cssi/SciSciGPT-SciSciNet huggingface dataset:
Community structure and metabolism through reconstruction of microbial genomes from the environment

Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.
Fetal Ventricular Mass Determination on Three-Dimensional Echocardiography Studies in Normal Fetuses and Validation Experiments

Background— Estimation of ventricular volume and mass is important for baseline and serial evaluation of fetuses with normal or abnormal hearts. Direct measurement of chamber wall volumes and mass can be made without geometric assumptions by 3D fetal echocardiography. Our goals were to determine the feasibility of using fast nongated 3D echocardiography for fetal volumetric and mass assessments, to validate the accuracy of the ultrasound system and the measurement technique, and if satisfactory, to develop normal values for fetal ventricular mass during the second and third trimesters. Methods and Results— This was a prospective outpatient study of 90 consecutive normal pregnancies during routine obstetric services at Oregon Health & Science University (Portland). Optimized 3D volumes of the fetal thorax and cardiac chambers were rapidly acquired and later analyzed for right and left ventricular mass by radial summation technique from manual epicardial and endocardial traces. Experiments to validate the u...
Territorial multi-robot task division

This work demonstrates the application of the distributed behavior-based approach to generating a multirobot controller for a group of mobile robots performing a clean-up and collection task. The paper studies a territorial approach to the task in which the robots are assigned individual territories that can be dynamically resized if one of the robots malfunctions, permitting the completion of the task. The described controller is implemented on a group of four IS Robotics R2e mobile robots. Using a collection of experimental robot data, we empirically derive and demonstrate most effective foraging in our domain, and show the decline of performance of the space division strategy with increased group size.
Wine, Beer, and Spirits Are They Really Horses of a Different Color?

The study of alcohol and its effects on health has a long history, ranging from anecdotal accounts in biblical times to more recent rigorous studies of populations with hundreds of thousands of participants. The largest studies suggest that men and women who drink 1 to 2 drinks per day on average have lower total mortality rates,1–3⇓⇓ reflected in lower incidence of coronary heart disease, diabetes, and in some populations, ischemic stroke. The clear benefit of moderate alcohol consumption on risk of coronary disease has been documented in almost 100 studies. The early hypothesis that the apparent benefit might be explained by inclusion of sicker individuals among the nondrinkers (“sick quitter effect”) has been decisively refuted in studies that excluded those with poor health at baseline or included only lifelong nondrinkers in the comparison group. Although no randomized trials with clinical end points have been conducted, further evidence for a causal link between moderate alcohol consumption and lower risk of coronary disease derives from genetic and metabolic studies. The finding of a strong interaction between alcohol intake and a common polymorphism in the gene for alcohol dehydrogenase4 strongly supports causality because such a result cannot plausibly be attributed to confounding factors (that is, the polymorphism can be considered as distributed at random with regard to other lifestyle practices like diet and exercise). Our understanding of the beneficial metabolic …
The cytohesin guanosine exchange factors (GEFs) are required to promote HGF‐mediated renal recovery after acute kidney injury (AKI) in mice

The lack of current treatment and preventable measures for acute kidney injury (AKI) in hospitalized patients results in an increased mortality rate of up to 80% and elevated health costs. Additionally, if not properly repaired, those who survive AKI may develop fibrosis and long-term kidney damage. The molecular aspects of kidney injury and repair are still uncertain. Hepatocyte growth factor (HGF) promotes recovery of the injured kidney by inducing survival and migration of tubular epithelial cells to repopulate bare tubule areas. HGF-stimulated kidney epithelial cell migration requires the activation of ADP-ribosylation factor 6 (Arf6) and Rac1 via the cytohesin family of Arf-guanine-nucleotide exchange factors (GEFs), in vitro. We used an ischemia and reperfusion injury (IRI) mouse model to analyze the effects of modulating this signaling pathway on kidney recovery. We treated IRI mice with either HGF, the cytohesin inhibitor SecinH3, or a combination of both. As previously reported, HGF treatment promoted rapid improvement of kidney function as evidenced by creatinine (Cre) and blood urea nitrogen (BUN) levels. In contrast, simultaneous treatment with SecinH3 and HGF blocks the ability of HGF to promote kidney recovery. Immunohistochemistry showed that HGF treatment promoted recovery of tubule structure, and had enhanced levels of active, GTP-bound Arf6 and GTP-Rac1. SecinH3 treatment, however, caused a dramatic decrease in GTP-Arf6 and GTP-Rac1 levels when compared to kidney sections from HGF-treated IRI mice. Additionally, SecinH3 counteracted the renal reparative effects of HGF. Our results support the conclusion that cytohesin function is required for HGF-stimulated renal IRI repair.
What Might Bring Regular Order Back to the House

It is not hard to find critics of how the U.S. Congress operates today. Two of the most prominent, Thomas Mann and Norman Ornstein, have bemoaned in particular Congress's failure to follow “regular order,” which in their 2006 book The Broken Branch they describe as a legislative process that incorporates “discussion, debate, negotiation, and compromise” (Mann and Ornstein 2006, 170).
Multiscale difference equation signal modeling and analysis techniques

A novel signal modeling technique in which an arbitrary sequence of data points is represented as samples of the solution to a multiscale difference equation is proposed. Such a model completely characterizes a number of higher derivatives of the signal as well as the signal itself. It provides a recursive signal interpolation mechanism as a function of scale. It also leads to multigrid type signal filtering, detection and estimation algorithms. The existence and uniqueness of L/sub 1/ and L/sub 2/ solutions to the multiscale difference equation are first investigated. The paper generalizes the results obtained for the two scale difference equation. Next, we provide conditions for the existence of unique solution to such an equation. Finally, techniques for modeling an arbitrary set of data samples as samples of the solution to a multiscale difference equation are presented. Specifically, we describe the encoding and decoding steps in these techniques. We also prevent audio signal modeling examples to illustrate multiscale difference equation models. >
The Million Dollar Letter: Some Hints on How to Write One.

This article suggests ways of writing a truly effective cover letter, an extremely important document in the search for a job. First, features gleaned from 13 model letters in technical writing textbooks yield figures on the number of words, sentences, and paragraphs per letter, plus the average number of words per sentence and paragraph, information helpful to those with little or no knowledge of how to write a strong cover letter. Second, the article surveys what the textbook writers offer as advice about the rhetorical principles that should be employed in composing cover letters. One piece of advice given by almost all of the experts is that writers should try to exude an energetic attitude, yet these same authorities do not delineate just how to display such a posture in the letters themselves. Third, examination of the letters reveals that one way that experts insert verve into cover letters is to use verbals, particularly gerunds, participles, and infinitives. In fact, 92.58% of the sentences in th...
Lithologically influenced geomorphic responses to Holocene climatic changes in the Southern Colorado Plateau, Arizona: A soil-geomorphic and ecologic perspective

Abstract The semiarid landscape occupied by the Navajo and Hopi peoples on the Colorado Plateau in northeastern Arizona in the southwestern United States is characterized by an extensive network of deeply incised arroyos. Since the early 20th century, many researchers have proposed that the recent formation of arroyos in this region and also many attributes of modern vegetation communities were caused directly by overgrazing of vegetation by domestic livestock of the Navajo. Other researchers, however, have proposed other causes for such features, such as climatic change. We believe that the landforms, soils and vegetation of a small area located on Antelope Mesa in this region, underlain by the highly erodible materials of the Miocene Bidahochi Formation, may have been more sensitive to minor climatic changes of the Holocene than landscapes of massive Mesozoic sandstones that dominate the Colorado Plateau. In the Antelope Mesa area, the presence of actively filling channels rather than arroyos in the upper parts of many drainage basins and associated soils and ecologic patterns indicate that the aggradation (1) was initiated in downstream reaches and within the past two centuries, (2) may be linked to recently accelerated slope erosion, and (3) is unrelated to past or ongoing grazing. This suggests the ongoing aggradation may be related to recent minor climatic changes. Geochronologic and soil-geomorphic evidence indicate that the most recent cycle of arroyo incision and filling may be a small-scale analogue for larger-magnitude, older cycles that produced regionally recognizable, paired terraces that are attributable to previous Holocene climate changes. We propose that climatic change, and more specifically, increases in precipitation, caused an acceleration in the erosion of the steep, typically minimally vegetated slopes of the Bidahochi Formation. The beginning of the ‘Neoglacial Period’ (ca. 2–3 ka), effects of which are documented by other proxy records in this region, may be the climatic change that triggered widespread deposition of a large, mid-Holocene alluvial unit in this region. Alternating episodes of eolian activity and soil formation in the study area and in this general region provide independent evidence of Holocene climatic changes. Our interpretations of the origin of the cut-and-fill cycles that emphasize the role of drainage basin lithology and differ significantly from previous interpretations emphasize the linkage of climatic changes, groundwater levels and arroyo incision. This study reveals the importance of integrating soil and ecologic studies with geomorphologic research; such an approach may be critical in helping understand how anthropogenically induced climatic changes of the next century could impact geomorphic processes and the ecology of arid and semiarid regions.
Atomic Structure of Bacteriophage Sf6 Tail Needle Knob

Podoviridae are double-stranded DNA bacteriophages that use short, non-contractile tails to adsorb to the host cell surface. Within the tail apparatus of P22-like phages, a dedicated fiber known as the “tail needle” likely functions as a cell envelope-penetrating device to promote ejection of viral DNA inside the host. In Sf6, a P22-like phage that infects Shigella flexneri, the tail needle presents a C-terminal globular knob. This knob, absent in phage P22 but shared in other members of the P22-like genus, represents the outermost exposed tip of the virion that contacts the host cell surface. Here, we report a crystal structure of the Sf6 tail needle knob determined at 1.0 Å resolution. The structure reveals a trimeric globular domain of the TNF fold structurally superimposable with that of the tail-less phage PRD1 spike protein P5 and the adenovirus knob, domains that in both viruses function in receptor binding. However, P22-like phages are not known to utilize a protein receptor and are thought to directly penetrate the host surface. At 1.0 Å resolution, we identified three equivalents of l-glutamic acid (l-Glu) bound to each subunit interface. Although intimately bound to the protein, l-Glu does not increase the structural stability of the trimer nor it affects its ability to self-trimerize in vitro. In analogy to P22 gp26, we suggest the tail needle of phage Sf6 is ejected through the bacterial cell envelope during infection and its C-terminal knob is threaded through peptidoglycan pores formed by glycan strands.
Person Perception, Self-Identity, and Ethnic Group Preference in Anglo, Black, and Chicano Preschool and Third-Grade Children

Seventy-two preschool and 68 third-grade Anglo, Black, and Chicano children were shown color photographs of young male adults from the same three ethnic groups as Ss. All children were able to discriminate between the photographs of the white and Black males, but the preschool Ss were unable to make the finer discrimination between the Anglo and Chicano photographs. All pools of Ss indicated the appropriate photograph when asked which looked most like them. Among the preschool Ss neither the Blacks nor the Chicanos expressed a significant preference for their own ethnic group, while a significant number of the Anglo Ss selected the Anglo photograph as the one they liked the most. At the third-grade level, only the Chicano Ss displayed a strong preference for their own ethnic group.
Nutrient Composition of Commercially Spray-Dried Egg Products

Abstract Nutrient composition analyses of three commercially spray-dried whole egg, white, and yolk products were conducted. Samples were obtained from industrial sources, pooled, packaged under a nitrogen atmosphere (except white), and stored under refrigeration. Values were obtained for total nitrogen, lipid, calories, ash, amino acids, minerals, fatty acids, and vitamins. An equation, whole egg = .28 egg white + .72 egg yolk, relates the amounts of each component in the three products. Prior to this work most data on egg products were adapted from shell egg values.
Management of carcinoma in situ of the bladder: best practice and recent developments

Management of carcinoma in situ of the bladder remains a complex and challenging endeavor due to its high rate of recurrence and progression. Although it is typically grouped with other nonmuscle invasive bladder cancers, its higher grade and aggressiveness make it a unique clinical entity. Intravesical bacillus Calmette-Guerin is the standard first-line treatment given its superiority to other agents. However, high rates of bacillus Calmette-Guerin failure highlight the need for additional therapies. Radical cystectomy has traditional been the standard second-line therapy, but additional intravesical therapies may be more appealing for non-surgical candidates and patients refusing cystectomy. The subject of this review is the treatment strategies and available therapies currently available for carcinoma in situ of the bladder. It discusses alternative intravesical treatment options for patients whose condition has failed to respond to bacillus Calmette-Guerin therapy and who are unfit or unwilling to undergo cystectomy.
The Bystander Effect in Radiation Oncogenesis: II. A Quantitative Model

Abstract Brenner, D. J., Little, J. B. and Sachs, R. K. The Bystander Effect in Radiation Oncogenesis: II. A Quantitative Model. There is strong evidence that biological response to ionizing radiation has a contribution from unirradiated “bystander” cells that respond to signals emitted by irradiated cells. We discuss here an approach incorporating a radiobiological bystander response, superimposed on a direct response due to direct energy deposition in cell nuclei. A quantitative model based on this approach is described for α-particle-induced in vitro oncogenic transformation. The model postulates that the oncogenic bystander response is a binary “all or nothing” phenomenon in a small sensitive subpopulation of cells, and that cells from this sensitive subpopulation are also very sensitive to direct hits from α particles, generally resulting in a directly hit sensitive cell being inactivated. The model is applied to recent data on in vitro oncogenic transformation produced by broad-beam or microbeam α-p...
Non-Euclidean Constructions

Always write in your books. You may be a silly person—for though your reading my book is rather a contrary presumption, yet it is not conclusive—and your observations may be silly or irrevelant, but you cannot tell what use they may be of long after you are gone where Budgeteers cease from troubling. (Budget, vol. 2, p. 265.)
Bandgap Guidance of High-order Modes in a Two-dimensional Induced Defect

We demonstrate high-order defect modes in an optically induced two-dimensional photonic lattice with a negative (low-index) defect. Experimental results are corroborated by numerical simulations.
Influence of electronic spin and spin-orbit coupling on decoherence in mononuclear transition metal complexes

Enabling the rational synthesis of molecular candidates for quantum information processing requires design principles that minimize electron spin decoherence. Here we report a systematic investigation of decoherence via the synthesis of two series of paramagnetic coordination complexes. These complexes, [M(C2O4)3](3-) (M = Ru, Cr, Fe) and [M(CN)6](3-) (M = Fe, Ru, Os), were prepared and interrogated by pulsed electron paramagnetic resonance (EPR) spectroscopy to assess quantitatively the influence of the magnitude of spin (S = (1)/2, (3)/2, (5)/2) and spin-orbit coupling (ζ = 464, 880, 3100 cm(-1)) on quantum decoherence. Coherence times (T2) were collected via Hahn echo experiments and revealed a small dependence on the two variables studied, demonstrating that the magnitudes of spin and spin-orbit coupling are not the primary drivers of electron spin decoherence. On the basis of these conclusions, a proof-of-concept molecule, [Ru(C2O4)3](3-), was selected for further study. The two parameters establishing the viability of a qubit are a long coherence time, T2, and the presence of Rabi oscillations. The complex [Ru(C2O4)3](3-) exhibits both a coherence time of T2 = 3.4 μs and the rarely observed Rabi oscillations. These two features establish [Ru(C2O4)3](3-) as a molecular qubit candidate and mark the viability of coordination complexes as qubit platforms. Our results illustrate that the design of qubit candidates can be achieved with a wide range of paramagnetic ions and spin states while preserving a long-lived coherence.
Love of Angiotensin-Converting Enzyme Inhibitors in the Time of Cholera

The highly acclaimed novel Love in the Time of Cholera by the Nobel Prize-winning Colombian author Gabriel Garcia Marquez is a brilliant exploration of the complexity of love, specifically the struggle between our attraction to the ideal and depraved dimensions of love and the importance of
Pregaming, Drinking Duration, and Movement as Unique Predictors of Alcohol Use and Cognitions Among Mandated College Students

ABSTRACTBackground: Pregaming is a common phenomenon among college students and is associated with increased risks such as heavy drinking, alcohol-related consequences, and violating campus alcohol policies. However, the mechanism by which pregaming increases student risk is unclear. Objectives: The current study aimed to delineate the role of personal endorsement of pregaming, duration of an entire drinking episode on the night of an alcohol violation, and movement from one location to another in predicting alcohol use and violation-related cognitions. Methods: Participants (N = 113) were college students who had received an alcohol violation. Hierarchical multiple regressions were conducted to investigate the predictive value of pregaming endorsement, duration of drinking, and movement on drinking behaviors [number of drinks consumed and estimated blood alcohol content (eBAC)] on the night of the alcohol violation as well as violation-related cognitions (responsibility, aversiveness). Results: Pregaming...
Relationship between Intelligence Development and Level of Gross Motor Function Classification in Children with Cerebral Palsy

Objective To investigate the level and structure of intelligence in children with cerebral palsy(CP) and to analyze the relationship between intelligence development and severity degree of gross motor function.Methods One hundred and eight children with CP were selected from Nanhai Maternity and Children's Hospital Affiliated to Guangzhou University of Traditional Chinese Medicine from Jan.2008 to Dec.2008.Their capability of motor behavior,language behavior,individual behavior and social behavior were assessed by Gesell Developmental Scale(GDS). Their gross motor function was evaluated by Gross Motor Function Classification System(GMFCS). The relationship between severity degree (GMFCS) and the development of motor,language,individual sociability and social adaptation were also discussed.Results One hundred and one children had been found with mental retardation among 108 cases,accounting for 93.5 percent.Scores of motor behavior was 29.08±18.05,scores of language behavior was 37.96±23.45,scores of individual behavior was 34.65±21.43,and scores of social behavior was 33.43±22.23.There was significant difference between scores of motor behavior and language behavior(Pa0.05).Gross function classification in children with CP was negatively correlated with their scores of GDS-DQ(r=-0.739,-0.632,-0.659,-0.679,Pa0.01).Conclusions Most children with CP have metal retardation,which is shown in the abnormal intelligence structure and the slow development of social adaptation,individual sociability,language behavior and motor behavior. A negative correlation was found between the severity degree of gross motor functions and the level of mental development. The higher GMFCS level is,the slower the intelligence develops. More attention should be paid to the recovery of intelligence development of the children with CP,especially those with serious motor retardation.
Research on Key Technologies of Information Security Protection for Industrial Control Systems

The risk of information security in industrial control system is rising fast recently. This paper puts forward a security protection research framework, which combines a protection system, specifications and standards, a security simulation platform, key technologies of attack and defense, research and development of security products, and so on. The paper provides an integrated solution covering the security protection system,specifications and standards, simulation validation, protection technologies, protection products and assessment service, which provides a full range of technical support for industrial control system.
Thinking of Speech Enhancement Technology and Strategy

For the speech signal,voice quality is greatly affected by the noise.Speech enhancement techniques must be used to suppress background noise,and improve voice quality and voice clear degrees.In this paper,the current speech enhancement algorithms are analyzed and researched from learning the history of the development of the speech enhancement algorithms.On the basis of these,the problems of speech enhancement algorithms meeting and being solved are further analyzed.
Research of Effect and Strategy about Negative Factors of Mass Media on China Contemporary Culture-shaping

The process of contemporary culture-shaping has a close relationship with mass communication that is the development of culture promotes the development of mass communication also the improvement of the the-ory on the mass media and the accumulation of practice made great impact on the formation and development of culture at the same time.However because of the negative factors of mass media as follow complex contents rigid mode limited technology weak gatekeeper and varying function and so on we should see that it is not all positive the mass media affects culture'formation and development.This article generalizes the relationship between mass media and culture-shaping analyzes the negative factors of mass media and the causes of it and summarizes the negative effects during the formation of culture.Furthermore it proposes the strategy of avoiding the negative effects so as to promote the positive effects of the mass communication's impact on cultural shaping.
Effect of Intragastric Balloons on Liver Enzymes: A Systematic Review and Meta-Analysis

Background Intragastric balloons (IGBs) are safe and effective in inducing weight loss in obese patients. The objective of this study was to review and analyze the available data of the effect of IGB on markers of nonalcoholic fatty liver disease (NAFLD) and liver enzymes.
In support of psychoanalyzing literary characters.

Psychanalyse appliquee a la litterature: psychanalyse du texte ou de son auteur? On etudie ici Paul, le heros d'un roman de DH Lawrence: «The Rocking Horse Winner»
Using Video in Web-Based Listening Tests

With sophisticated multimedia technology, there is a renewed interest in the relationship between visual and auditory channels in assessing listening comprehension (LC). Research on the use of visuals in assessing listening has emerged with inconclusive results. Some learners perform better on tests which include visual input (Wagner, 2007) while others have found no difference in the performance of participants on the two test formats (Batty, 2015). These mixed results make it necessary to examine the role of using audio and video in LC as measured by L2 listening tests. The current study examined the effects of two different types of listening support on L2 learners’ comprehension: (a) visual aid in a video with input modified with redundancy and (b) no visuals (audio-only input) with input modified with redundancy. The participants of this study included 246 Spanish students enrolled in two different intermediate Spanish courses at a large Midwestern university who participated in four listening tasks either with video or with audio. Findings of whether the video serves as a listening support device and whether the course formats differ on intermediate-level Spanish learners’ comprehension will be shared as well as participants’ preferences with respect to listening support.
Reconfigurable analog classifier for knee-joint rehabilitation

We present a System-On-Chip Field Programmable Analog Array (FPAA) for analyzing and processing the signals off an accelerometer for a wearable joint health assessment device. FPAAs have been shown to compute with an efficiency of 1000 times, as well as area efficiencies of 100 times, more than digital solutions. This work presents a low power signal processing system which allows us to extract features from the output of the accelerometer. These features are used by the classifier, implemented using a vector matrix multiplication and a two output 1-winner-take-all, to detect flexion and extension cycles in the subject. The compiled design consumes 0.636 μW of power for the front end analog signal processing chain where as the single layer classifier uses 13 μW of power. Thus the system is highly suitable for wearable applications where power consumption is a major concern. The current FPAA is fabricated in a 0.35 μm CMOS process and is operated at a power supply of 2.5 volts. The Gm-C filters and other circuits are operated in the subthreshold regime of the transistor to obtain the highest transconductance to current ratio offered by the process.
Neurally-based algorithms for image processing

One of the more difficult problems in image processing is segmentation. The human brain has an ability that is unmatched by any current technology for breaking down the world into distributed features and reconstructing them into distinct objects. Neurons encode information both in the number of spikes fired in a given time period, which indicates the strength with which a given local feature is present, and in the temporal code or relative timing of the spike, indicating whether the individual features are part of the same or different objects. Neurons that respond to contiguous stimuli produce synchronous oscillations, while those that are not fire independently. Thus, neural synchrony could be used as a tag for each pixel in an image indicating to which object it belongs. We have developed a simulation based on the primary visual cortex. We found that neurons that respond to the same object oscillate synchronously while those that respond to different objects fire independently.
Rapamycin Eye Drops Suppress Lacrimal Gland Inflammation In a Murine Model of Sjögren's Syndrome.

Purpose To evaluate the efficacy of topical rapamycin in treating autoimmune dacryoadenitis in a mouse model of Sjogren's syndrome. Methods We developed rapamycin in a poly(ethylene glycol)-distearoyl phosphatidylethanolamine (PEG-DSPE) micelle formulation to maintain solubility. Rapamycin or PEG-DSPE eye drops (vehicle) were administered in a well-established Sjogren's syndrome disease model, the male nonobese diabetic (NOD) mice, twice daily for 12 weeks starting at 8 weeks of age. Mouse tear fluid was collected and tear Cathepsin S, a putative tear biomarker for Sjogren's syndrome, was measured. Lacrimal glands were retrieved for histological evaluation, and quantitative real-time PCR of genes associated with Sjogren's syndrome pathogenesis. Tear secretion was measured using phenol red threads, and corneal fluorescein staining was used to assess corneal integrity. Results Lymphocytic infiltration of lacrimal glands from rapamycin-treated mice was significantly (P = 0.0001) reduced by 3.8-fold relative to vehicle-treated mice after 12 weeks of treatment. Rapamycin, but not vehicle, treatment increased tear secretion and decreased corneal fluorescein staining after 12 weeks. In rapamycin-treated mice, Cathepsin S activity was significantly reduced by 3.75-fold in tears (P < 0.0001) and 1.68-fold in lacrimal gland lysates (P = 0.003) relative to vehicle-treated mice. Rapamycin significantly altered the expression of several genes linked to Sjogren's syndrome pathogenesis, including major histocompatibility complex II, TNF-α, IFN-γ, and IL-12a, as well as Akt3, an effector of autophagy. Conclusions Our findings suggest that topical rapamycin reduces autoimmune-mediated lacrimal gland inflammation while improving ocular surface integrity and tear secretion, and thus has potential for treating Sjogren's syndrome-associated dry eye.
A novel physiological role for ARF1 in the formation of bidirectional tubules from the Golgi

Capitalizing on CRISPR/Cas9 gene-editing techniques and super-resolution nanoscopy, we explore the role of the small GTPase ARF1 in mediating transport steps at the Golgi. Besides its well-established role in generating COPI vesicles, we find that ARF1 is also involved in the formation of long (∼3 µm), thin (∼110 nm diameter) tubular carriers. The anterograde and retrograde tubular carriers are both largely free of the classical Golgi coat proteins coatomer (COPI) and clathrin. Instead, they contain ARF1 along their entire length at a density estimated to be in the range of close packing. Experiments using a mutant form of ARF1 affecting GTP hydrolysis suggest that ARF1[GTP] is functionally required for the tubules to form. Dynamic confocal and stimulated emission depletion imaging shows that ARF1-rich tubular compartments fall into two distinct classes containing 1) anterograde cargoes and clathrin clusters or 2) retrograde cargoes and coatomer clusters.
Two-Phase Flow

This chapter is the third that presents an example application of TCAT to a porous medium flow and transport problem. Single-phase flow was modeled in Chap. 9. The analysis considered three entities: a fluid phase, w, a solid phase, s, and the interface between the phases, ws. In Chap. 10, the additional feature of chemical species transport was added to the analysis.
Generalized integrated framework for modelling communications and electric power infrastructure resilience

This paper presents a quantitative framework for modeling electric power and communications infrastructures resilience. While in the past, resilience models applied to these infrastructures have focused on technological aspects, a fundamental novel aspect of the herein presented framework is the integral inclusion of models for human-driven processes, such as logistics, that influences recovery speed. Another fundamental novel aspect of the presented modeling framework is the generalized representation of dependencies and the characterization of the role that service buffers, such as energy storage, have on representing dependencies of associated services. Infrastructure system models combine three interconnected domains, each mathematically represented by at least one graph: a physical domain, a human/organizational domain, and a cyber domain. Each of the graphs that form the proposed framework represent the provision of a service. Thus, modeling of functional dependencies is inherently part of the developed models.
Association of Pathological Fibrosis With Renal Survival Using Deep Neural Networks.

Introduction Chronic kidney damage is routinely assessed semiquantitatively by scoring the amount of fibrosis and tubular atrophy in a renal biopsy sample. Although image digitization and morphometric techniques can better quantify the extent of histologic damage, we need more widely applicable ways to stratify kidney disease severity. Methods We leveraged a deep learning architecture to better associate patient-specific histologic images with clinical phenotypes (training classes) including chronic kidney disease (CKD) stage, serum creatinine, and nephrotic-range proteinuria at the time of biopsy, and 1-, 3-, and 5-year renal survival. Trichrome-stained images processed from renal biopsy samples were collected on 171 patients treated at the Boston Medical Center from 2009 to 2012. Six convolutional neural network (CNN) models were trained using these images as inputs and the training classes as outputs, respectively. For comparison, we also trained separate classifiers using the pathologist-estimated fibrosis score (PEFS) as input and the training classes as outputs, respectively. Results CNN models outperformed PEFS across the classification tasks. Specifically, the CNN model predicted the CKD stage more accurately than the PEFS model (κ = 0.519 vs. 0.051). For creatinine models, the area under curve (AUC) was 0.912 (CNN) versus 0.840 (PEFS). For proteinuria models, AUC was 0.867 (CNN) versus 0.702 (PEFS). AUC values for the CNN models for 1-, 3-, and 5-year renal survival were 0.878, 0.875, and 0.904, respectively, whereas the AUC values for PEFS model were 0.811, 0.800, and 0.786, respectively. Conclusion The study demonstrates a proof of principle that deep learning can be applied to routine renal biopsy images.
The Effect of Crowding on Urban Families

Many, but not all, studies of crowding in animal populations show that compressed living conditions cause marked declines in health, life expectancy, maternal care and increases in aggression and aberrant social behavior (2, 4, 11). While some observers apply these findings directly to human populations, others suggest that man’s advanced ability to adapt makes such application questionable at best (6).
Extracorporeal Photopheresis Improves Survival in Hematopoietic Cell Transplant Patients with Bronchiolitis Obliterans Syndrome without Significantly Impacting Measured Pulmonary Functions

Abstract We carried out the first matched retrospective cohort study aimed at studying the safety and efficacy of extracorporeal photopheresis (ECP) for bronchiolitis obliterans syndrome (BOS) after allogeneic hematopoietic cell transplantation (HCT). Medical records of 1325 consecutive adult patients who underwent HCT between 2005 and 2015 were reviewed. Seventy-four patients (median age, 51 years) with a diagnosis of BOS were included in the study. After propensity-score matching for BOS severity, 26 patients who underwent ≥3 months of ECP were matched to 26 non–ECP-treated patients, who were assigned an index date corresponding to the ECP start date for their matched pairs. The rate of decline in FEV1 percentage predicted (FEV1PP) decreased after ECP initiation (and after index date in the non-ECP group), with no significant difference between the 2 groups (P = .33). On a multivariable analysis that included baseline transplant and pulmonary function test variables, matched related donor HCT (HR, .1; 95% CI, .03 to .5; P = .002), ECP (HR, .1; 95% CI, .01 to .3; P = .001), and slower rate of decline in FEV1PP before the ECP/index date (HR, .7; 95% CI, .6 to .8; P = .001) were associated with a better overall survival. At last follow-up, non–ECP-treated patients were more likely to be on >5 mg daily dose of prednisone (54% versus 23%; P = .04) and had a greater decline in their Karnofsky performance score (mean difference, −9.5 versus −1.6; P = .06) compared with ECP-treated-patients. In conclusion, compared with other BOS-directed therapies, ECP was found to improve survival in HCT patients with BOS, without significantly impacting measured pulmonary functions. These findings need prospective validation in a larger patient cohort.
Neural correlates of global and specific cognitive deficits in schizophrenia.

Abstract Cognitive deficits are a core feature of schizophrenia, but the neural mechanisms that contribute to these characteristics are not fully understood. This study investigated whether volume of the dorsal lateral prefrontal cortex (DLPFC), inferior frontal gyrus (IFG), hippocampus, and white matter were associated with impairment in specific cognitive domains, including executive functioning, working memory, verbal memory, verbal fluency, processing speed, versus global functioning. The multi-site data used in this study was collected from the Bipolar and Schizophrenia Network on Intermediate Phenotypes (B-SNIP), and consisted of 206 healthy controls and 247 individuals with either schizophrenia or schizoaffective disorder. The neuroimaging data was segmented based on the Destrieux atlas in FreeSurfer. Linear regression analyses revealed that global cognition, executive functioning, working memory, and processing speed were associated with all brain structures, except the DLPFC was only associated with executive fucntion. When controlling for the global cognitive deficit, executive function was trending significance with white matter, but continued to be associated with the DLPFC and IFG, as did the association between processing speed and the hippocampus. These findings suggest that volumes of the DLPFC, IFG, hippocampus, and white matter are associated with the global cognitive impairment seen in schizophrenia, but some brain structures may also be specifically related to domain-specific deficits (primarily executive function) over-and-beyond the global cognitive deficit.
Laws of Programming: The Algebraic Unification of Theories of Concurrency

I began my academic research career in 1968, when I moved from industrial employment as a programmer to the Chair of Computing at the Queen’s University in Belfast. My chosen research goal was to discover an axiomatic basis for computer programming. Originally I wanted to express the axioms as algebraic equations, like those which provide the basis of arithmetic or group theory. But I did not know how. After many intellectual vicissitudes, I have now discovered the simple secret. I would be proud of this discovery, if I were not equally ashamed at taking so long to discover it.
Inflammation and Disease: Modelling and Modulation of the Inflammatory Response to Alleviate Critical Illness.

Abstract Critical illness, a constellation of interrelated inflammatory and physiological derangements occurring subsequent to severe infection or injury, affects a large number of individuals in both developed and developing countries. The prototypical complex system embodied in critical illness has largely defied therapy beyond supportive care. We have focused on the utility of data-driven and mechanistic computational modelling to help address the complexity of critical illness and provide pathways towards discovering potential therapeutic options and combinations. Herein, we review recent progress in this field, with a focus on both animal and computational models of critical illness. We suggest that therapy for critical illness can be posed as a model-based dynamic control problem, and discuss novel theoretical and experimental approaches involving biohybrid devices aimed at reprogramming inflammation dynamically. Together, these advances offer the potential for Model-based Precision Medicine for critical illness.
Water in the American West, Water Policy and Management, and the Role of Environmental Security

This chapter examines the substantial literature on water policy, as there are numerous dimensions, divisions, and sub-topics from a variety of contributors. The literature germane to a discussion of water in the American West can be divided into three groups. The first body of work examines the particular dynamics of western U.S. water issues, and includes authors that come from a journalism or activist background, as well as traditional scholarship from a diverse set of academic fields such as geoscience, economics, sociology, public policy, and political science, as well as anthropology. The second portion of the literature is a broader set of contributions that examine water policy and management more broadly. This group covers many issues of water management and policy that extend beyond the American West and are typically drawn from the public policy literature, covering topics such as collaborative agreements, agricultural water issues, pollution control, and institutional or regulatory reform. The third group of literature is from the emerging sub-field of environmental security. Originally, the domain of political science, environmental security has grown to include a wide range of scholarly fields including geography, sociology, economics, and others. This chapter weaves together these three different strands of literature.
The state of phosphorus balance on 58 Virginia dairy farms.

Managing a sustainable dairy farm requires balancing phosphorus (P) imports and exports that enter and leave through the farm gate. Over the long term, P surpluses will elevate soil-test P concentrations above crop requirements through routine land applications of manure. The objectives of this study were aimed at Virginia dairy farms (a) to determine P mass balances, (b) to define potential guidelines for a sustainable and feasible zone of operation based on P balance and P use efficiency, and (c) to assess risk factors driving P surplus and P use inefficiencies. Data on farm-gate P imports and exports via feed, manure, crops, fertilizers, bedding, animals, and milk were collected for 58 dairy farms in Virginia. There was no relationship between farm P balance and milk production, indicating that a P surplus was not necessary for good milk productivity. A feasible P balance limit was calculated below which 75% of farms could operate, and this was 18.7 kg P ha-1 . Two risk factors were identified for farms having a P balance above this limit: (a) land application of poultry litter and (b) excessive import of P through feed. Combined dairy and beef operations generally had more land and a lower P balance, whereas having combined dairy and poultry did not raise the P balance as long as poultry litter was exported. Dairy farms in Virginia can operate with a sustainable P balance as long as they avoid using excessive poultry litter and pay attention to P imported through purchased feed.
Analysis of Sinus Balloon Catheter Dilation Providers Based on Medicare Provider Utilization and Payment Data

BackgroundThe use of balloon catheter dilation (BCD) to treat chronic rhinosinusitis has increased dramatically since its conception, necessitating further characterization of BCD providers and tre...
From the Transcriptome to Electrophysiology: Searching for the Underlying Cause of Diabetes.

Cells within the islet of Langerhans are heterogeneous. Camunas-Soler et al. (2020) implement a patch-seq technique to collect both transcriptomic and electrophysiological data from the same cell. By doing so, they discover new genes that correlate with functional heterogeneity and find that shifts in these correlations indicate β cell compensation in type 2 diabetes.
Expertise in Political Contexts: Latour Avec the Third Wave in Science and Technology Studies

The interdiscipline of science and technology studies (‘STS’) has been characterized by its descriptive analyses of the presumptions and practices of scientific communities, and by numerous theoretical internal debates over the proper framework of analysis of science. While STS has not been characterized by a powerful effect on law and government, both of which are consumers of scientific expertise, an opportunity arises for engagement in public policy disputes due to the willful ignorance regarding science in the Trump administration, and the negative effects of political agendas and conflicts of interest therein. The urgent need for reliable expertise in such political contexts is addressed in the so-called third wave of STS that is based on Harry Collins and Rob Evans’s innovative ‘architecture of expertise.’ Two recent book chapters, namely Darrin Durant’s essay on ignoring experts and Martin Weinel’s essay on counterfeit scientific controversies, serve as practical examples of third-wave theory. Bruno Latour, who was engaged in a debate with Collins (and others in STS) concerning their respective approaches during the 1990s, also recently addressed the need for expertise (particularly climate expertise) in government contexts. Nowadays, Collins and Latour both promote consensus expertise and identify its reliance (for its authority) on science as a trusted institution. This article compares the similarities (and acknowledges the differences) between Collins and Latour with respect to their pragmatic strategies, and concludes that notwithstanding internal debates, STS scholars should join Collins (with Evans) and Latour to look outward toward critique and correction of governments that ignore scientific expertise.