cssi/SciSciGPT-SciSciNet huggingface dataset:
Carbon fixation in trees as a micro optimization process: an example of combining ecology and economics

This paper demonstrates how optimization procedures commonly used in microeconomics can be directly applied in studying ecological systems. Two alternative economic-analog models of carbon fixation in trees are developed that yield mutually exclusive, testable hypotheses regarding plant functioning. The first is a relatively straight-forward economic analog where carbon serves as the currency and the plant is modeled as a maximizer of net carbon gain (a profit analog). The second models carbon ‘revenue’ as the minimum of two functions that relate carbon gain to leaf and root biomass, respectively. The plant is then modeled with a MAXMIN operator, such that the minimum net revenue is maximized. Both models imply that leaves and roots are simultaneously limiting factors, but the second (MAXMIN) model implies that they are not ‘equally’ limiting. A parameterized version of the hiAXMIN model is developed, and sensitivity analysis performed to demonstrate how the model behaves biologically.
Determination of Si/SiO/sub 2/ interface roughness using weak localization

The interface roughness of intentionally textured Si/SiO/sub 2/ interfaces was measured using the quantum weak localization (WL) correction to the electrical conductivity at low temperatures. The deduced roughness was confirmed by observation of the Si surface replicas by atomic force microscopy (AFM). Quantitative agreement between the two methods was found ( Delta =1.2 to 1.4 AA from WL and 1.35 AA from AFM). For a surface with artificially induced texture, it is found that WL can easily distinguish a significant increase in roughness relative to the smooth surfaces. AFM confirms this qualitative conclusion. >
Integration of silicon photonics in bulk CMOS

The first monolithic process flow integrating silicon photonics on operational bulk CMOS has been developed. Features include deep-trench isolation, polysilicon waveguides, grating couplers, filters, modulators, and detectors. Fully functional on-chip CMOS enables Tx/Rx operation while minimizing interconnect parasitics. With the addition of an external 1280nm source, a fully functional optical link (5Gb/s 2.8pJ/b), capable of wavelength division multiplexing, has been demonstrated. In addition to the polysilicon resonant detector used in the link, a monolithically-integrated Silicon-Germanium selective epitaxial growth based photodetector was developed.
An automatic parallelization framework for OpenAxiom

Each polynomial pj can be computed using sequential nested loops. Our framework is able to transform the sequential computation to its parallel version. The transformed version computes the denominator and numerator of each term pi using a parallel reduction function, respectively. The list of the terms (X xj) in the numerator, and the terms (xi xj) in the denominator are computed via calling a parallel map function. The transformation relies on the fact that the multiplication operator over any field and the multiplication operator over univariate polynomials are monoid operators, i.e., the operators are associative and each has an identity element. In general, such algebraic properties are domain-specific knowledge and are dicult to infer systematically. This framework provides linguistic support to express them directly in code:
Shields, Swords, and the Moral Autonomy of Jurors

Using ideas rooted in fact-finding accuracy, courts hold that defendants open the door to illegally-obtained evidence when they use exclusion as a "sword" to offer contradicted evidence or arguments. Yet the metaphor holding that rules excluding evidence can function "as shield, but not a sword" is inapt when applied to rules that promote non fact-finding goals. Whether the door is opened to admission of evidence excluded by such rules must depend on a contextual analysis of the rule's purpose. Finding that defendants cannot use the constitutional exclusionary rule to advance contradicted evidence or argument negates its necessary deterrent function. Defendants should lose immunity against illegally-obtained evidence only when they offer evidence derived from the same unlawful search or interrogation, or ask the jury to consider why the prosecution did not produce the suppressed evidence. The waiver rule allows the exclusionary rule to accomplish its purpose while protecting the integrity of our fact-finding process, which occasionally values social goals above fact-finding accuracy. By distinguishing arguments about the absence of suppressed evidence from those equivalent to assertions by witnesses required to lie about events to prevent jurors from learning of suppressed evidence, the waiver rule protects jurors from the assault on rational autonomy to which Kant objected. Whether Kant would find sufficient evidence law’s respect for jurors’ right not to be lied to or insist upon their right to all available evidence, we cannot expect evidence rules to function without limiting the evidence that jurors consider. As long as we do, courts must assure that their decisions about opening the door do not undermine the goals that exclusion is designed to achieve.
Sum-rate-optimal dual-QoS MIMO multicasting over medium-voltage NB-PLC networks

We propose a multiple-input multiple-output (MIMO) orthogonal frequency-division multiplexing system for narrowband power-line communication applications in multiuser medium-voltage (MV) multicast networks. The 3-phase MV multicast network is modeled as a 2-input / 3-output MIMO spatial channel over the 3–500 kHz frequency band. We optimize the precoder design to maximize the signal-to-interference-plus-noise ratio at each receive node assuming either a matched filter receiver or a minimum mean square error linear receiver. The performance is evaluated in terms of the achievable sum-rate for a group-based multicast network under two different grouping criteria. The first is an equal-priority criterion where the users in each group receive the same message and all network users operate at the same bit error rate. The second criterion is quality-of-service based and guarantees a lower bit error rate to the premium users compared to the standard users. We quantify the sum-rate gains of multicasting over broadcasting where all users are combined in one group.
HMG-CoA reductase regulation: use of structurally diverse first half-reaction squalene synthetase inhibitors to characterize the site of mevalonate-derived nonsterol regulator production in cultured IM-9 cells

The activity of HMG-CoA reductase (HMGR) is tightly regulated, in part through post-transcriptional mechanisms that are mediated by nonsterol products of mevalonate metabolism. Previous reports have suggested that these mediators are derived from farnesyl pyrophosphate (FPP). Recent studies have implicated FPP hydrolysis products (e.g., farnesol), the squalene synthetase (SQS) reaction products presqualene pyrophosphate (PSQPP) and squalene, or their metabolites. To distinguish among these possible mediators, we evaluated the ability of HMGR and SQS inhibitors to induce compensatory increases in HMGR activity in cultured IM-9 cells. Mevinolin (HMGR inhibitor) produced predicted increases in HMGR activity that were related to the degree of cholesterolgenesis inhibition (e.g., 4-fold, 9-fold, and 17-fold increases relative to 50%, 76%, and 90% inhibition, respectively). By contrast, a variety of structurally distinct reversible, competitive, first half-reaction SQS inhibitors all reduced cholesterolgenesis by up to 90% with no appreciable increases in HMGR activity. These observations strongly suggest that nonsterol-mediated post-transcriptional mechanisms regulating HMGR activity remain intact after SQS first half-reaction inhibition, indicating that nonsterol regulator production is independent of SQS action and ruling out PSQPP, squalene and their metabolites as possible mediators. Unexpectedly, the SQS mechanism-based irreversible inactivator, zaragozic acid A (ZGA) exhibited the greatest degree of HMGR modulation, producing 5-fold, 11-fold, and 40-fold increases in HMGR activity at concentrations that produced 25%, 50%, and 75% cholesterolgenesis inhibition, respectively. The markedly greater magnitude of HMGR stimulation by ZGA versus mevinolin at similar levels of cholesterolgenesis inhibition suggests that ZGA may directly interfere with the production or action of the nonsterol regulator. —Petras, S. F., S. Lindsey, and H. J. Harwood, Jr. HMG-CoA reductase regulation: use of structurally diverse first half-reaction squalene synthetase inhibitors to characterize the site of mevalonate-derived nonsterol regulator production in cultured IM-9 cells. J. Lipid Res. 1999. 40: 24–38.
Reassessing the hemostatic disorder associated with acute promyelocytic leukemia.

of the prothrombin (PT), activated partial thromboplastin (PTT) and thrombin times (TT), increased levels of fibrin degradation products (FDPs), and hypofibrin~genemia.~~~"~~~~~ These findings are not diagnostic of any single coagulation disorder, but reflect a complex interaction of several pathophysiologic processes depicted in Fig 1. The first and most generally recognized abnormality is the release of procoagulants from the APL cells resulting in DIC. Several types of procoagulant activity have been found in APL cells capable of activating factor X through both intrinsic and extrinsic pathways, including tissue factorlike
Paul Ehrlich in His Time: A Historian’s View

As a historian, unversed in natural sciences, I will try to put a few aspects of science to the historical framework of the past 150 years: its role in history has been steadily changing, and its many different aspects have never been fully recognized by historians. There is a famous, but shameful gap between the humanities and the natural sciences, which were described by C.P. Snow as the two cultures. When I was taking an interest in some representatives of science in Germany in the decades preceding and following the First World War — Haber, Einstein and their circle, as well as the politicoscientific culture surrounding them — I was interested in man, in man with his love for science, which was still innocent at that time. The passion leading to great achievements was to be felt, but what were the conditions of involvement and success? What did “science as a profession” mean? What was the scientific ethos of that time, the prerequisite for creativity?
System Requirements for Delivery of Telemedicine Services

The objectives of this chapter are to review the system requirements of delivery telemedicine services for the clinical implementation of a Telemanagement of Inflammatory Bowel Disease (IBD) program. The concept of developing a successful and sustainable telemedicine program is a significant undertaking that includes purchasing and deploying a telemedicine platform, testing and training all clinical and support staff, creating documentation for clinician and patients participating in the program, and finally creating a support structure to troubleshoot and resolve any technical challenges that might occur during a telemedicine encounter. The creation of a scope of work document and technology assessment review also play major parts in the system development of the program. These factors, while all are very important, also hinge on the telemedicine endorsement and adoption of the technology with physicians, nurses, executive leadership, and patients. Technical simplicity is also a major factor in the success of the program. The chapter provides the necessary requirements to protect the privacy of the patient and clinicians during a telemedicine visit. The chapter also provides recommendations on video etiquette or the “dos and don’ts” of where and how the attendees should be participating using the video technology. The chapter stresses interoperability of the video technology as well as devices utilized to keep the costs at a minimum for the patient. Lastly, this chapter provides some insight on building a support structure to provide technical support for hardware and software for the clinicians and patients.
RADIONUCLIDE TECHNIQUES FOR EVALUATING CARDIAC FUNCTION

Publisher Summary This chapter describes a radionuclide technique for evaluating cardiac function. Assessment of regional wall motion by this technique has been limited by traditional geometric analysis. Analysis of the radionuclide ventriculogram can be approached either by evaluation of wall motion or by indices dependent on count rate and, therefore, dependent on changes in blood volume. The former approach relies on edge tracking and is limited by the spatial resolution of the image and by the constraints of two-dimensional imaging. The ventricular wall is assessed best where it is tangential to the imaging device. Previous assessments of regional left ventricular function by gated equilibrium angiocardiography have generally included standard angiographic descriptions of either segmental axis shortening or extent of akinetic segments derived from traced end-diastolic and end-systolic perimeters of the left ventricular blood pool. Techniques that are dependent on changes in count rate observe the hemodynamic events occurring throughout the left ventricle and are sensitive to alterations in ventricular contraction independent of their location with respect to the camera; analysis is, therefore, three dimensional. The accuracy of this technique is limited by the accuracy with which background is subtracted.
Plant Defense Inhibitors Affect the Structures of Midgut Cells in Drosophila melanogaster and Callosobruchus maculatus

Plants produce proteins such as protease inhibitors and lectins as defenses against herbivorous insects and pathogens. However, no systematic studies have explored the structural responses in the midguts of insects when challenged with plant defensive proteins and lectins across different species. In this study, we fed two kinds of protease inhibitors and lectins to the fruit fly Drosophila melanogaster and alpha-amylase inhibitors and lectins to the cowpea bruchid Callosobruchus maculatus. We assessed the changes in midgut cell structures by comparing them with such structures in insects receiving normal diets or subjected to food deprivation. Using light and transmission electron microscopy in both species, we observed structural changes in the midgut peritrophic matrix as well as shortened microvilli on the surfaces of midgut epithelial cells in D. melanogaster. Dietary inhibitors and lectins caused similar lesions in the epithelial cells but not much change in the peritrophic matrix in both species. We also noted structural damages in the Drosophila midgut after six hours of starvation and changes were still present after 12 hours. Our study provided the first evidence of key structural changes of midguts using a comparative approach between a dipteran and a coleopteran. Our particular observation and discussion on plant–insect interaction and dietary stress are relevant for future mode of action studies of plant defensive protein in insect physiology.
Trichoplax, the simplest known animal, contains an estrogen-related receptor: Implications for the evolution of vertebrate and invertebrate estrogen receptors

Although, as their names imply, vertebrate and invertebrate estrogen receptors (ERs) and estrogen-related receptors (ERRs) are related transcription factors, their evolutionary relationships to each other are not fully understood. We searched recently sequenced genome of Trichoplax, the simplest known animal, and genomes from three lophotrochozoans: Capitella, a worm, Helobdella robusta, a leech, and Lottia gigantea, a snail, to elucidate the origins and evolution of ERs and ERRs. BLAST found an ERR in Trichoplax, but no ER. BLAST searches of the lophotrochozaons found ERRs in all three and invertebrate ERs in Capitella and Lottia, but not in Helobdella. These database searches and a phylogenetic analyses indicate that invertebrate ERs arose in a protostome, and vertebrate ERs arose later in deuterostome.
Applied Proteomics in Breast Cancer

Breast cancer is the most commonly diagnosed cancer and remains the second most common cause of cancer-related deaths in women. Proteomics has been used in biomedical research for 20 years. However, the application of proteomics in breast cancer remains a small fraction of breast cancer research. Comprehensive analysis of proteins is seldom used in clinical practice. Analysis of single proteins still remains the standard practice in clinical laboratories. Despite the use of multiplex methods for protein analysis in preclinical research, it is challenging to apply these techniques in the clinical setting. In this review, we summarize the commonly implemented array-based and mass spectrometry-based proteomic techniques, and the application of biomarkers for a specific purpose or mechanisms involved in breast cancer biology. The ultimate goal of this review is to help clinicians and scientists for choosing the right techniques and understanding their potential with respect to prognosis and prediction of the treatment outcome.
Suppression of apoptosis by BRAF inhibitors through off-target inhibition of JNK signaling.

8537 Background: The advent of targeted therapy has revolutionized the treatment of cancer. The mutant BRAFV600E protein is found in over 50% of melanomas and thyroid carcinomas, resulting in eleva...
Wavelength division multiplexed light source monolithically integrated on a silicon photonics platform.

We demonstrate monolithic integration of a wavelength division multiplexed light source for silicon photonics by a cascade of erbium-doped aluminum oxide (Al2O3:Er3+) distributed feedback (DFB) lasers. Four DFB lasers with uniformly spaced emission wavelengths are cascaded in a series to simultaneously operate with no additional tuning required. A total output power of −10.9 dBm is obtained from the four DFBs with an average side mode suppression ratio of 38.1±2.5 dB. We characterize the temperature-dependent wavelength shift of the cascaded DFBs and observe a uniform dλ/dT of 0.02 nm/°C across all four lasers.
The Number of Monodromy Representations of Abelian Varieties of Low $p$-Rank

Abstract Let A g be an abelian variety of dimension g and p-rank λ ≤ 1 over an algebraically closed field of characteristic p > 0 . We compute the number of homomorphisms from π 1 et ( A g , a ) to G L n ( F q ) , where q is any power of p. We show that for fixed g, λ, and n, the number of such representations is polynomial in q, and give an explicit formula for this polynomial. We show that the set of such homomorphisms forms a constructible set, and use the geometry of this space to deduce information about the coefficients and degree of the polynomial. In the last section we prove a divisibility theorem about the number of homomorphisms from certain semidirect products of profinite groups into finite groups. As a corollary, we deduce that when λ = 0 , # Hom ( π 1 et ( A g , a ) , G L n ( F q ) ) | G L n ( F q ) | is a Laurent polynomial in q.
History of Childhood Maltreatment and College Academic Outcomes: Indirect Effects of Hot Execution Function.

Abstract In typical college samples, approximately one-third of students may have a history of childhood maltreatment, placing them at risk for struggles with college adaptation and achievement. Surprisingly little research has been conducted exploring this relationship. In the current study, we conducted an exploratory analysis to determine the degree to which executive function (EF) mediates the association between self-reported maltreatment history and college adaptation and academic achievement. Consistent with contemporary EF research, we distinguished between relatively “cool” EF tasks (i.e., performed in a context relatively free of emotional or motivational valence) and “hot” EF tasks that emphasize performance under greater more emotionally arousing conditions. Sixty-one male and female college undergraduates self-reported childhood maltreatment history (emotional abuse and neglect, physical abuse and neglect, and sexual abuse) on the Childhood Trauma Questionnaire (CTQ), and were given two EF measures: 1) Go-No-Go (GNG) test that included a Color Condition (cool); Neutral Face Condition (warm); and Emotion Face condition (hot), and 2) Iowa Gambling Task (IGT), a measure of risky decision making that reflects hot EF. Academic outcomes were: 1) grade point average (GPA: first-semester, cumulative, and semester concurrent with testing), and 2) Student Adaptation to College Questionnaire (SACQ). Correlational patterns suggested two EF scores as potential mediators: GNG reaction time (RT) in the Neutral Face condition, and IGT Block 2 adaptive responding. Indirect effects analyses indicated that IGT Block 2 adaptive responding mediated the relationship between CTQ Total score and 1st semester GPA, and between CTQ Emotional Abuse and concurrent GPA. Regarding college adaptation, we identified a consistent indirect effect of GNG Neutral Face RT on the relationship between CTQ Emotional Neglect and SACQ total, academic, social, and personal-emotional adaption scores. Our results demonstrate that higher scores on a child maltreatment history self-report negatively predict college academic outcomes as assessed by GPA and by self-reported adaptation. Further, relatively "hot" EF task performance on the IGT and GNG tasks serves as a link between child maltreatment experiences and college achievement and adaptation, suggesting that hot EF skills may be a fruitful direction for intervention efforts to improve academic outcomes for this population.
No pain no gain? Adjuvant effects of alum and monophosphoryl lipid A in pertussis and HPV vaccines

Development of non-infectious subunit vaccines is hampered by a slow pipeline of new adjuvants to replace or enhance alum in part because expectations of safety are high. Transient vaccine side effects are not clinical priorities because they cause no lasting harm and vaccine development has appropriately been focused on avoidance of serious adverse events. As a result, surprisingly little is known about the extent to which side effects caused by a vaccine's reactogencicity are predictive of successful immunization outcomes. Recent clinical studies of pertussis and human papillomavirus vaccines adjuvanted with alum or the TLR4 agonist monophosphoryl lipid A can be used to advance understanding of the relationship between vaccine side effects and immunization outcomes.
Functional brain connectivity in resting-state fMRI using phase and magnitude data.

Abstract Background The output of BOLD fMRI consists of a pair of magnitude and phase components. While the magnitude data has been widely accepted for brain function analysis, we can also make use of the phase data (unwrapped) since this is a good representation of the internal magnetic field. In this work, we discuss the use of fMRI phase data for brain function analysis. New methods The fMRI phase data taken from 100 subjects are preprocessed using standard SPM approaches. Group independent component analysis (ICA) is applied to the magnitude and phase data separately. We then compare the spatial patterns for both magnitude and phase data using an empirical spatial smoothing procedure. We also evaluate the magnitude and phase functional network connectivity (FC) matrices. Results We observed the positive/negative correlation-balanced functional connectivity in phase data, which is distinct from the positive correlation prevalence in magnitude data. The phase FC (pFC) structure is quite different from the magnitude FC (mFC) in functional clusters (on-diagonal blocks or cliques) and inter-cluster couplings (off-diagonal blocks). Comparison with existing Methods since both the magnitude and phase data of the fMRI signals are generated from the same magnetic source, either can be useful for brain function analysis from different perspective (per different measurements). Herein, we report on making use of resting-state fMRI phase data for brain functional analysis in comparison with magnitude data. This exploration in phase fMRI may provide a new arena for more comprehensive brain function analysis.
A 25 Gb/s 60 GHz digital power amplifier in 28nm CMOS

This paper presents a 60 GHz class-E digital power amplifier (DPA) that generates energy-efficient, non-constant envelope modulations up to 25 Gb/s. The DPA achieves a peak drain efficiency of 17.7% at a V sat of 7.4 dBm. By means of direct digital amplitude modulation of the 6-bit output stage, the DPA produces error-free, high-order constellations (16-QAM, 32-QAM, 64-QAM) up to 5 GSym/s with error vector magnitudes (EVMs) 3.5X higher data rates at comparable average efficiencies is achieved.
Matrices and Determinants

We have already noticed that a linear map o: k → k is completely determined by its value on one element of k, e.g., on 1. Also we noted that a linear map $$ \varphi :k^2 \to k $$ is determined by φ(1,0) and φ(0,1). We Will now see how a linear map $$ \varphi :V \to W $$ (V, W being vector over k of dimensions n, m) is determined by nm elements of k.
Plasmodesmata and Noncell Autonomous Signaling in Plants

Plasmodesmata are fundamental intercellular communication channels in plants that are essential for coordination of physiological and developmental signaling processes across cellular boundaries. The fact that creation of these membranous structures is considered one of the most crucial factors in the evolution of higher plants clearly states their unparalleled significance in plant systems. Plasmodesmata are also unique in their structure, in that they establish an endomembrane as well as a cytoplasmic continuum throughout the whole plant body by forming cytoplasmic strands that are lined with plasma membrane externally and endoplasmic reticulum internally. These structures, when assembled during cytokinesis by entrapment of endoplasmic reticular strands in the expanding cell plate, are called primary plasmodesmata. It is remarkable that plant cells have acquired an additional mechanism to produce secondary plasmodesmata by de novo biosynthesis postcytokinetically across existing cell walls, which in essence is necessary to maintain or increase symplasmic connectivity between expanding cells. This process is thought to occur through cell wall loosening and membrane fusion followed by deposition of new cell wall materials around the nascent protoplasmic strands. Perhaps, it is one of the most fascinating discoveries in plant biology that plasmodesmata are highly dynamic channels with the capacity to dilate and facilitate macromolecular trafficking despite the physical constraint imposed by the surrounding cell wall. It is also this activity through which plasmodesmata can act as supracellular checkpoint over intercellular transfer of signaling or information molecules. Exciting future discoveries in plasmodesmal biology are expected to be made by uncovering the molecular composition, anatomy, and transport mechanism of this fascinating yet incredibly recalcitrant biological structure.
Hypoglycemia and Hypoglycemia Unawareness During and Following Exercise

Attention to diet, including meal composition and timing, is integral to all athletes’ training programs. Athletes with type 1 diabetes mellitus (type 1 DM) face the added task of administering insulin to carefully match energy availability and requirements. Avoiding both hyper- and hypoglycemia is a continual challenge for all patients with type 1 DM but is even more difficult for athletes who experience extreme changes in fuel utilization between periods of rest and exercise.
Optical coherence tomography in neurophthalmology

Optical coherence tomography (OCT), widely used in the management of macular disorders and glaucoma, has proved its usefulness in many neurophthalmic disorders. OCT can quantify the retinal nerve fiber layer thickness and ganglion cell layer thickness and provides an idea about the neuronal integrity of the anterior visual pathway, which cannot be picked up by routine fundoscopy. Here, we are discussing some neurophthalmic and neurologic diseases where OCT can contribute to the diagnosis, disease monitoring and can provide prognostic information.
PD-1 blockade alters fate commitment of myeloid progenitors during tumor-mediated “emergency” myelopoiesis

PD-1 is an immune inhibitory receptor for which blocking agents have achieved significant success as anti-cancer therapeutics. The mechanism(s) of the how PD-1 compromises anti-tumor function and how such effect is reversed by PD-1 blockade remain poorly understood. The rapid change in hematopoietic output that occurs in response to immunologic stress is known as “emergency” myelopoiesis. This process is co-opted by tumors to enhance the generation of tumor-promoting myeloid cells, mostly undifferentiated myeloid-derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs). We analyzed the myeloid compartment of tumor-bearing mice and determined that myeloid cells express PD-1 and PD-L1. Using PD-1 KO mice or WT mice treated with PD-1 blocking antibody in cancer-driven myelopoiesis experiments we determined a cell-switch fate from MDSCs to effector myeloid cells. PD-1 deletion or blockade, which impaired tumor growth and metastases, stimulated the differentiation of hematopoietic progenitor cells and resulted in increase of Ly6C hi monocytes and monocyte-derived DC (mo-DC). Abrogation of PD-1 signaling enhanced the maturation of MDSCs by inducing the lineage commitment transcription factors IRF8, IRF4 and RORC1. IRF8 and IRF4 promote monocytes/macrophage and hinder granulocyte differentiation, whereas RORC1 is required for expansion of Ly6C hi monocytes and resolution of inflammation. These results reveal a role of the PD-1:PD-L1 pathway in the differentiation of lineage-committed myeloid progenitors to promote undifferentiated MDSCs and suppress effector monocytes/DCs. Switch of myeloid progenitor fate commitment might be a key mechanism by which PD-1 blockade mediates anti-tumor function.
Scholarship as conversation: Using book reviews to think about scholarly communication

I n the ACRL white paper “Intersections of Scholarly Communication and Information Literacy: Creating Strategic Collaborations for a Changing Academic Environment,” the authors suggested librarians should reach out to “formal undergraduate research programs where faculty are paired one-on-one with undergraduate students.” By partnering with research groups, librarians could introduce the concepts behind scholarly communication and the information cycle, thereby enhancing the undergraduate research experience.
Help Needed: Best Practices, Collaborative Advantage, and Library Websites

Around the world, building and managing library websites calls for solving problems. For instance, library administrators must resolve technical issues, like broken hyperlinks, as well as organizat...
Partially Shuffling the Training Data to Improve Language Models.

Although SGD requires shuffling the training data between epochs, currently none of the word-level language modeling systems do this. Naively shuffling all sentences in the training data would not permit the model to learn inter-sentence dependencies. Here we present a method that partially shuffles the training data between epochs. This method makes each batch random, while keeping most sentence ordering intact. It achieves new state of the art results on word-level language modeling on both the Penn Treebank and WikiText-2 datasets.
Gene regulation through dynamic actin control of nuclear structure

Bone marrow mesenchymal stem cells exist in a multipotential state, where osteogenic and adipogenic genomes are silenced in heterochromatin at the inner nuclear leaflet. Physical force, generated i...
Adversarial aircraft diversion and interception using missile herding techniques

When being pursued by guided munitions, a fixed wing aircraft is likely to attempt to avoid interception. If a team of autonomous missiles can learn how their motion affects the induced motion of their target, the exploitation of this knowledge can facilitate controlled diversion and interception of the target. Motivated by recent advances in the field of herding control, this paper details a novel control and estimation strategy for a team of missiles tasked with diverting a target aircraft from its planned path and intercepting it somewhere on a prescribed “safe" trajectory. A neural network-based estimation scheme is used to approximate the uncertain missile-target interactions online. The missile controllers leverage these estimates to ensure that the diversion and interception objectives are achieved. A rigorous Lyapunov-based analysis examines the stability of the closed loop error system.
Assessing Tumor Microenvironment of Metastasis Doorway-Mediated Vascular Permeability Associated with Cancer Cell Dissemination using Intravital Imaging and Fixed Tissue Analysis.

The most common cause of cancer related mortality is metastasis, a process that requires dissemination of cancer cells from the primary tumor to secondary sites. Recently, we established that cancer cell dissemination in primary breast cancer and at metastatic sites in the lung occurs only at doorways called Tumor MicroEnvironment of Metastasis (TMEM). TMEM doorway number is prognostic for distant recurrence of metastatic disease in breast cancer patients. TMEM doorways are composed of a cancer cell which over-expresses the actin regulatory protein Mena in direct contact with a perivascular, proangiogenic macrophage which expresses high levels of TIE2 and VEGF, where both of these cells are tightly bound to a blood vessel endothelial cell. Cancer cells can intravasate through TMEM doorways due to transient vascular permeability orchestrated by the joint activity of the TMEM-associated macrophage and the TMEM-associated Mena-expressing cancer cell. In this manuscript, we describe two methods for assessment of TMEM-mediated transient vascular permeability: intravital imaging and fixed tissue immunofluorescence. Although both methods have their advantages and disadvantages, combining the two may provide the most complete analyses of TMEM-mediated vascular permeability as well as microenvironmental prerequisites for TMEM function. Since the metastatic process in breast cancer, and possibly other types of cancer, involves cancer cell dissemination via TMEM doorways, it is essential to employ well established methods for the analysis of the TMEM doorway activity. The two methods described here provide a comprehensive approach to the analysis of TMEM doorway activity, either in naive or pharmacologically treated animals, which is of paramount importance for pre-clinical trials of agents that prevent cancer cell dissemination via TMEM.
An Updated Approach to Evaluation and Treatment of Helicobacter pylori Infection

Helicobacter pylori is a chronic bacterial infection that can lead to peptic ulcer disease, chronic gastritis, and gastric cancer. Its prevalence in the United States is lower than in most of the world, although specific populations are at particular risk for disease-related complications, including those with lower socioeconomic status and older adults. Since its discovery, there have been advances in H. pylori diagnosis and treatment, which are the focus of this review for general practice. Practice guidelines have expanded the role for treatment, despite traditional management algorithms resulting in diminished effectiveness as a result of increasing antibiotic resistance. In this context, new approaches warrant discussion. As such, this review aims to provide a clinical context and framework for the testing and rational treatment of H. pylori infection consistent with the available evidence.
WAYFINDING STUDY IN VIRTUAL ENVIRONMENTS: THE ELDERLY VS. THE YOUNGER-AGED GROUPS

This study aims to examine the impact of architectural wayfinding aids on wayfinding performances in comparison of the elderly group and the younger aged group. An ambulatory healthcare facility was simulated using Virtual Reality (VR) to develop two levels of wayfinding aids for the same environments. The base model included minimal wayfinding aids, and the design model included more wayfinding aids. The VR environment was presented in the form of video in order to test wayfinding performances at three different wayfinding decision points. Results showed that age and wayfinding aids impacted wayfinding performances. The younger-aged group performed wayfinding better compared to the elderly group. Participants who were tested in the design model were more successful in wayfinding compared to the elderly group. The elderly group reported that more salient wayfinding aids such as a big logo and paint colors helped their wayfinding while the younger-aged group reported less salient aids such as door designs as helpful wayfinding aids. When there were minimal wayfinding aids, the elderly participants needed to rely mostly on memory recall by remembering turns or paying close attention. When participants felt that the wayfinding test was difficult, their performances were less successful. Findings in this study suggest that wayfinding design for the elderly should consider the limited ability of recall and therefore, design wayfinding aids more frequently with more salient aids to avoid confusion. The elderly group needed to rely on their limited cognitive ability when there were not enough wayfinding aids, which make them experience difficulties in wayfinding.
The Effect of War on the U.S. Federal Courts of Appeals: an Analysis of U.S. Appeals Court Treatment of War Related Cases

How is judicial decisionmaking in the United States affected by the presence of war? To contribute to this question we analyzed changes in U.S. Courts of Appeals decisions during times of war and peace, bridging current analyses by assessing the influence of war on the outcome of civil rights cases and criminal rights cases and on war related cases only. Going beyond the sample database to identify cases related to the wars in question and using a measure that captures the intensity of war, we show that the courts are not immune to the changed circumstances during times of war and that judges on the U.S. Courts of Appeals tend to vote more conservatively in times of war and with increased intensity of war. These influences are even more pronounced in cases related to war and while war appears to produce changes in judicial behavior in non-trivial ways.
Color Terms, Linguistics of

The study of the linguistics of color terms has mostly been concerned with isolating the ‘basic’ color terms of a language: the smallest set of linguistically simplex expressions of the language with which a speaker can name any color.
Review of Physical Evidence in Forensic Science

The authors do not state the audience that this book was written for, but, judging from the level of the material and its length and breadth, it seems apparent that they had criminal investigators in mind. This is supported by the contents of the last chapter on legal aspects of forensic science, which deals almost exclusively with search and seizure issues.
The accuracy of self-reported hearing loss in older Latino-American adults.

The purpose of this study was to examine the accuracy of self-reported hearing loss in older Latino-American adults. Fifty-nine individuals, 32 women (mean age 62.2 years) and 27 men (mean age 62.4 years), participated. The questionnaire addressed hearing loss, hearing aid use, and other people's views of their hearing abilities. Based on the question, ‘Do you feel you have a hearing loss?’, the prevalence of self-reported hearing loss was 57.6%, with 56.3% of women and 59.3% of men reporting a hearing loss. Sensitivity, specificity, and accuracy were calculated using this question and compared to the pure-tone average (PTA) at 500, 1000, 2000, and 4000 Hz in the poorer ear. Overall, sensitivity was 75.7%, specificity was 72.7%, and accuracy was 74.6%. Results of this smaller scale study suggest that a single question, used as a screening measure, is both sensitive and specific for hearing loss in older Latino-American adults and may overcome language and cultural barriers. This question can be easily imp...
Scaling the data mining step in knowledge discovery using oceanographic data

Knowledge discovery from large acoustic images is a computationally intensive task. The data-mining step in the knowledge discovery process that involves unsupervised learning (clustering) consumes the bulk of the computation. We have developed a technique that allows us to partition the data, distribute it to different processors for training, and train a single system to join the results of the independent categorizers. We report preliminary results using this approach for knowledge discovery with large acoustic images having more than 10, 000 training instances.
Genetic dissection of DNA binding and luminescence gene activation by the Vibrio fischeri LuxR protein.

The Vibrio fischeri luminescence (lux) genes are regulated by the 250-amino-acid-residue LuxR protein and a V. fischeri metabolite termed autoinducer. The V. fischeri lux regulon consists of two divergently transcribed units. Autoinducer and LuxR activate transcription of the luxICDABE operon and autoregulate the luxR transcriptional unit. LuxR proteins with C-terminal truncations of up to 40 amino acid residues coded by plasmids with luxR 39-deletion mutations are functional in negative autoregulation as demonstrated by using a luxR::lacZ transcriptional fusion as a luxR promoter probe in Escherichia coli. The truncated LuxR proteins showed little or no ability to activate transcription of luxICDABE, as indicated by using luminescence as a sensitive indicator of promoter strength in E. coli. Besides having no detectable activity as positive regulators of luxICDABE, LuxR proteins with C-terminal truncations of more than 40 amino acid residues had reduced or no detectable activity as negative autoregulators. The results suggest that amino acid residues in LuxR prior to no. 211 are sufficient for lux DNA binding. Residues in the region of 211 to 250 constitute a C-terminal tail that appears to be involved in activation of luxICDABE transcription either by interacting physically with the transcription initiation complex or by affecting lux DNA in the vicinity of the promoter. Images
Spatial Heterogeneity of Bacterial Assemblages in Marine Sediments: The Influence of Deposit Feeding by Balanoglossus aurantiacus.

Abstract Densities and substrate utilization patterns of the bacterial assemblages of three intertidal sandflats were contrasted to investigate spatial heterogeneity. Possible influence of deposit-feeding Balanoglossus aurantiacus (Enteropneusta: Ptychoderidae) was also studied by comparing samples taken from the faecal mounds with surrounding sediments. While there were no significant differences in total bacterial abundance, carbon source utilization patterns, determined using Biolog GN microtitre plates, differed among the sandflats and within the sandflats for samples from grids more than 10 m apart. No consistent quantitative or qualitative differences were detected among clusters of ambient sediment samples taken less than 0·5 m apart. Qualitative differences in microbial assemblages were found between faecal mounds and ambient (>10 cm apart) sediment within a single intertidal flat. These differences were in part due to digestive removal of bacteria, as heterotrophic plate counts and response in Biolog plates (average well colour development, AWCD) were significantly higher for the surrounding sediment. However, when Biolog profiles were normalized to AWCD, it became clear that gut passage resulted in structural shifts in bacterial assemblages. These changes were due to digestion of a subset of ingested bacteria with the concomitant stimulation (or inoculation) of other groups, which were largely unculturable under the conditions employed. These findings illustrate that deposit feeding effects spatial heterogeneity in sedimentary bacterial assemblages. Given the ephemeral nature of these disturbed patches, however, it is not yet clear that deposit feeding is a primary determinant of microbial community structure in this sedimentary landscape.
Urokinase-type plasminogen activator receptor crosslinking in an NK cell line increases integrin surface expression by the MAP kinase/ERK 1/2 signaling pathway.

Urokinase-type plasminogen activator receptor (uPAR) is attached to cell membranes by a glycosylphosphatidylinositol (GPI) anchor, and as such is devoid of an intracellular domain, but is nevertheless able to initiate signal transduction. Herein, we report a relationship between integrins and uPAR on the surface of the human NK cell line, YT. Our data reveals that crosslinking uPAR, which mimics uPAR clustering at focal adhesion sites, causes increases in expression of the αM, αV, and β2 integrins on the surface of YT cells. Activation of the MEK/ERK signaling cascade occurs following uPAR crosslinking, as phosphorylation of both MEK 1/2 and ERK 1/2 results from receptor clustering. The MEK-specific inhibitors PD98059 and U0126 blocked MAP kinase phosphorylation; furthermore, PD98059 inhibited the increase in integrin expression induced by uPAR clustering. This study suggests that uPAR is a signaling receptor and regulator of integrins in NK cells and may impact NK cell function, including the potential for their accumulation within tumor metastases following adoptive transfer. J. Cell. Biochem. 89: 279–288, 2003. © 2003 Wiley-Liss, Inc.
Temperature-Dependent Sorption of Naphthalene, Phenanthrene, and Pyrene to Low Organic Carbon Aquifer Sediments

Sorption experiments were conducted with naphthalene, phenanthrene, and pyrene on low organic carbon sediments at 4 and 26 °C using batch and column techniques. Experimental controls ensured the absence of biologic and photolytic activity and colloid-free solution supernatants. Equilibrium distribution coefficients (Kd) increased 1.1−1.6 times with a decrease in temperature of 22 °C. Fraction instantaneous sorption (F) values did not change significantly with a decrease in temperature of 22 °C. Desorption rate constants (k2) decreased 1.2−2.6 times with a decrease in temperature of 22 °C. Times to equilibrium were at least 40 h. The magnitude of observed Kd and k2 values and the effect of temperature on Kd (e.g., low enthalpy of sorption) are consistent with sorbate partitioning between the aqueous phase and small amounts of organic matter (foc = 0.02%) on the sediments. The temperature dependence of Kd and k2 may be small as compared to the effects of heterogeneities in field-scale aquifer systems. Thus,...
Does establishing a bariatric surgery fellowship training program influence operative outcomes

Background Roux-en-Y gastric bypass (RYGB) has a long learning curve that may be reflected in operative outcomes. This study sought to assess whether training a fellow has an impact on the operative outcomes of the training program.
Tuning in to a single molecule: vibrational spectroscopy with atomic resolution

It has recently been shown that the scanning tunneling microscope can be used to obtain the vibrational spectrum of a single molecule on a surface. The ability to obtain both spatial and precise energetic information with angstrom-scale resolution should lead to an enhancement in our ability to understand and engineer surfaces at the atomic level.
Water relations and humidity-related metabolism of the desert snail Rabdotus schiedeanus (Pfeiffer) (Helicidae)

Abstract 1. 1. Rates of water loss for Rabdotus schiedeanus varies inversely with shell-free weight and aperture area among deat snails, but these factors did not influence water loss in living animas. 2. 2. Greater water-loss rates were found for dead snails than for inactive one, suggesting cutaneous regulation 3. 3. Small snails drank and retained proportionately greater amounts of water than did large snails. 4. 4. Oxygen consumption at 25°C increased with increasing humidity.