2019, and is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is a pandemic with an estimated death rate between 1% and 5%; and an estimated R 0 between 2.2 and 6.7 according to various sources. As of March 28th, 2020, there were over 649,000 confirmed cases and 30,249 total deaths, globally. In the United States, there were over 115,500 cases and 1891 deaths and this number is likely to increase rapidly. It is critical to detect clusters of COVID-19 to better allocate resources and improve decision-making as the outbreaks continue to grow. Using daily case data at the county level provided by Johns Hopkins University, we conducted a prospective spatial-temporal analysis with SaTScan. We detect statistically significant space-time clusters of COVID-19 at the county level in the U.S. between January 22nd-March 9th, 2020, and January 22nd-March 27th, 2020. The space-time prospective scan statistic detected “active” and emerging clusters that are present at the end of our study periods – notably, 18 more clusters were detected when adding the updated case data. These timely results can inform public health officials and decision makers about where to improve the allocation of resources, testing sites; also, where to implement stricter quarantines and travel bans. As more data becomes available, the statistic can be rerun to support timely surveillance of COVID-19, demonstrated here. Our research is the first geographic study that utilizes space-time statistics to monitor COVID-19 in the U.S.
Clinical and pathologic factors associated with survival in BRAFV600E colorectal cancers.

4047Background: BRAFV600E mutations occur in fewer than 10% of all patients (pts) with metastatic colorectal cancer (mCRC) and arise from sessile serrated adenomas. Despite efficacy with targeted t...
The Effects of Lavender Essential Oil on Wound Healing: A Review of the Current Evidence.

Background: The commercialization of essential oils has expanded their presence in the United States, and emerging studies demonstrate that they may have a place in Western medicine. One oil with a...