cssi/SciSciGPT-SciSciNet huggingface dataset:
Regional Economic Policy

The model of regional growth developed in the previous chapter can be used to investigate the long-run implications of various regional growth policies. A policy’s objectives and immediate impact might differ significantly from its long-term effects. It is not possible to evaluate an economic policy without fully understanding its long-term effects. This problem does not arise in models that are static or that lack interactions between demand and supply within a region and interregional interactions through input flows and trade flows. Once these elements are included, the long-run effects of a policy cannot be inferred from its short-run impact, for the magnitude and even the direction of the effect of the policy will be determined by complex inter-temporal and interregional as well as intraregional feedbacks.
A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions.

Background Identifying conserved regions in protein sequences is a fundamental operation, occurring in numerous sequence-driven analysis pipelines. It is used as a way to decode domain-rich regions within proteins, to compute protein clusters, to annotate sequence function, and to compute evolutionary relationships among protein sequences. A number of approaches exist for identifying and characterizing protein families based on their domains, and because domains represent conserved portions of a protein sequence, the primary computation involved in protein family characterization is identification of such conserved regions. However, identifying conserved regions from large collections (millions) of protein sequences presents significant challenges. Methods In this paper we present a new, alignment-free method for detecting conserved regions in protein sequences called NADDA (No-Alignment Domain Detection Algorithm). Our method exploits the abundance of exact matching short subsequences (k-mers) to quickly detect conserved regions, and the power of machine learning is used to improve the prediction accuracy of detection. We present a parallel implementation of NADDA using the MapReduce framework and show that our method is highly scalable. Results We have compared NADDA with Pfam and InterPro databases. For known domains annotated by Pfam, accuracy is 83%, sensitivity 96%, and specificity 44%. For sequences with new domains not present in the training set an average accuracy of 63% is achieved when compared to Pfam. A boost in results in comparison with InterPro demonstrates the ability of NADDA to capture conserved regions beyond those present in Pfam. We have also compared NADDA with ADDA and MKDOM2, assuming Pfam as ground-truth. On average NADDA shows comparable accuracy, more balanced sensitivity and specificity, and being alignment-free, is significantly faster. Excluding the one-time cost of training, runtimes on a single processor were 49s, 10,566s, and 456s for NADDA, ADDA, and MKDOM2, respectively, for a data set comprised of approximately 2500 sequences.
Tumor-Derived Exosomes and Their Role in Tumor-Induced Immune Suppression.

Tumor-derived exosomes (TEX) are emerging as critical components of an intercellular information network between the tumor and the host. The tumor escapes from the host immune system by using a variety of mechanisms designed to impair or eliminate anti-tumor immunity. TEX carrying a cargo of immunoinhibitory molecules and factors represent one such mechanism. TEX, which are present in all body fluids of cancer patients, deliver negative molecular or genetic signals to immune cells re-programming their functions. Although TEX can also stimulate immune activity, in the microenvironments dominated by the tumor, TEX tend to mediate immune suppression thus promoting tumor progression. The TEX content, in part resembling that of the parent cell, may serve as a source of cancer biomarkers. TEX also interfere with immune therapies. A better understanding of TEX and their contribution to cancer progression and cancer patients’ response to immune therapies represents a challenging new field of investigation.
Evidential Reasoning Based Fault Diagnosis

Fault diagnosis in IT environments is complicated because (i) most monitors have shared specificity (high amount of memory utilization can result from a large number of causes), (ii) it is hard to deploy and maintain enough sensors to ensure adequate coverage, and (iii) some functionality may be provided as-a-service by external parties with limited visibility and simultaneous availability of alert data. To systematically incorporate uncertainty and to be able to fuse information from multiple sources, we propose the use of Dempster-Shafer Theory (DST) of evidential reasoning for fault diagnosis and show its efficacy in the context of a distributed application.
Polymorphic malware detection using sequence classification methods and ensembles

Identifying malicious software executables is made difficult by the constant adaptations introduced by miscreants in order to evade detection by antivirus software. Such changes are akin to mutations in biological sequences. Recently, high-throughput methods for gene sequence classification have been developed by the bioinformatics and computational biology communities. In this paper, we apply methods designed for gene sequencing to detect malware in a manner robust to attacker adaptations. Whereas most gene classification tools are optimized for and restricted to an alphabet of four letters (nucleic acids), we have selected the Strand gene sequence classifier for malware classification. Strand's design can easily accommodate unstructured data with any alphabet, including source code or compiled machine code. To demonstrate that gene sequence classification tools are suitable for classifying malware, we apply Strand to approximately 500 GB of malware data provided by the Kaggle Microsoft Malware Classification Challenge (BIG 2015) used for predicting nine classes of polymorphic malware. Experiments show that, with minimal adaptation, the method achieves accuracy levels well above 95% requiring only a fraction of the training times used by the winning team's method.
The Caregiving Quandary

Long before I became a cancer caregiver, I worried about families. Providing care without a script, expanding their workload, solo decision making, incessant worrying, managing expectations, overseeing medications-that is the lay caregiver's all-consuming world. However, when cancer entered my residence, I started living what I had historically observed from a distance. The double-duty caregiving at work and home overwhelmed me. Years of experience did little to prepare me for the emotional tsunami and physical toll caregiving took on me. I questioned my ability to make decisions, I got my husband's medications mixed up, and I had trouble asking for and accepting help, despite how much I needed it. .
An Examination of American College of Surgeons NSQIP Surgical Risk Calculator Accuracy

Background The American College of Surgeons NSQIP offers a Surgical Risk Calculator (SRC) that provides detailed, patient-level, risk assessments for many adverse outcomes to surgeons, patients, and the general public. The SRC calculator was designed to help guide discussion and decisions by providing generally applicable (not hospital-specific) information about surgical risk using easily understood and broadly available preoperative variables. Although large, internal evaluations have shown that the SRC has good accuracy (model discrimination and calibration), external validations have been inconsistent and tend to favor a conclusion of inadequate performance. Study Design External studies, attempting to validate the SRC, were examined with respect to 3 design features: sample size (small samples reduce reliability), case-mix homogeneity (homogeneity reduces discrimination); and number of institutions providing data (few institutions reduces generalizability). The impact of each feature was then examined in several sets of simulation studies. Results Each of the 3 design features has the potential to act as an artifactual cause for apparent SRC predictive failure. In addition, demonstrations that SRC estimates are inferior to those from models that use additional (sometimes operation-specific) predictor variables were seen as not relevant with respect to the SRC's intended scope. Conclusions The SRC predictive failures, reported by studies with the described design limitations, should not be misunderstood as disqualifying the SRC as an accurate and appropriate tool for its intended purpose of providing a general purpose risk calculator, applicable across many surgical domains, using easily understood and generally available predictive information.
A scholar, colleague and friend

AbstractThe unique personality known as the Abilene Paradox man. A man who lived and breathed stories and story telling, the likes of “Swatting Flies and Telling Lies.”
Effect of Biofuel on Agricultural Supply and Land Use

While biofuels were introduced, in part, to reduce greenhouse gas emissions through replacing fossil fuels, comparing their impact to conventional sources has been difficult. This is largely due to the challenges of quantifying indirect land use change due to biofuels, which has proved controversial. This paper introduces a stylized, dynamic framework to analyze the evolution of land use expansion as well as deforestation over time. Our analysis suggests that land use change is a dynamic process and that relationships between variables are not regular over time and space. Technological change and effective environmental policy, of both agriculture and forests, can curtail deforestation. Outcomes of the model are illustrated with empirical data from the U.S. and Brazil. In the United States, deforestation does not lead directly to cropland expansion, as there is a transition period during which land is used as pasture or left idle. In Brazil, with four times more land in pasture or underutilized land than in cropland, there is significant potential for cropland expansion from this underutilized land.
Human Papillomavirus Genome Integration and Head and Neck Cancer

We conducted a critical review of human papillomavirus (HPV) integration into the host genome in oral/oropharyngeal cancer, reviewed the literature for HPV-induced cancers, and obtained current data for HPV-related oral and oropharyngeal cancers. In addition, we performed studies to identify HPV integration sites and the relationship of integration to viral-host fusion transcripts and whether integration is required for HPV-associated oncogenesis. Viral integration of HPV into the host genome is not required for the viral life cycle and might not be necessary for cellular transformation, yet HPV integration is frequently reported in cervical and head and neck cancer specimens. Studies of large numbers of early cervical lesions revealed frequent viral integration into gene-poor regions of the host genome with comparatively rare integration into cellular genes, suggesting that integration is a stochastic event and that site of integration may be largely a function of chance. However, more recent studies of head and neck squamous cell carcinomas (HNSCCs) suggest that integration may represent an additional oncogenic mechanism through direct effects on cancer-related gene expression and generation of hybrid viral-host fusion transcripts. In HNSCC cell lines as well as primary tumors, integration into cancer-related genes leading to gene disruption has been reported. The studies have shown that integration-induced altered gene expression may be associated with tumor recurrence. Evidence from several studies indicates that viral integration into genic regions is accompanied by local amplification, increased expression in some cases, interruption of gene expression, and likely additional oncogenic effects. Similarly, reported examples of viral integration near microRNAs suggest that altered expression of these regulatory molecules may also contribute to oncogenesis. Future work is indicated to identify the mechanisms of these events on cancer cell behavior.
Opinion: "Plan S" falls short for society publishers-and for the researchers they serve.

Over the course of my long scientific career, I have had experience with academic publishing from several perspectives: as an author, as an associate editor of both academic and for-profit journals, as chair of a society’s journals board, as editor-in-chief of a major society journal ( Science ), and now as the chief executive of a membership organization (the National Academy of Sciences) that publishes a highly regarded society journal (PNAS). While for-profit publishers do bring value to the overall enterprise, ultimately I decided to direct my own research output (whenever it was my choice to make), time, and talent to nonprofit scientific society publishing. I see merit in redirecting publishing profits to enhance the welfare of the research community through the variety of society programs that support students, underrepresented minorities, community engagement, and other worthy causes—rather than having those monies benefit for-profit shareholders. The proposal known as Plan S has the admirable aim of achieving full OA across a wide swath of journal publications. But the path currently suggested has serious drawbacks that could jeopardize nonprofit science societies. Image credit: Dave Cutler (artist). In recent decades, society publishers have responded to a number of changes in the publishing landscape. In all cases, these responses have been guided by the wisdom of leading researchers serving on oversight boards charged with ensuring the overall health of the research enterprise. This charge is, of course, broader than simply the broadest dissemination of the research or necessarily the lowest-cost publication model. I continue to monitor that landscape, knowing that further changes are inevitable and part of scholarly publishing’s evolution as it aspires to serve science and society. Hence, I, like many in scientific society leadership and publishing, have been following with great interest the ambitious plan (“Plan S”) put forward in September by a group … [↵][1]1Email: MMcNutt{at}nas.edu. [1]: #xref-corresp-1-1
Topological insulators in longitudinally driven waveguides: Lieb and kagome lattices

Topological insulators are studied via tight-binding approximations of longitudinally driven photonic lattices with three lattice sites per unit cell. Two cases are considered in detail: Lieb and kagome lattices. The lattice is decomposed into three sublattices, each of which is allowed to move independently of the others. Emphasis is placed on periodic driving induced by laser-etched helical coils along the direction of propagation. The linear Floquet bands are constructed for various intersublattice rotation patterns such as different radii, different frequency, phase offset, and quasi-one-dimensional motion. Depending on the nature of the band structure, bulk spectral bands with nonzero Chern number are found to support topologically protected edge states which can move unidirectionally. In this case, the modes move scatter-free around defects due to underlying topological protection. Intriguing mode dynamics are found including bidirectional topological modes and bulk-edge leakage, i.e., excitation of bulk modes at a defect for edge modes with dispersion frequencies near the bulk bands. Finally, certain nonlinear edge modes are also found to propagate unidirectionally and scatter-free around lattice defects.
Advocating a preferred legislative style while constituting a bipartisan collective identity: Women senators’ strategic use of constitutive and polarizing rhetoric

ABSTRACTOn October 1, 2013 the U.S. federal government buckled under the pressure of partisanship and shut down for 16 days. News coverage of the event focused on how the women of the 113th Senate ...
Long‐term outcomes and management considerations after parathyroidectomy in the dialysis patient

Parathyroidectomy (PTX) remains an important intervention for dialysis patients with poorly controlled secondary hyperparathyroidism (SHPT), though there are only retrospective and observational data that show a mortality benefit to this procedure. Potential consequences that we seek to avoid after PTX include persistent or recurrent hyperparathyroidism, and parathyroid insufficiency. There is considerable subjectivity in defining and diagnosing these conditions, given that we poorly understand the optimal PTH targets (particularly post PTX) needed to maintain bone and vascular health. While lowering PTH after PTX decreases bone turnover, long-term changes in bone activity have been poorly explored. High turnover bone disease, usually present at the time a PTX is considered, often swings to a state of low turnover in the setting of sufficiently low PTH levels. It remains unclear if all low bone turnover equate with disease. However, such changes in bone turnover appear to predispose to vascular calcification, with positive calcium balance after PTX being a potential contributor. We know little of how the post-PTX state resets calcium balance, how calcium and VDRA requirements change or what kind of adjustments are needed to avoid calcium loading. The current consensus cautions against excessive reduction of PTH although there is insufficient evidence-based guidance regarding the management of chronic kidney disease - mineral bone disease (CKD-MBD) parameters in the post-PTX state. This article aims to compile existing research, provide an overview of current practice with regard to PTX and post-PTX chronic management. It highlights gaps and controversies and aims to re-orient the focus to clinically relevant contemporary priorities in CKD-MBD management after PTX.
Influence of Early Lactation Assistance on Inpatient Exclusive Breastfeeding Rates.

BackgroundHuman milk feeding reduces the incidence and costs of several maternal and childhood illnesses. Initiation and success of human milk feeding are influenced by race, socioeconomic status, ...
Association of doxycycline and mortality in patients hospitalized with pneumonia

Background: Despite clinical practice guideline recommendations to use doxycycline as part of combination therapy for some patients hospitalized with pneumonia there is minimal research supporting this. Therefore, the purpose of our study was to examine the association between doxycycline use, as part of combination antibiotic therapy, and mortality for patients hospitalized with pneumonia. Methods: We identified patients > 65 years of age admitted to any US Department of Veterans Affairs hospital in fiscal years 2002-2012 with a discharge diagnosis of pneumonia. We excluded those patients who did not receive antibiotic therapy concordant with the 2019 ATS/IDSA clinical practice guidelines. Using a multilevel regression model, we examined the association of doxycycline on 30-day mortality, adjusting for demographics, comorbid conditions, severity of illness, prior outpatient medications, and admitting hospital. Results: Our cohort was comprised of 83,961 patients with a mean age of 77.8 (standard deviation 7.4) years, 98% were male, and 7.4% received doxycycline. Unadjusted mortality was 8.6% for those who received doxycycline vs. 11.7% in those who did not (p Conclusions: In this observational cohort study, we found that doxycycline use, as part of guideline-concordant antibiotic therapy, was associated with significantly lower mortality. While this supports the safety and efficacy of antibiotic regimes that include doxycycline, additional studies, especially randomized clinical trials, are needed to confirm this.
High-fat diet-fed ovariectomized mice are susceptible to accelerated subcutaneous tumor growth potentially through adipose tissue inflammation, local insulin-like growth factor release, and tumor associated macrophages.

BACKGROUND The association between obesity and colorectal cancer (CRC) risk has been well established. This relationship appears to be more significant in men than in women, which may be attributable to sex hormones. However, controlled animal studies to substantiate these claims and the mechanisms involved are lacking. MATERIALS AND METHODS MC38 murine colon adenocarcinoma cells were injected subcutaneously into high-fat diet (HFD) fed male, female and ovariectomized (OVX) female C57BL/6 mice. RESULTS HFD increased tumor growth (main effect) that was consistent with metabolic perturbations (P < 0.01). HFD OVX mice exhibited the most significant tumor growth compared to HFD male and female mice (p < 0.05) and this was associated with increased subcutaneous adipose tissue (p < 0.05). Further, the subcutaneous adipose tissue depots within HFD OVX mice exhibited more severe macrophage associated inflammation compared to female (P < 0.01), but not male mice. Conditioned media from subcutaneous adipose tissue of HFD OVX contained higher IGF-1 levels compared to male (P < 0.01), but not female mice. Finally, HFD OVX mice had increased M2-like gene expression in their tumor-associated macrophages (TAMs) compared to female mice (P < 0.01). CONCLUSIONS This work provides evidences suggesting adiposity, adipose specific IGF-1, macrophage associated adipose inflammation, and TAMs as potential mechanisms driving obesity-enhanced CRC in females lacking ovarian hormones.
Dissertation Chapter 3: McVeigh, Family Members, and Survivors: Relationships, the Law, and Memory

This chapter explores how family members and survivors negotiated their relationships with McVeigh and the criminal justice system. It analyzes these relationships chronologically from McVeigh's arrest through his trial and ultimately execution. It first outlines the victim-offender relationship that was perceived to exist between family members/survivors and McVeigh, exploring its para-social origins. The implications of this relationship, in which McVeigh was seen as a defiant offender, posed a potential barrier to the construction of social mnemetic frameworks. This chapter then links the para-social relationship to the behavior of family members and survivors through the federal trials of McVeigh and Nichols, elucidating how family members and survivors perceived the criminal justice system by analyzing their opinions on the death penalty, the trial and execution. Though McVeigh was held accountable for the bombing, the trial did not facilitate memory work for family members and survivors. Finally, this chapter examines the state of family members' and survivors' impressions of McVeigh immediately prior to his execution, including their ability to forgive, their willingness to meet with him in person, and their expectations concerning his conduct at the execution. Their impressions reflect the degree to which McVeigh's defiance unsettled them, revealing how participants' attitudes towards the perpetrators and the criminal justice system affected processes of mnemetic reconstruction.
Matrix and agent-based modeling of threats to a diamond-backed terrapin population

Abstract Population models are important tools for evaluating human impacts and potential management approaches on declining species. However, often studies are limited by constraints of the specific modeling approach. In this study we considered the persistence of a diamond-backed terrapin (Malaclemys terrapin) population using two distinct modeling approaches. Two of the models were deterministic matrix models. Analysis of the discrete non-spatial models showed that female adult survival rate had the largest positive impact on population growth while delaying sexual maturity decreased population growth. The matrix models also demonstrated that an increase in crab traps skewed the sex ratio of the population in favor of females. The third model was a stochastic agent-based formulation that evaluated how increases in the number of crab traps and frequency of nest disturbances affected the long-term viability of diamond-backed terrapins. The spatial agent-based model revealed how terrapin mortality was highly sensitive to the proximity of traps to the primary terrapin habitat. Results from this project improve our understanding of threats to diamond-backed terrapins and can be used to guide conservation efforts.
Food Insecurity during the Time of COVID-19: Vulnerability, Health Conditions, and Taking Action.

Since the report of the first cases of a “viral pneumonia” in Wuhan, China in late 2019, the global spread of what would be identified as SARS-Co V-2 or COVID-19 has been rapid and virulent. As of ...
Comparison of SUSY spectra generators for natural SUSY and string landscape predictions

Models of natural supersymmetry give rise to a weak scale m_{weak}~m_{W,Z,h}~ 100 GeV without any (implausible) finetuning of independent contributions to the weak scale. These models, which exhibit radiatively driven naturalness (RNS), are expected to arise from statistical analysis of the string landscape wherein large soft terms are favored, but subject to a not-too-large value of the derived weak scale in each pocket universe of the greater multiverse. The string landscape picture then predicts, using the Isajet SUSY spectra generator Isasugra, a statistical peak at m_h~ 125 GeV with sparticles generally beyond current LHC search limits. In this paper, we investigate how well these conclusions hold up using other popular spectra generators: SOFTSUSY, SPHENO and SUSPECT (SSS). We built a computer code DEW4SLHA which operates on SUSY Les Houches Accord files to calculate the associated electroweak naturalness measure \Delta_{EW}. The SSS generators tend to yield a Higgs mass peak ~125-127 GeV with a superparticle mass spectra rather similar to that generated by Isasugra. In an Appendix, we include loop corrections to \Delta_{EW} in a more standard notation.
Evaluation of Methyl-Binding Domain Based Enrichment Approaches Revisited

Methyl-binding domain (MBD) enrichment followed by deep sequencing (MBD-seq), is a robust and cost efficient approach for methylome-wide association studies (MWAS). MBD-seq has been demonstrated to be capable of identifying differentially methylated regions, detecting previously reported robust associations and producing findings that replicate with other technologies such as targeted pyrosequencing of bisulfite converted DNA. There are several kits commercially available that can be used for MBD enrichment. Our previous work has involved MethylMiner (Life Technologies, Foster City, CA, USA) that we chose after careful investigation of its properties. However, in a recent evaluation of five commercially available MBD-enrichment kits the performance of the MethylMiner was deemed poor. Given our positive experience with MethylMiner, we were surprised by this report. In an attempt to reproduce these findings we here have performed a direct comparison of MethylMiner with MethylCap (Diagenode Inc, Denville, NJ, USA), the best performing kit in that study. We find that both MethylMiner and MethylCap are two well performing MBD-enrichment kits. However, MethylMiner shows somewhat better enrichment efficiency and lower levels of background “noise”. In addition, for the purpose of MWAS where we want to investigate the majority of CpGs, we find MethylMiner to be superior as it allows tailoring the enrichment to the regions where most CpGs are located. Using targeted bisulfite sequencing we confirmed that sites where methylation was detected by either MethylMiner or by MethylCap indeed were methylated.
NIHSS/EIC Mismatch Explains the > 1/3 MCA Conundrum

To the Editor: The controversy about the significance of early ischemic changes (EIC) on CT after acute stroke by von Kummer, Lyden, and Davis and Donnan1–3 nicely summarizes the issues except for what, in my mind, is the most likely explanation for the discrepancy between the NINDS and ECASS conclusions on this subject. I would also like to propose an alternative way of looking at the “more or less than one third MCA territory” controversy. The aim of treatment with intravenous tPA is to reperfuse tissue that is hypoperfused but still viable (penumbra). While there are undoubtedly other variables that are important, the overwhelming burden of animal and human data have shown that time is critical for the existence of penumbra; penumbral tissue is more plentiful the earlier the patient is treated after the stroke onset. Therefore, when NINDS patients were treated on average 90 minutes after stroke onset, the core of already infarcted tissue, represented by areas of EIC on CT, was in most cases likely still surrounded by substantial salvageable, normally appearing penumbral brain tissue on CT. Such patients could, and did, benefit from reperfusion after intravenous tPA. However, 240 to 300 minutes after the stroke, when the average ECASS patient was treated, the core would be larger (hence more patients with EIC in >⅓ MCA), and the regions of EIC would most likely be surrounded by relatively less penumbra. The result of treating such patients, therefore, is risk with less likelihood of much benefit. This logically would explain why EIC by themselves, whatever their extent, did not predict lack of benefit from tPA treatment in the NINDS patients, but why extensive EIC were associated with risk and no benefit in ECASS. This hypothesis is supported by clinical observation of patients seen within 3 hours of stroke …
The ATP binding site on rho protein. Affinity labeling of Lys181 by pyridoxal 5'-diphospho-5'-adenosine.

We have labeled the nucleoside triphosphate-binding domain of Escherichia coli rho factor with the ATP affinity analog [3H]pyridoxal 5′-diphospho-5′-adenosine (PLP-AMP). PLP-AMP completely inactivates the RNA-dependent ATPase activity of rho upon incorporation of 3 mol of reagent/mol of hexameric rho protein. Although the potency of PLP-AMP is enhanced when an RNA substrate such as poly(C) is present, the stoichiometry for inhibition remains the same as in the absence of poly(C). The nucleotide substrate ATP competes very effectively for the binding site and protects against PLP-AMP inactivation. A domain of rho called N2, which comprises the distal two-thirds of the molecule (residues 152-419) and encompasses the region proposed to bind ATP, is labeled specifically in the presence of poly(C). Amino acid sequence analysis of the single [3H]PLP-AMP labeled proteolytic fragment showed Lys181 to be the site of modification, suggesting that this residue normally interacts with the gamma-phosphoryl of bound ATP. These results agree with our proposed tertiary structure for the ATP-binding domain of rho that places this lysine residue in a flexible loop above a hydrophobic nucleotide-binding pocket comprised of several parallel beta-strands, similar to adenylate kinase, F1-ATPase, and related ATP-binding proteins. Parallel studies of rho structure and function by site-directed mutagenesis and chemical modification support this interpretation.
Induction of Autoimmune Hemolytic Disease by Diffusible Substances from the Thymus of NZB/Bl Mice

Mice of four strains were thymectomized neonatally and implanted with Millipore diffusion chambers containing thymic tissue from newborn mice of the NZB/Bl strain. Of a total of 60 surviving animals, 50 developed a positive Coombs’ test and other evidences of autoimmune hemolytic disease. Controls remained negative. Various possibilities concerning the nature of the membrane-passing factor or agent are considered.
Stimulation of vascular cell proliferation by beta-galactoside specific lectins.

An investigation was conducted to assess the effects of various beta-galactoside specific lectins on the growth of vascular cells in vitro. The plant lectins from peanut (Arachis hypogaea), mushroom (Agaricus bisporus), and coral tree (Erythrina corallodendron) were used in these studies with the ultimate purpose of comparing those findings with data derived with the lectin isolated from rat lung. Peanut lectin was added to confluent and subconfluent cultures of smooth muscle cells (SMC), pulmonary arterial (PEC), and aortic endothelial cells (BAEC) at concentrations of 2, 3.5, and 7.0 micrograms/ml. There was a dose-dependent increase in cell proliferation for both confluent and subconfluent SMC, with maximal stimulation noted between 3.5 and 7 micrograms/ml of peanut lectin. A dose-dependent stimulation of PEC proliferation was also found with maximal stimulation between 3.5 and 7.0 micrograms/ml. Peanut lectin did not stimulate BAEC to multiply. The stimulation of PEC and SMC by peanut lectin could be ...
Developing a Systems Biology Approach to Study Disease Progression Caused by Heterodera glycines in Glycine max

Introduction advent of molecular biology caused a reductionist “fever” to spread throughout the biological research community that continues to this day. The new molecular insights and techniques enabled researchers to probe the constituent parts of complex biological systems at unprecedented scale and detail. The reductionist approach naturally emerged: if we could now isolate and study the component parts of a system, we should be able to synthesize the information about the individual components into a unifi ed understanding of the whole system. However, this “naive reductionism” (Bloom, 2001) needs to be balanced with a systems approach for a simple reason: the complex dynamics of a biological system often produce behaviors and properties that cannot be explained by the presence of a single component, but rather emerge from the interactions of the components of the system (so-called emergent
Production of 2,3-butylene glycol from citrus wastes. II. The Bacillus polymyxa fermentation.

The conditions required for production of levo 2,3-butylene glycol by Bacillus polymyxa from citrus molasses were studied. Starter cultures required acclimatization to the substrate prior to inoculation of the fermentation medium. Maximal production of butylene glycol with minimal residual sugar was obtained with a medium consisting of molasses, diluted to 20 degrees Brix, and 0.4% urea. Optimal environmental conditions included aeration at 0.11 volumes of air per volume of medium per minute, maintenance of pH at 6.0 to 6.2, a fermentation temperature of 30 C, and a stirring rate of 420 rev/min. The concentration of butylene glycol obtained in the fermentation beer ranged from 2.3 to 4.4%. The optical rotation of the glycol ranged from [alpha](D) (23 degrees ) = -1.01 degrees to -10.45 degrees . The variation in rotation was probably due to the presence of contaminating substances in the distillate.
Pattern-based ontology design

In this chapter, we present ontology design patterns (ODPs), which are reusable modeling solutions that encode modeling best practices. ODPs are the main tool for performing pattern-based design of ontologies, which is an approach to ontology development that emphasizes reuse and promotes the development of a common “language” for sharing knowledge about ontology design best practices. We put specific focus on content ODPs (CPs) and show how they can be used within a particular methodology. CPs are domain-dependent patterns, the requirements of which are expressed by means of competency questions, contextual statements, and reasoning requirements. The eXtreme Design (XD) methodology is an iterative and incremental process, which is characterized by a test-driven and collaborative development approach. In this chapter, we exemplify the XD methodology for the specific case of CP reuse. The XD methodology is also supported by a set of software components named XD Tools, compatible with the NeOn Toolkit, which assist users in the process of pattern-based design.
The Role of Information Extraction in the Design of a Document Triage Application for Biocuration

Traditionally, automated triage of papers is performed using lexical (unigram, bigram, and sometimes trigram) features. This paper explores the use of information extraction (IE) techniques to create richer linguistic features than traditional bag-of-words models. Our classifier includes lexico-syntactic patterns and more-complex features that represent a pattern coupled with its extracted noun, represented both as a lexical term and as a semantic category. Our experimental results show that the IE-based features can improve performance over unigram and bigram features alone. We present intrinsic evaluation results of full-text document classification experiments to determine automatically whether a paper should be considered of interest to biologists at the Mouse Genome Informatics (MGI) system at the Jackson Laboratories. We also further discuss issues relating to design and deployment of our classifiers as an application to support scientific knowledge curation at MGI.
Using the right tools and techniques leads to successful testing of MCMs

The secret to successfully testing MCM prototype products is to perform the right amount of testing. Attempting to test every transistor inside of each chip in the MCM is likely to result in a failed project, because most MCMs are too complex to test as though they are one large IC. The formula used for several successful projects was to (1) obtain functional ICs, (2) devise tests that verify the ICs are properly interconnected, and (3) run some simple functional tests to verify the MCM performs properly as a unit. Obtaining good chips is usually not a big problem, since most IC manufacturers perform relatively complete testing of the bare ICs. Generating interconnect tests is a straightforward task for many designs. Sometimes design-for-testability (DFT) is required to make the design more readily testable. Functional tests, even very limited ones, are best developed using logic simulation, allowing coverage and correctness to be verified before going to the tester. A brief sampling is presented of specific approaches to consider when planning the strategy.
Inclusion, Accommodation, and Recognition: Accounting for Differences Based on Religion and Sexual Orientation

This Article analyzes the rights claims and theoretical frameworks deployed by Christian Right and gay rights cause lawyers in the context of gay-inclusive school programming to show how two movements with conflicting normative positions are using similar representational and rhetorical strategies. Lawyers from both movements cast constituents as vulnerable minorities in a pluralistic society, yet they do so to harness the homogenizing power of curriculum and thereby entrench a particular normative view. Exploring how both sets of lawyers construct distinct and often incompatible models of pluralism as they attempt to influence schools’ state-sponsored messages, this Article exposes the strengths as well as the limitations of both movements’ strategies. Christian Right lawyers’ free speech strategy - articulating religious freedom claims through the secular language of free speech doctrine - operates within an inclusion model of pluralism. This model stresses public participation and engagement with difference. After making significant advances over the past several years, lawyers have begun to employ the inclusion model with some success in the school programming domain, despite significant doctrinal and remedial limitations. At the same time, Christian Right lawyers assert parental rights and free exercise claims in curricular challenges. Such claims rely on an accommodation model of pluralism that permits selective withdrawal based on religious beliefs and thereby resists active engagement with difference. This strategy struggles in the face of a well-accepted view of civic education that values exposure to diversity - a view bound up with the success of the Christian Right’s inclusion model of pluralism. Gay rights lawyers respond to Christian Right claims by drawing on a left multicultural model of pluralism. This model constitutes lesbians and gay men as identity holders (rather than sex actors), and in doing so succeeds in justifying the inclusion of sexual orientation in programming that prioritizes diversity. The left multicultural claim stalls, however, when it demands the state’s affirmative cultivation of respect by asserting students’ rights to gay-inclusive instruction. In the end, both the Christian Right and gay rights movements make important advances yet face significant tensions as they craft doctrinal claims that operate within competing models of pluralism.
Interactions between cumulus convection and its environment as revealed by the MC3E sounding array

This study attempts to understand interactions between midlatitude convective systems and their environments through a heat and moisture budget analysis using the sounding data collected from the Midlatitude Continental Convective Clouds Experiment (MC3E) in central Oklahoma. Distinct large-scale structures and diabatic heating and drying profiles are presented for cases of weaker and elevated thunderstorms as well as intense squall line and supercell thunderstorm events during the campaign. The elevated cell events were nocturnal convective systems occurring in an environment having low convective available potential energy (CAPE) and a very dry boundary layer. In contrast, deeper convective events happened during the morning into early afternoon within an environment associated with large CAPE and a near-saturated boundary layer. As the systems reached maturity, the diagnosed diabatic heating in the latter deep convective cases was much stronger and of greater vertical extent than the former. Both groups showed considerable diabatic cooling in the lower troposphere, associated with the evaporation of precipitation and low-level clouds. The horizontal advection of moisture also played a dominant role in moistening the lower troposphere, particularly for the deeper convective events, wherein the near surface southeasterly flow allows persistent low-level moisture return from the Gulf of Mexico to support convection. The moisture convergence often was present before these systems develop, suggesting a strong correlation between the large-scale moisture convergence and convection. Sensitivity tests indicated that the uncertainty in the surface precipitation and the size of analysis domain mainly affected the magnitude of these analyzed fields rather than their vertical structures.
1.2.1 Self‐Directed Teams for Systems Engineering

A systems engineering functional group within a matrix organization provides technical skills to system development projects. Effective systems engineering requires a balanced emphasis on people, technology, and process activities. This balance can be achieved through the use of self-directed teams in place of the traditional hierarchical organization. Using defined team tasks, clear interfaces, and a metrics program, self-directed systems engineering teams were piloted. Results were measured in project performance, team performance, and involvement by systems engineers in developing and improving the technology skills and processes necessary for future company growth.
Healthcare epidemiology is the paradigm for patient safety.

I was honored to receive the 2001 Lectureship Award from the Society for Healthcare Epidemiology of America (SHEA). It was my intent during the talk to review our field and implications that some of the new initiatives called “patient safety” have for our expertise. This article is based on the SHEA Lectureship that was given April 1, 2001, at the SHEA Annual Meeting in Toronto, Ontario, Canada.This article consists of four sections. First, I review lessons learned from colleagues during the 33 years that I have been associated with the field of hospital epidemiology and infection control, since my first days at the Centers for Disease Control and Prevention (CDC). Second, I explore issues raised by the Institute of Medicine (IOM) report on patient safety, adverse events, and medical errors, evaluating research that went into the extrapolation of the numbers of preventable deaths that this report highlighted. Those deaths gained everyone's attention. Third, I review the field of healthcare epidemiology, highlighting the three decades of success in our field in enhancing the safety of patients, improving their outcomes, and making a difference in the quality of medical care received in the United States. Finally, I discuss the challenges that hospital epidemiology currently faces and the opportunities that come with the expertise we have developed during more than 30 years.
The structure of trans-1,4-diisocyanocyclohexane in solution, in the solid state, and as a ligand bridging bulky tungsten(II) complexes

Abstract The conformational structures of the bridging ligand trans -1,4-diisocyanocyclohexane were determined in solution, as a solid, and as a ligand bridging bulky seven-coordinate tungsten(II) complexes. In solution CNC 6 H 10 NC exists as an equilibrium mixture of diaxial and diequatorial conformers, with the diequatorial conformer preferred in a 2 : 1 ratio. Infrared data indicate that the bulk solid does not consist of the diequatorial conformer, and a single-crystal study verifies that the diaxial conformer is preferred in the solid state. The crystal data found for CNC 6 H 10 NC are: space group P 2 1 /n, Z = 2, a = 5.996(1) A, b = 7.203(2) A, c = 8.972(3) A, β = 96.89(2)°, and V = 384.7(2) A 3 . 13 C NMR bandshape analysis provides a low activation barrier (40.7(4) kJ mol −1 ) in CH 2 Cl 2 solution for diaxial—diequatorial conversion. In spite of the accessibility of both conformers in solution, the ligand unexpectedly adopts the diaxial conformation in the bimetallic complex (Br 2 (PEt 3 ) 2 (CO) 2 W) 2 CNC 6 H 10 NC. The crystal data found for (Br 2 (PEt 3 ) 2 (CO) 2 W) 2 CNC 6 H 10 NC are: space group Pca 2 1 , Z = 4, a = 17.162(5) A, b = 16.226(6) A, c = 18.233(3) A, and V = 5077.3(25) A 3 .
Physician attitudes toward treatment of depression in older medical inpatients.

Objectives: To better understand low treatment (<50%) and psychiatry referral rates (<10%) of depressed older medical patients, we examined medical physicians’ characteristics, attitudes and practices regarding treatment. Methods: Physicians caring for a consecutive series of 1000 depressed older patients during medical hospitalization and/or after discharge were asked about their general attitudes and behaviors related to the treatment of depression in older patients. Results: Of 422 physicians responding to questionnaires, less than half (48%) usually started more than two patients a month on antidepressants. Even fewer (14%) referred more than two patients a month for counseling; 37% usually referred none. Only 11% referred more than two patients a month to psychiatrists; nearly 40% usually referred none. Antidepressants, counseling, and psychiatric referral were seldom thought very effective. Physicians out of their training and those in primary care specialties (especially family practice) were more ...
Kinetic studies in mass spectrometry—IX: Competing [M NO2] and [M NO] reactions in substituted nitrobenzenes. Approximate activation energies from ionization and appearance potentials

Ionization (IP) and appearance potentials (AP) have been secured for apparently competing [M NO2] cleavage and [M NO] rearrangement reactions in a series of m-and p-X substituted nitrobenzene molecular ions. Approximate activation energies AP–IP were within the experimental reproducibility for most substituents for the [M NO2] reaction of m-and p-X isomer pairs of compounds, but outside it for the [M NO] process. This is interpreted as either effective substituent randomization in the reacting molecular ions or as fortuitously similar activation energies for the [M NO2] cleavage. Assuming the latter, AP–IP for both reactions gave acceptably linear correlations of negative slope when plotted against σ or σ+, which has been interpreted mechanistically in terms of a degree of positive charge dissipation in the rate limiting transition states. These findings are in direct contrast to the energetics of the [M CH3] and [M CH2O] reactions recently studied in substituted anisoles, where plots of AP–IP vs. σ+ displayed positive slopes. The advantages of AP–IP over peak relative abundance as a mechanistic probe are discussed, and corresponding plots of logZ/Z0vs. σ(σ+) and log [A0]/[M0] (1 – f) vs. σ(σ+) for the same reactions are presented and discussed. The disadvantages and limitations of IP and AP measurements are also emphasized.