cssi/SciSciGPT-SciSciNet huggingface dataset:
Dutch Burghers and Portuguese Mechanics: Eurasian Ethnicity in Sri Lanka

Historians and anthropologists in Sri Lanka have tended to migrate in opposite directions, but away from the multiethnic confusion of the port cities. Typi- cally, the heterogeneous, semi-Westernized, postcolonial urban society of Colombo and the larger towns has been only a transit point on intellectual journeys outbound to European archives or inbound to “traditional culture.” This was certainly my viewpoint as I arrived “inbound” in Sri Lanka for my first anthropological fieldwork. I took only passing notice of the clerks of mixed European and Sri Lankan descent who sold me stationery supplies at Cargill's and mosquito nets at Carvalho's. These people are given the official designation of Burghers in the government census: they are the racially mixed descendants of the Portuguese, Dutch, and British personnel who occupied the island during four and a half centuries of colonial rule.
Designing a Living Snow Fence for Snow Drift Control

Abstract Blowing and drifting snow continues to be a transportation and safety hazard with significant economic costs. Critical design criteria for the construction of a living (vegetated) snow fence are reviewed and presented using the most currently available design equations. Coupled with an analysis of climate and topographical data, the design criteria are applied to an area in Rocky Mountain National Park historically prone to snow drifting. The long-term average snow accumulation season (period beginning with the first blowing snow and ending with maximum drift density) was calculated from air temperature as between 4 November and 10 April, and these dates compared well with those based on nearby snow observations. Over the snow accumulation season, the potential for snow transport based on wind characteristics was 21.4 tonnes m−1 (all wind directions), of which 21.0 tonnes m−1 occurred along a mean drifting direction of 259° (nearly perpendicular to the road at the study site). The potential for s...
Homogeneity of isostatic pressure-assisted sintering of agglomerated powder

This article is dedicated to the modeling of the pressure-assisted sintering of agglomerated powders by the grain-boundary and the surface diffusion transport. Agglomerates are treated as volumes with dense particle packing. Kinetics of sintering during consolidation is estimated by a direct numerical analysis of the matter redistribution by diffusion around a single neck between identical spherical particles. Type of packing is introduced into the model through the definition of the packing angle and a special symmetry boundary condition for diffusion fluxes. The numerical analysis of sintering parameters for a single neck allows the evaluation of macroscopic viscosities of the material for different types of the particle packing and enables the estimation of the densification rate of agglomerates and non-agglomerated elements of powder compacts. Calculations show that, despite low initial density and low initial viscosity of a loose powder around agglomerates, isostatic pressing cannot provide a complete equalization of local densities in an agglomerated powder. In all considered cases, agglomerates have reached final density faster than elements with looser packing.
Prenatal Exposure to Tobacco: II Effects on Cognitive Functioning at Age Three

Three-year-old children, born to women who smoked ten or more cigarettes at the beginning of pregnancy and identified at the time of registration for prenatal care, were assessed by the McCarthy Scales of Children's Abilities and the Minnesota Child Development Inventory. Children whose mothers quit smoking during pregnancy relative to children whose mothers persisted in smoking performed at a statistically significant higher level on the General Cognitive Index of the McCarthy and on each of the three subscales from which the General Cognitive Index is derived. The scores on the Minnesota Child Development Inventory were similar in showing a higher performance in the children of quitters. Statistical adjustment for environmental factors, characteristics of the child, and fetal maturity did not account for the observed differences between children of women who quit smoking and those of women who continued to smoke.
Beyond Landsat: a comparison of four satellite sensors for detecting burn severity in ponderosa pine forests of the Gila Wilderness, NM, USA

Methods of remotely measuring burn severity are needed to evaluate the ecological and environmental impacts of large, remote wildland fires. The challenges that were associated with the Landsat program highlight the need to evaluate alternative sensors for characterising post-fire effects. We compared statistical correlations between 55 Composite Burn Index field plots and spectral indices from four satellite sensors varying in spatial and spectral resolution on the 2003 Dry Lakes Fire in the Gila Wilderness, NM. Where spectrally feasible, burn severity was evaluated using the differenced Enhanced Vegetation Index (dEVI), differenced Normalised Difference Vegetation Index (dNDVI) and the differenced Normalised Burn Ratio (dNBR). Both the dEVI derived from Quickbird and the dNBR derived from the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) showed similar or slightly improved correlations over the dNBR derived from Landsat Thematic Mapper data (R2 = 0.82, 0.84, and 0.78 respectively). The relatively coarse resolution MODIS-derived NDVI image was weakly correlated with ground data (R2 = 0.38). Our results suggest that moderately high-resolution satellite sensors like Quickbird and ASTER have potential for providing accurate information about burn severity. Future research should develop stronger links between higher-resolution satellite data and burn severity across a range of environments.
Practical Rate Adaptation in Mobile environments

Channel asymmetry and high fluctuation of channel conditions are two salient characteristics of wireless channels in mobile environments. Therefore, when using IEEE 802.11 devices in mobile environments such as vehicular networks, it is critical to have an effective rate adaptation scheme that can deal with these issues. In this paper, we propose a practical rate adaptation scheme called RAM (Rate Adaptation in Mobile environments) and implement it in the Madwifi device driver. RAM uses a receiver-based approach to handle channel asymmetry and a conservative SNR prediction algorithm to deal with high channel fluctuation. More importantly, RAM allows the receiver to convey the feedback information in a creative manner via ACK transmission rate variation, which does not require changes to the device firmware and hence is implementable at the device driver level. The effectiveness of RAM is demonstrated through experimental evaluation in indoor static and mobile environments and outdoor vehicular environments, as well as simulation study based on SNR traces collected from the experiments.
Eastern North American transport climatology during high- and low-ozone days

A synoptic scale transport climatology during days with high and low ozone concentrations was established for "ve summers from 1991 to 1995 over eastern North America. The airmass transport patterns were estimated from source impact regions derived from forward airmass histories. Daily maximum ozone concentrations were used to de"ne locally and regionally high- (90th percentile) and low- (10th percentile) ozone days. Examination of transport during locally high-ozone days revealed that there is poor transport in the central part of the domain, i.e. from Tennessee to northern Indiana, and in the South from Texas to South Carolina due to stagnating or recirculating air masses. However, high ozone concentrations over the western and northern sections of the domain occurred during strong and persistent southerly and westerly winds, respectively. In addition, on average, high ozone concentration surrounding the central part of the domain were associated with transport from this region. These results support the notion that ozone exceedances in the central and Southeastern US are predominately ‘homegrowna while the western and northern section of the domain are also in#uenced by regional transport. In contrast, on low-ozone days, the transport was predominantly from outside (e.g., Canada and the Gulf of Mexico) into the Eastern US. The transport conditions during regionally high-ozone days were characterized by slow meandering transport over Kentucky, Tennessee, and West Virginia, with a strong clockwise transport around this region of stagnation. ( 2001 Elsevier Science Ltd. All rights reserved.
Achieving high throughput for data transfer over ATM networks

File-transfer rates for ftp are often reported to be relatively slow, compared to the raw bandwidth available in emerging gigabit networks. While a major bottleneck is disk I/O, protocol issues impact performance as well. Ftp was developed and optimized for use over the TCP/IP protocol stack of the Internet. However, TCP has been shown to run inefficiently over ATM. In an effort to maximize network throughput, data-transfer protocols can be developed to run over UDP or directly over IP, rather than over TCP. If error free transmission is required, techniques for achieving reliable transmission can be included as part of the transfer protocol. However, selected image-processing applications can tolerate a low level of errors in images that are transmitted over a network. In this paper we report on experimental work to develop a high-throughput protocol for unreliable data transfer over ATM networks. We attempt to maximize throughput by keeping the communications pipe full, but still keep packet loss under five percent. We use the Bay Area Gigabit Network Testbed MAN as our experimental platform.
Transport by weak electrostatic density drift fluctuations

Expressions are derived for transport by weak electrostatic microfluctuations driven unstable by a density gradient perpendicular to a uniform magnetic field in a Vlasov plasma. These expressions, which are evaluated for the universal and lower-hybrid density drift instabilities, provide improved physical interpretations for various wave-particle exchange frequencies previously reported. It is demonstrated that wave-particle effects generally reduce the free energy driving these instabilities, and that some forms of steady-state distribution functions are inappropriate for nonlinear theory.
Fine-scale genetic structure of the ringtail (Bassariscus astutus) in a Sky Island mountain range

Landscape complexity provides opportunities for local adaptation and creates population genetic structure at limited geographic scales. We determined if fine-scale genetic structure was evident in a population of ringtails (Bassariscus astutus) inhabiting the Guadalupe Mountains, a small, isolated, and ecologically diverse mountain range in the southwest United States. We hypothesized that ringtails would exhibit either a genetic pattern of isolation by distance (IBD), because their small body size would most likely limit dispersal distances, or a pattern of isolation by resistance (IBR), because the topographical complexity of the mountain range would result in complex dispersal patterns. To investigate for the presence of fine-scale genetic structure in this population, we genotyped 153 ringtails at 15 microsatellite loci and described genetic structure using 2 Bayesian clustering techniques. Six genetic clusters were identified revealing complex spatial genetic structure within a localized geographic a...
On the Derivation of Higher Order Root-Finding Methods

High order root-finding algorithms are constructed based on some canonical conditions and a generalized Taylor series. The convergence order is automatically determined using these canonical conditions. The proposed approaches resulted in deriving methods of any desired order including the Newton, Halley, and Ostrowski iterations. It is also shown that, when zeros are simple, higher order methods may be obtained by applying lower order methods such as Newton Iteration to new functions which have same zeros as the original function. These functions are constructed so that the first few derivatives beyond the first vanish. Several examples are given for constructing methods of higher order for computing the zeros of the entire function sin(z).
Changes of Variability in Response to Increasing Greenhouse Gases. Part I: Temperature

This study documents the temperature variance change in two different versions of a coupled ocean– atmosphere general circulation model forced with estimates of future increases of greenhouse gas (GHG) and aerosol concentrations. The variance changes are examined using an ensemble of 8 transient integrations for the older model version and 10 transient integrations for the newer one. Monthly and annual data are used to compute the mean and variance changes. Emphasis is placed upon computing and analyzing the variance changes for the middle of the twenty-first century and compared with those found in a control integration. The large-scale variance of lower-tropospheric temperature (including surface air temperature) generally decreases in high latitudes particularly during fall due to a delayed onset of sea ice as the climate warms. Sea ice acts to insolate the atmosphere from the much larger heat capacity of the ocean. Therefore, the near-surface temperature variance tends to be larger over the sea ice–covered regions, than the nearby ice-free regions. The near-surface temperature variance also decreases during the winter and spring due to a general reduction in the extent of sea ice during winter and spring. Changes in storminess were also examined and were found to have relatively little effect upon the reduction of temperature variance. Generally small changes of surface air temperature variance occurred in low and midlatitudes over both land and oceanic areas year-round. An exception to this was a general reduction of variance in the equatorial Pacific Ocean for the newer model. Small increases in the surface air temperature variance occur in mid- to high latitudes during the summer months, suggesting the possibility of more frequent and longer-lasting heat waves in response to increasing GHGs.
Initial Development of the Student's Life Satisfaction Scale:

This article describes the development of a brief research instrument to measure global life satisfaction in children, the Student's Life Satisfaction Scale (SLSS). A preliminary version of the SLS...
Increased Expression of Enzymes of Triglyceride Synthesis Is Essential for the Development of Hepatic Steatosis

Molecular mechanisms underpinning nonalcoholic fatty liver disease (NAFLD) are not well understood. The earliest step of NAFLD is hepatic steatosis, which is one of the main characteristics of aging liver. Here, we present a molecular scenario of age-related liver steatosis. We show that C/EBPα-S193D knockin mice have age-associated epigenetic changes and develop hepatic steatosis at 2 months of age. The underlying mechanism of the hepatic steatosis in old wild-type (WT) mice and in young S193D mice includes increased amounts of tripartite p300-C/EBPα/β complexes that activate promoters of five genes that drive triglyceride synthesis. Knockdown of p300 in old WT mice inhibits hepatic steatosis. Indeed, transgenic mice expressing dominant-negative p300 have fewer C/EBPα/β-p300 complexes and do not develop age-dependent hepatic steatosis. Notably, the p300-C/EBPα/β pathway is activated in the livers of patients with NAFLD. Thus, our results show that p300 and C/EBP proteins are essential participants in hepatic steatosis.
Insulin-stimulated Activation of eNOS Is Independent of Ca2+ but Requires Phosphorylation by Akt at Ser1179

Vasodilator actions of insulin are mediated by activation of endothelial nitric-oxide synthase (eNOS) and subsequent production of NO. Phosphatidylinositol 3-kinase and Akt play important roles in insulin-signaling pathways leading to production of NO in vascular endothelium. Here we dissected mechanisms whereby insulin activates eNOS by using the fluorescent dye DAF-2 to directly measure NO production in single cells. Insulin caused a rapid increase in intracellular NO in NIH-3T3(IR) cells transiently transfected with eNOS. The stimulation of NO production by lysophosphatidic acid (LPA) was abrogated by pretreatment of cells with the calcium chelator 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid. Remarkably, in the same cells, insulin-stimulated production of NO was unaffected. However, cells expressing the eNOS-S1179A mutant (disrupted Akt phosphorylation site) did not produce detectable NO in response to insulin, whereas the response to LPA was similar to that observed in cells expressing wild-type eNOS. Moreover, production of NO in response to insulin was blocked by coexpression of an inhibitory mutant of Akt, whereas the response to LPA was unaffected. Phosphorylation of eNOS at Ser(1179) was observed only in response to treatment with insulin, but not with LPA. Interestingly, platelet-derived growth factor treatment of cells activated Akt but not eNOS. Results from human vascular endothelial cells were qualitatively similar to those obtained in transfected NIH-3T3(IR) cells, although the magnitude of the responses was smaller. We conclude that insulin regulates eNOS activity using a Ca(2+)-independent mechanism requiring phosphorylation of eNOS by Akt. Importantly, phosphorylation-dependent mechanisms that enhance eNOS activity can operate independently from Ca(2+)-dependent mechanisms.
Temporalis tendon transfer as part of a comprehensive approach to facial reanimation.

Objective: To report an approach to facial paralysis in patients for whom dynamic adjacent muscle transfer is determined to be the best treatment option. Methods: Retrospective review of 7 consecut...
Magnitude- and time-scaling of state-variable equations for analog/hybrid computation:

The programming of differential equations on an ana log or hybrid computer usually requires that the system be scaled in both magnitude and time to pre vent overloading the amplifiers and to obtain the desired speed of solution. This paper, which is tutorial in nature, presents a systematic matrix method which may be used to scale differential equa tions written in state variable format. The proce dure requires estimates of the maximum values of each computer variable, and the technique is shown to be appZicabZe to both linear and nonlinear systems. The description of the method is followed by two illustrative examples, one linear and one nonlinear, and comments on an effective rescaling algorithm.
Hypoxia/Hypoxemia-Induced Activation of the Procoagulant Pathways and the Pathogenesis of Ischemia-Associated Thrombosis

Although oxygen deprivation has long been associated with triggering of the procoagulant pathway and venous thrombosis, blood hypoxemia and stasis by themselves do not lead to fibrin formation. A pathway is outlined through which diminished levels of oxygen activate the transcription factor early growth response-1 (Egr-1) leading to de novo transcription/translation of tissue factor in mononuclear phagocytes and smooth muscle cells, which eventuates in vascular fibrin deposition. The procoagulant response is magnified by concomitant suppression of fibrinolysis by hypoxia-mediated upregulation of plasminogen activator inhibitor-1. These data add a new facet to the biology of thrombosis associated with hypoxemia/stasis and imply that interference with mechanisms causing Egr-1 activation in response to oxygen deprivation might prevent vascular fibrin deposition occurring in ischemia without directly interfering with other pro/anticoagulant pathways.
A family-based, genome-wide association study of young-onset breast cancer: inherited variants and maternally mediated effects

Young-onset breast cancer shows certain phenotypic and etiologic differences from older-onset breast cancer and may be influenced by some distinct genetic variants. Few genetic studies of breast cancer have targeted young women and no studies have examined whether maternal variants influence disease in their adult daughters through prenatal effects. We conducted a family-based, genome-wide association study of young-onset breast cancer (age at diagnosis <50 years). A total of 602 188 single-nucleotide polymorphisms (SNPs) were genotyped for 1279 non-Hispanic white cases and their parents or sisters. We used likelihood-based log-linear models to test for transmission asymmetry within families and for maternally mediated genetic effects. Three autosomal SNPs (rs28373882, P=2.8 × 10(-7); rs879162, P=9.2 × 10(-7); rs12606061, P=9.1 × 10(-7)) were associated with risk of young-onset breast cancer at a false-discovery rate below 0.20. None of these loci has been previously linked with young-onset or overall breast cancer risk, and their functional roles are unknown. There was no evidence of maternally mediated, X-linked, or mitochondrial genetic effects, and no notable findings within cancer subcategories defined by menopausal status, estrogen receptor status, or by tumor invasiveness. Further investigations are needed to explore other potential genetic, epigenetic, or epistatic mechanisms and to confirm the association between these three novel loci and young-onset breast cancer.
Military service, deployments, and exposures in relation to amyotrophic lateral sclerosis etiology.

Abstract Background Factors underlying a possible excess of amyotrophic lateral sclerosis (ALS) among military veterans remain unidentified. Limitations of previous studies on this topic include reliance on ALS mortality as a surrogate for ALS incidence, low statistical power, and sparse information on military-related factors. Objectives We evaluated associations between military-related factors and ALS using data from a case-control study of U.S. military veterans. Methods From 2005 to 2010, we identified medical record-confirmed ALS cases via the National Registry of Veterans with ALS and controls via the Veterans Benefits Administration's Beneficiary Identification and Records Locator System database. In total, we enrolled 621 cases and 958 frequency-matched controls in the Genes and Environmental Exposures in Veterans with Amyotrophic Lateral Sclerosis study. We collected information on military service and deployments and 39 related exposures. We used unconditional logistic regression models to estimate odds ratios (ORs) and 95% confidence intervals (CIs). We used inverse probability weighting to adjust for potential bias from confounding, missing covariate data, and selection arising from a case group that disproportionately included long-term survivors and a control group that may or may not differ from U.S. military veterans at large. Results The odds of ALS did not differ for veterans of the Air Force, Army, Marines, and Navy. We found higher odds of ALS for veterans whose longest deployment was World War II or the Korean War and a positive trend with total years of all deployments (OR = 1.27; 95% CI: 1.06, 1.52). ALS was positively associated with exposure to herbicides for military purposes, nasopharyngeal radium, personal pesticides, exhaust from heaters or generators, high-intensity radar waves, contaminated food, explosions within one mile, herbicides in the field, mixing and application of burning agents, burning agents in the field, and Agent Orange in the field, with ORs between 1.50 and 7.75. Conclusions Although our results need confirmation, they are potentially important given the large number of U.S. military veterans, and they provide clues to potential factors underlying the apparent increase of ALS in veteran populations.
Information-theoretic analysis of x-ray photoabsorption based threat detection system for check-point

In this work we present an information-theoretic framework for a systematic study of checkpoint x-ray systems using photoabsorption measurements. Conventional system performance analysis of threat detection systems confounds the effect of the system architecture choice with the performance of a threat detection algorithm. However, our system analysis approach enables a direct comparison of the fundamental performance limits of disparate hardware architectures, independent of the choice of a specific detection algorithm. We compare photoabsorptive measurements from different system architectures to understand the affect of system geometry (angular views) and spectral resolution on the fundamental limits of the system performance.
Semi-supervised learning in the presence of novel class instances

In this paper, we present an approach for learning in the semi-supervised setting in the presence of novel class instances. In this setting, data consists of a labeled portion and an unlabeled portion that contains novel class instances along with unlabeled known class instances. Novel class instances are instances from concepts that do not have labeled training examples. This setting is appropriate for the case in which data is abundant and labeling the entire data is prohibitively expensive. We provide a model and an inference framework that allow for a direct control over the portion of novel class instances in the unlabeled data. Experiments on synthetic data demonstrate the usefulness of the proposed approach. Comparison to state-of-the-art approaches for learning in the presence of novel class instances using unlabeled data illustrates the advantage in using the proposed method in term of accuracy.
Author, King, and Christ in Shakespeare’s Histories

By the time he completed Henry V in 1599, Shakespeare had written or co-written two four-part sequences of English history plays. Taken together, these two tetralogies formed a coherent historical narrative, a cycle. No other dramatist for the Elizabethan public theaters had ever attempted such a cycle; none had even written more than a two-part sequence of plays. The only significant analogue to Shakespeare’s achievement were the miracle plays that in earlier times had been performed in towns such as York and Chester during the festival of Corpus Christi. These cycles, dozens of plays apiece, were religious drama, telling the history of the world from the Creation to the Last Judgment. They were also Catholic drama, and the Protestant Church eventually shut them down. But the Corpus Christi cycles lasted long enough for Shakespeare, his fellow actors, and members of his audience to have been able to witness them.1 Why did Shakespeare take the unprecedented step of imitating or emulating these old religious plays with a commercial theatrical cycle of his own?2
Restricting Time in Bed in Early Adolescence Reduces Both NREM and REM Sleep but Does Not Increase Slow Wave EEG

Author(s): Campbell, Ian G; Kraus, Amanda M; Burright, Christopher S; Feinberg, Irwin | Abstract: Study objectivesSchool night total sleep time decreases across adolescence (9-18 years) by 10 min/year. This decline is comprised entirely of a selective decrease in NREM sleep; REM sleep actually increases slightly. Decreasing sleep duration across adolescence is often attributed to insufficient time in bed. Here we tested whether sleep restriction in early adolescence produces the same sleep stage changes observed on school nights across adolescence.MethodsAll-night sleep EEG was recorded in 76 children ranging in age from 9.9 to 14.0 years. Each participant kept 3 different sleep schedules that consisted of 3 nights of 8.5 h in bed followed by 4 nights of either 7, 8.5, or 10 h in bed. Sleep stage durations and NREM delta EEG activity were compared across the 3 time in bed conditions.ResultsShortening time in bed from 10 to 7 hours reduced sleep duration by approximately 2 hours, roughly equal to the decrease in sleep duration we recorded longitudinally across adolescence. However, sleep restriction significantly reduced both NREM (by 83 min) and REM (by 47 min) sleep. Sleep restriction did not affect NREM delta EEG activity.ConclusionsOur findings suggest that the selective NREM reduction and the small increase in REM we observed longitudinally across 9-18 years are not produced by sleep restriction. We hypothesize that the selective NREM decline reflects adolescent brain maturation (synaptic elimination) that reduces the need for the restorative processes of NREM sleep.
Insights into cellulase‐lignin non‐specific binding revealed by computational redesign of the surface of green fluorescent protein

Biological-mediated conversion of pretreated lignocellulosic biomass to biofuels and biochemicals is a promising avenue toward energy sustainability. However, a critical impediment to the commercialization of cellulosic biofuel production is the high cost of cellulase enzymes needed to deconstruct biomass into fermentable sugars. One major factor driving cost is cellulase adsorption and inactivation in the presence of lignin, yet we currently have a poor understanding of the protein structure-function relationships driving this adsorption. In this work, we have systematically investigated the role of protein surface potential on lignin adsorption using a model monomeric fluorescent protein. We have designed and experimentally characterized 16 model protein variants spanning the physiological range of net charge (-24 to +16 total charges) and total charge density (0.28-0.40 charges per sequence length) typical for natural proteins. Protein designs were expressed, purified, and subjected to in silico and in vitro biophysical measurements to evaluate the relationship between protein surface potential and lignin adsorption properties. The designs were comparable to model fluorescent protein in terms of thermostability and heterologous expression yield, although the majority of the designs unexpectedly formed homodimers. Protein adsorption to lignin was studied at two different temperatures using Quartz Crystal Microbalance with Dissipation Monitoring and a subtractive mass balance assay. We found a weak correlation between protein net charge and protein-binding capacity to lignin. No other single characteristic, including apparent melting temperature and 2nd virial coefficient, showed correlation with lignin binding. Analysis of an unrelated cellulase dataset with mutations localized to a family I carbohydrate-binding module showed a similar correlation between net charge and lignin binding capacity. Overall, our study provides strategies to identify highly active, low lignin-binding cellulases by either rational design or by computational screening genomic databases. Biotechnol. Bioeng. 2017;114: 740-750. © 2016 Wiley Periodicals, Inc.
Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli.

ABSTRACT YbeY is part of a core set of RNases in Escherichia coli and other bacteria. This highly conserved endoribonuclease has been implicated in several important processes such as 16S rRNA 3′ end maturation, 70S ribosome quality control, and regulation of mRNAs and small noncoding RNAs, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. Thus, YbeY likely interacts with numerous protein or RNA partners that are involved in various aspects of cellular physiology. Using a bacterial two-hybrid system, we identified several proteins that interact with YbeY, including ribosomal protein S11, the ribosome-associated GTPases Era and Der, YbeZ, and SpoT. In particular, the interaction of YbeY with S11 and Era provides insight into YbeY’s involvement in the 16S rRNA maturation process. The three-way association between YbeY, S11, and Era suggests that YbeY is recruited to the ribosome where it could cleave the 17S rRNA precursor endonucleolytically at or near the 3′ end maturation site. Analysis of YbeY missense mutants shows that a highly conserved beta-sheet in YbeY—and not amino acids known to be important for YbeY’s RNase activity—functions as the interface between YbeY and S11. This protein-interacting interface of YbeY is needed for correct rRNA maturation and stress regulation, as missense mutants show significant phenotypic defects. Additionally, structure-based in silico prediction of putative interactions between YbeY and the Era-30S complex through protein docking agrees well with the in vivo results. IMPORTANCE Ribosomes are ribonucleoprotein complexes responsible for a key cellular function, protein synthesis. Their assembly is a highly coordinated process of RNA cleavage, RNA posttranscriptional modification, RNA conformational changes, and protein-binding events. Many open questions remain after almost 5 decades of study, including which RNase is responsible for final processing of the 16S rRNA 3′ end. The highly conserved RNase YbeY, belonging to a core set of RNases essential in many bacteria, was previously shown to participate in 16S rRNA processing and ribosome quality control. However, detailed mechanistic insight into YbeY’s ribosome-associated function has remained elusive. This work provides the first evidence that YbeY is recruited to the ribosome through interaction with proteins involved in ribosome biogenesis (i.e., ribosomal protein S11, Era). In addition, we identified key residues of YbeY involved in the interaction with S11 and propose a possible binding mode of YbeY to the ribosome using in silico docking.
Anticoagulation in Penetrating Trauma

Anticoagulation following injury can be a slippery slope. Many patient present with overt coagulopathy, while others will only develop trauam-associated coaguloapthy after resuscitatiion and injury repair. The decision to anticoagulate even the most complex vascualr reconstruction was be carefully weighed with the risks related to the remainder of the trauma burden.
Diffusiophoretic Focusing of Suspended Colloids

Using a microfluidic system to impose and maintain controlled, steady-state multicomponent pH and electrolyte gradients, we present systems where the diffusiophoretic migration of suspended colloids leads them to focus at a particular position, even in steady-state gradients. We show that naively superpositing effects of each gradient may seem conceptually and qualitatively reasonable, yet is invalid due to the coupled transport of these multicomponent electrolytes. In fact, reformulating the classic theories in terms of the flux of each species (rather than local gradients) reveals rather stringent conditions that are necessary for diffusiophoretic focusing in steady gradients. Either particle surface properties must change as a function of local composition in solution (akin to isoelectric focusing in electrophoresis), or chemical reactions must occur between electrolyte species, for such focusing to be possible. The generality of these findings provides a conceptual picture for understanding, predicting, or designing diffusiophoretic systems.
Towards constructing “Super Gene Sets” regulatory networks

In this article, we described a new computational framework to construct “Super Gene Sets”-Pathways, Annotated list, and Gene signatures (PAGs), regulatory (r-type) PAG-PAG relationships. To construct PAGs, we aggregate singleton PAGs (sPAGs) upstream/downstream of a common shared multi-gene PAG (mPAGs). Then, we iteratively remove a member gene to calculate its Cohesion Coefficient (CoCo), which helps assess the degree of biological relevance beyond random chance, until the CoCo score achieves the maximal value at a specific level. The new relationship between aggregated mPAG (m'PAG) and the shared mPAG will, therefore, have distinct m'PAG-mPAG relationships. Our results suggest the following. First, the new m'PAGs have sufficiently high CoCo scores, suggesting high biological relevance, and distinct gene ontology annotations different from their regulated PAG targets; however, there are significant enrichments of shared GO annotations between each pair of identified m'PAG-mPAG relationships. Second, new m'PAGs are relatively robust against data noise based on noise characteristic simulations. Third, by applying our framework to real cancer microarray analysis data, we demonstrated that our new framework is effective in helping build multi-scale biomolecular systems models that are easy to interpret by biologists.
Remembering the Alamosaurus: Jensen Relocates Gilmore's Alamosaurus Quarry, USNM 15560, North Horn Formation, Emery County, Utah, and Discovers a Second Individual Alamosaurus

Alamosaurus sanjuanensis was originally described from a left scapula (USNM 10846) and right ischium (USNM 10847) discovered in the Late Cretaceous Ojo Alamo Formation of New Mexico in 1921 (USNM quarry 15560). In 1937 a second specimen was found in the North Horn Formation of Utah, consisting of a partial skeleton (USNM 15560), comprised of a mostly complete pelvis and caudal vertebral series, from the Late Cretaceous. A sacral complex with five vertebrae was observed in the field but was not collected. In 1966 James “Jim” Jensen of the Brigham Young University Earth Science Museum relocated the Gilmore quarry and found the sacrum, which, by then, had “rotted down into brown soil” and could not be recovered. Nearby, Jensen discovered the proximal heads of a humerus and femur and an isolated proximal caudal vertebra, none of which belonged to USNM 15560. Mike Morales and a team from the University of California at Berkeley discovered additional caudal vertebrae in the vicinity also, none of which belonged to the specimen collected by Gilmore. The specimens recovered by Jensen and Morales are significant because they indicate the presence of additional Alamosaurus specimens in the North Horn Formation. Additionally, the humerus is the most complete Alamosaurus humeral head yet discovered.
Immunotherapies: Exploiting the Immune System for Cancer Treatment

Cancer is a condition that has plagued humanity for thousands of years, with the first depictions dating back to ancient Egyptian times. However, not until recent decades have biological therapeutics been developed and refined enough to safely and effectively combat cancer. Three unique immunotherapies have gained traction in recent decades: adoptive T cell transfer, checkpoint inhibitors, and bivalent antibodies. Each has led to clinically approved therapies, as well as to therapies in preclinical and ongoing clinical trials. In this review, we outline the method by which these 3 immunotherapies function as well as any major immunotherapeutic drugs developed for treating a variety of cancers.
Geometric calibration for a next-generation digital breast tomosynthesis system using virtual line segments

Our next-generation tomosynthesis (NGT) system prototype introduces additional geometric movements to conventional Digital Breast Tomosynthesis (DBT) acquisition geometries, to provide isotropic super-resolution. These movements include x-ray source movement in the posteroanterior (PA) direction and detector movement in the z-direction (perpendicular to the breast support). The desired benefits of the NGT system are only achievable with precise geometric calibration. In our previous work, a geometric phantom with 24 point-like ball bearings (BB’s) at four different magnifications was designed and a geometric calibration method that minimizes the difference between the projected locations and the calculated locations of BB’s was tested. This study investigates a new calibration method using the same phantom, utilizing projected 2D equations of virtual line segments created by any two BB’s for more precise reconstruction of the various acquisition modes of the NGT system. The geometric parameters were solved with two approaches: (1) solving each projection individually and (2) solving all projections simultaneously. Furthermore, two algorithms to compensate for any possible inaccuracy in BB locations within the phantom, presumably by less than desired manufacturing precision, were developed and compared: (1) manually identifying and removing poorly positioned BB’s and (2) performing an iteration to re-calculate the BB locations. Magnification digital breast tomosynthesis was also performed to test the calibration method further. Tomographic image reconstructions successfully demonstrated isotropic super-resolution and magnified super-resolution.
Expression and Function of Chemokines CXCL9-11 in Micturition Pathways in Cyclophosphamide (CYP)-Induced Cystitis and Somatic Sensitivity in Mice

Changes in urinary bladder function and somatic sensation may be mediated, in part, by inflammatory changes in the urinary bladder including the expression of chemokines. Male and female C57BL/6 mice were treated with CYP (75 mg/kg, 200 mg/kg, i.p.) to induce bladder inflammation (4 hr, 48 hr, chronic). We characterized the expression of CXC chemokines (CXCL9, CXCL10 and CXCL11) in the urinary bladder and determined the effects of blockade of their common receptor, CXCR3, at the urinary bladder level on bladder function and somatic (hindpaw and pelvic) sensation. qRT-PCR and ELISAs were used to determine mRNA and protein expression of CXCL9, CXCL10, and CXCL11 in urothelium and detrusor. In urothelium of female mice treated with CYP, CXCL9 and CXCL10 mRNA significantly (p ≤ 0.01) increased with CYP treatment whereas CXC mRNA expression in the detrusor exhibited both increases and decreases in expression with CYP treatment. CXC mRNA expression in the urothelium and detrusor of male mice was more variable with both significant (p ≤ 0.01) increases and decreases in expression depending on the specific CXC chemokine and duration of CYP treatment. CXCL9 and CXCL10 protein expression was significantly (p ≤ 0.01) increased in the urinary bladder with 4 hr CYP treatment in female mice whereas CXC protein expression in the urinary bladder of male mice did not exhibit an overall change in expression. CXCR3 blockade with intravesical instillation of AMG487 (5 mg/kg) significantly (p ≤ 0.01) increased bladder capacity, reduced voiding frequency and reduced non-voiding contractions in female mice treated with CYP (4 hr, 48 hr). CXCR3 blockade also reduced (p ≤ 0.01) hindpaw and pelvic sensitivity in female mice treated with CYP (4 hr, 48 hr). CXC chemokines may be novel targets for treating urinary bladder dysfunction and somatic sensitization resulting from urinary bladder inflammation.
Chireix amplifier with enhanced bandwidth using active load

The use of an active load has been recently proposed for the realization of power-efficient broadband balanced amplifiers. The application of an active load to a dual-input Chireix amplifier is investigated in this paper for the purpose of increasing their bandwidth. An embedding device model is used to established the optimal non-Foster loads required for both the transistors to remain operating in class F as the operating frequency deviates from the center frequency. Given the transistors must operate with a constant voltage swing between backoff and peak, it is found necessary for the two transistors to operate with different load impedances as the frequency varies. The required load impedance and outphasing angles for the Chireix operation are obtained using a generalized eigenvalue problem using the Y-matrix of the Chireix combiner loaded with the active load. It is verified that using an active load, it is possible to maintain a high efficiency not only at peak power but also under various backoff power levels over a bandwidth of 1 GHz. Within a 200 MHz bandwidth, the PA is predicted to be able to maintain an efficiency larger than 79% for 6 dB backoff. Further work is required to experimentally validate the proposed technique.
The Monkey and the Sea Horse

Bilateral excisions of medial temporal lobe structures (uncinate-amygdaloid region, hippocampus, and hippocampal gyrus) in patients suffering from long-standing psychotic, or epileptic, symptoms resulted in a well-known severe anterograde amnesia (Scoville, 1954; Scoville and Milner, 1957). Subsequent clinical evidence pointed to the hippocampus as the critical structure in the defect. Thus, amnesia developed in one patient when excision of uncus and hippocampal zone was added to a partial unilateral lobectomy, with a preexisting lesion in the corresponding area of the contralateral temporal lobe (Scoville and Milner, 1957). Also, the severity of the memory loss for visual or verbal material was found to be correlated with the extent of hippocampal tissue removed (Penfield and Milner, 1958; Milner and Teuber, 1968). The role of the hippocampus in memory was reemphasized when, in one of the amnesic patients with unilateral left temporal lobectomy, autopsy revealed an extensive atrophy of the right hippocampus (Milner et al., 1968).
Phylogenomics of Thecamoebida (Discosea, Amoebozoa) with the Description of Stratorugosa tubuloviscum gen. nov. sp. nov., a Freshwater Amoeba with a Perinuclear MTOC.

Thecamoebida Smirnov and Cavalier-Smith, 2011 (Discosea, Amoebozoa) has been molecularly understudied. The group until recently consisted of three genera containing species that live in terrestrial or aquatic environments. Here, we describe a fourth genus, Stratorugosa tubuloviscum gen. nov. sp. nov., which was isolated from a freshwater Amoeba proteus Ward’s Science culture. Although this species most closely morphologically resembles a large, rugose Thecamoeba, S. tubuloviscum gen. nov. sp. nov. can be differentiated from Thecamoeba spp. by the following: 1) the presence of definitive finger-like (lobate-like) subpseudopodia extending at both the anterior and lateral parts of the cell during locomotion; 2) a peculiar locomotive mechanism with two sections, frontal and back, of the cells moving in a pulling and piggyback movement, respectively; 3) the presence of fibrillar cytoplasmic microtubules (MTs) organized by a prominent, perinuclear microtubule-organizing center (MTOC). A phylogenomic analysis of 511 genes assembled from transcriptomic data showed that this new genus was highly supported as sister to Stenamoeba. Despite the variance in gross morphology, Stenamoeba and S. tubuloviscum gen nov. sp. nov. both have MTOCs unlike two Thecamoeba spp., which display dot-like cytoplasmic MTs and lack an MTOC.
A Human-Centric Cloud and Fog-Assisted IoT Platform for Disaster Management

Natural and man-made disasters pose an ever-present threat to our community and society. Effective information and communication platform are important for disaster response. However, under disaster scenarios, network infrastructure, such as power grid, cellular tower and backbone networks can be damaged. In addition, the communication channels often become congested by exceptionally high levels of data traffic, as people impacted by the disaster are trying to contact with their family and friends and seeking for help; disaster responders are working to deploy rescue resources, and lots of citizens are broadcasting the disaster by uploading pictures or videos. In this paper, we propose an emergency information platform that is suitable for a challenged environment where the traditional communication paradigms either completely fail or poorly perform. We utilize the vast deployment of Internet of Things (IoT) and citizens in the community to bring benefits in terms of data network resilience in face of disaster. In particular, we propose a software-defined communication network that combines IoT technology, Fog computing, Cloud computing, peer-to-peer computing and delay-tolerant network together to enable an effective emergency-response information platform. It integrates the power of community, and citizen with IoT devices and existing partially damaged communication platform to address critical disaster communication problems.