cssi/SciSciGPT-SciSciNet huggingface dataset:
Cytochrome Content of Two Pseudomonads Containing Mixed-Function Oxidase Systems

The cytochrome and nonheme iron protein content of two pseudomonads, Pseudomonas oleovorans and P. putida, containing mixed function oxidase systems was examined. The mixed function oxidase system of P. oleovorans and P. putida had previously been shown to be present in cells which had been grown on hexane and camphor, respectively, as energy source. The content of protoheme was found to increase significantly when the organisms were grown on the substrates for mixed function oxidation. The nonheme iron protein content increased significantly in the case of P. putida and was constant in P. oleovorans. The cytochrome c content was essentially constant in both pseudomonads. The content of cytochrome P-450 in P. putida increased from an immeasurably low amount to 0.15 nmoles per mg (dry weight). The content of cytochrome o in P. oleovorans increased by a factor of 4.5. P. oleovorans was not found to contain detectable quantities of cytochrome P-450 either in the presence or absence of the mixed function oxidase system.
Adoption of a Plant-Based Diet by Patients with Recurrent Prostate Cancer

The Western diet has been associated with prostate cancer incidence as well as risk of disease progression after treatment. Conversely, plant-based diets have been associated with decreased risks. A pilot clinical trial of a 6-month dietary change and stress reduction intervention for asymptomatic, hormonally untreated patients experiencing a consistently rising PSA level, the first sign of recurrence of prostate cancer after surgery or radiation therapy, was conducted to investigate the level of intake of plant-based foods and the relationship between intake and the change in the rate of PSA rise. A pre-post design was employed in which each patient served as his own control. In this multifaceted intervention, patients and their spouses were encouraged to adopt and maintain a plant-based diet. The prestudy rate of PSA rise (from the time of posttreatment recurrence to the start of the study) was ascertained by review of patients' medical records. Dietary assessments were performed and prostate-specific antigen (PSA) levels ascertained at baseline, prior to the start of intervention, and at 3 and 6 months. Changes in numbers of servings of plant-based food groups were calculated and compared with rates of PSA rise over the corresponding time intervals. Median intake of whole grains increased from 1.7 servings/d at baseline to 6.9 and 5.0 servings/d at 3 and 6 months, respectively. Median intake of vegetables increased from 2.8 servings/d at baseline to 5.0 and 4.8 servings/d at 3 and 6 months, respectively. The rate of PSA rise decreased when comparing the prestudy period (0.059) to the period from 0 to 3 months (-0.002, P < .01) and increased slightly, though not significantly, when comparing the period from 0 to 3 months to the period from 3 to 6 months (0.029, P = .4316). These results provide preliminary evidence that adoption of a plant-based diet is possible to achieve as well as to maintain for several months in patients with recurrent prostate cancer. Changes in the rate of rise in PSA, an indicator of disease progression, were in the opposite direction as changes in the intake of plant-based food groups, raising the provocative possibility that PSA may have inversely tracked intake of these foods and suggesting that adoption of a plant-based diet may have therapeutic potential in the management of this condition.
The evolution and functional repertoire of translation proteins following the origin of life.

The RNA world hypothesis posits that the earliest genetic system consisted of informational RNA molecules that directed the synthesis of modestly functional RNA molecules. Further evidence suggests that it was within this RNA-based genetic system that life developed the ability to synthesize proteins by translating genetic code. Here we investigate the early development of the translation system through an evolutionary survey of protein architectures associated with modern translation. Our analysis reveals a structural expansion of translation proteins immediately following the RNA world and well before the establishment of the DNA genome. Subsequent functional annotation shows that representatives of the ten most ancestral protein architectures are responsible for all of the core protein functions found in modern translation. We propose that this early robust translation system evolved by virtue of a positive feedback cycle in which the system was able to create increasingly complex proteins to further enhance its own function. This article was reviewed by Janet Siefert, George Fox, and Antonio Lazcano (nominated by Laura Landweber)
The Mutational Specificity of the Dbh Lesion Bypass Polymerase and Its Implications

The Dbh polymerase of Sulfolobus solfataricus is a member of the recently described family of low fidelity DNA polymerases involved in bypass of DNA lesions. To investigate the enzymatic properties of Dbh, we characterized the errors made by this polymerase in vitro. Not only is Dbh much less accurate than the "classical" polymerases, but it showed a remarkable tendency to skip over a template pyrimidine positioned immediately 3' to a G residue, generating a single-base deletion. Single-turnover kinetic measurements suggest possible mechanisms. First, Dbh shows a bias in favor of dCTP, such that the rate of incorporation of dCTP opposite a template G is about 10-fold faster than for the other three dNTPs opposite their complementary partners. On a DNA substrate corresponding to a frameshift hotspot, the rate of frameshift insertion of dCTP opposite a template G that is one residue 5' to the expected templating position is approximately equal to the rate of the non-frameshifted C-dGTP insertion. We suspect that the unusual mutational specificity of Dbh (which is shared with other polymerases from the DinB branch of the bypass polymerase family) may be related to the type of DNA lesion(s) that it serves to bypass in vivo.
Demonstration on computed tomography of tracheomalacia in tracheobronchomegaly (Mounier-Kuhn syndrome).

The appearances on computed tomography (CT) (Shin et al, 1988) and magnetic resonance imaging (MRI) (Rindsberg et al, 1987) in single cases of tracheobronchomegaly (TBM) have been described. These reports emphasize the tracheal and proximal bronchial dilatation with diverticulosis of the main bronchi. In a recent case examined by us, these features were also present but even more striking was extreme thinning and deformation of the tracheal wall and indentation anteriorly by the brachiocephalic artery. This finding reflects the tracheomalacia found in this condition. As in previously reported cases, TBM was first detected in this patient on CT after numerous negative chest radiographs.
Temporal Change in Risk of Metachronous Contralateral Renal Cell Carcinoma: Influence of Tumor Characteristics and Demographic Factors

PURPOSE: To determine the relative risk (RR) of developing a metachronous contralateral renal tumor after an initial diagnosis of renal cell carcinoma (RCC), with stratification by renal tumor characteristics, demographic factors, and follow-up duration, in order to develop an improved risk-based surveillance strategy. PATIENTS AND METHODS: The 1973 to 1997 Surveillance, Epidemiology, and End Results database was used to determine the observed and expected number of metachronous contralateral renal tumors developing after an initial diagnosis of RCC. RESULTS: A total of 43,483 patients had a first diagnosis of RCC. Contralateral RCC developed subsequently in 155 (0.4%) of 40,049 patients with follow-up who had no synchronous diagnosis of RCC, with 10.81 expected cases (RR, 14.3; 95% CI, 12.2 to 16.8). The respective RRs (and 95% CIs) for contralateral RCC for white men and women were 16.0 (11.1 to 22.3) and 13.7 (7.7 to 22.6) at less than 2 years, 8.8 (5.0 to 14.3) and 10.5 (5.0 to 19.3) at 2 to 5 years, ...
REPRESENTATIONALISM AND THE ARGUMENT FROM HALLUCINATION

: Representationalism is sometimes advertised as providing a novel response to the argument from hallucination, one that accepts the presence of a ‘common factor’ between veridical and hallucinatory experience without positing sensory intermediaries between the mind and the world. I argue that much of the attractiveness of representationalism stems from a failure in the literature to distinguish between two distinct possible versions of representationalism, what I call ‘content-based representationalism’ and ‘vehicle-based representationalism’. Generically, representationalism appears to have a response to the argument from hallucination that avoids a commitment to qualia or sense-data. But once the distinction between content-based representationalism and vehicle-based representationalism is recognized, this response to the argument from hallucination fails.
Dynamic fracture of linear medium density polyethylene under impact loading conditions

In the present study three-point-bend impact experiments were conducted using a Modified Split Hopkinson Pressure Bar (MHPB) to better understand the correlation between impact velocity and critical dynamic energy release rate at crack initiation in linear medium density polyethylene (LMDPE). The MHPB experiments were conducted at impact velocities ranging from 1 to 7 m/s. The dynamic energy release rate at crack initiation was determined from the force–displacement history of the load point obtained from measurements of input and reflected strain profiles on the incident bar. Moreover, extensive scanning electron microscopy was used to elucidate the micro- and macro-failure mechanisms operative during the dynamic fracture event. In particular two micro-mechanisms of failure were of primary interest: (a) formation of a craze zone at the notch root, and (b) the development of shear lips at the surface of the specimen following crack initiation. The results of this investigation were compared to those obtained by other investigators on linear low-density polyethylene (LLDPE) and linear high-density polyethylene (LHDPE).
Efficacy of an Anaerobic Swab Transport System to Maintain Aerobic and Anaerobic Microorganism Viability after Storage at −80°C

An Amies agar gel swab transport system was evaluated for its ability to maintain bacterial viability and relative quantity after freezing at 280uC. Nine American Type Culture Collection (ATCC) bacterial strains were used: 3 anaerobic strains (Propionibacterium acnes, Peptostreptococcus anaerobius, and Clostridium sporogenes) and 6 facultative or strict aerobic bacterial strains (Stenotrophomonas maltophilia, Escherichia coli ((ATCC 25922 and ATCC 11775), Salmonella enterica subsp. enterica serovar Typhimurium, Staphylococcus saprophyticus, and Lactobacillus casei). The bacterial species were chosen because they corresponded to bacteria identified in psittacine feces and cloacal samples. There were no significant differences between growth scores at baseline and after storage at 280uC for 40 days for any of the bacteria examined after 48 and 72 hr of incubation, with the exception of P. anaerobius. For P. anaerobius, there was a significant reduction (P , 0.001) in the growth score after storage at 280uC for 40 days from that of the baseline; however, the bacteria were still viable. The tested swab transport system may be useful when lengthy storage and transport times necessitate freezing samples prior to culture.
Persistence of Overseeded Cool-Season Grasses in Bermudagrass Turf

Cool-season grass species are commonly overseeded into bermudagrass turf for winter color. When the overseeded grass persists beyond the spring; however, it becomes a weed. The ability of perennial ryegrass, Italian (annual) ryegrass, intermediate ryegrass, and hybrid bluegrass to persist in bermudagrass one year after seeding was determined. Perennial ryegrass, intermediate ryegrass, and Italian ryegrass produced acceptable ground cover in the spring after fall seeding. Hybrid bluegrass did not establish well, resulting in unacceptable cover. Perennial ryegrass generally persisted the most one year after seeding, either because of summer survival of plants or because of new germination the following fall. Plant counts one year after seeding were greater in the higher seeding rate treatment compared to the lower seeding treatment rate of perennial ryegrass, suggesting new germination had occurred. Plant counts one year after seeding plots with intermediate ryegrass or Italian ryegrass were attributed primarily to latent germination and not summer survival. Applications of foramsulfuron generally did not prevent overseeded species stand one year after seeding, supporting the conclusion of new germination. Although quality is less with intermediate ryegrass compared to perennial ryegrass, it transitions out easier than perennial ryegrass, resulting in fewer surviving plants one year later.
Presynaptic alpha2-adrenoceptors inhibit excitatory synaptic transmission in rat brain stem

The synaptic connection between the commissural portion of the nucleus tractus solitarius (ComNTS) and the dorsal motor nucleus of the vagus (DMV) was studied in rat brain stem slices, using the patch-clamp technique. The excitatory postsynaptic currents (EPSC) evoked by stimulation of the ComNTS were blocked by kynurenic acid (1 mM) and, in Mg2+-free solution, were sensitive to both the N-methyl-D-aspartic acid (NMDA) receptor blocker 3-[(RS)-2-carboxypiperazine-4-yl] -propyl-1-phosphonic acid (20 microM) and the non-NMDA receptor blocker 2,3-dihydro-6-nitro-7-sulfamoyl-benzo(f)quinoxaline (5 microM). Norepinephrine (NE, 1-100 microM) inhibited the EPSC, and the inhibition was attenuated by the alpha2-adrenoceptor antagonists idazoxan (1 microM) and yohimbine (10 microM) but not by the beta-adrenoceptor antagonist nadolol (50 microM). The NE-releasing agent tyramine (100 microM) reduced the EPSC, and the inhibition was attenuated by 1 microM idazoxan. NE (30 microM) did not affect the membrane input resistance but reduced the paired-pulse depression, demonstrating that NE acts on presynaptic alpha2-adrenoceptors. The results indicate the existence of a glutamatergic pathway from the ComNTS to the DMV neurons modulated by presynaptic NE receptors. This pathway might be a component of the vagovagal reflex regulating gastrointestinal function.
Atomic structure of salutaridine reductase from the opium poppy (Papaver somniferum).

Abstract The opium poppy (Papaver somniferum L.) is one of the oldest known medicinal plants. In the biosynthetic pathway for morphine and codeine, salutaridine is reduced to salutaridinol by salutaridine reductase (SalR; EC 1.1.1.248) using NADPH as coenzyme. Here, we report the atomic structure of SalR to a resolution of ∼1.9 A in the presence of NADPH. The core structure is highly homologous to other members of the short chain dehydrogenase/reductase family. The major difference is that the nicotinamide moiety and the substrate-binding pocket are covered by a loop (residues 265–279), on top of which lies a large “flap”-like domain (residues 105–140). This configuration appears to be a combination of the two common structural themes found in other members of the short chain dehydrogenase/reductase family. Previous modeling studies suggested that substrate inhibition is due to mutually exclusive productive and nonproductive modes of substrate binding in the active site. This model was tested via site-directed mutagenesis, and a number of these mutations abrogated substrate inhibition. However, the atomic structure of SalR shows that these mutated residues are instead distributed over a wide area of the enzyme, and many are not in the active site. To explain how residues distal to the active site might affect catalysis, a model is presented whereby SalR may undergo significant conformational changes during catalytic turnover.
Ten Thousand Democracies: Politics and Public Opinion in American School Districts

Ten Thousand Democracies: Politics and Public Opinion in American School Districts. By Michael B. Berkman and Eric Plutzer. Washington, DC: Georgetown University Press, 2005. 226p. $26.95. An important and ambitious empirical study of policymaking in the (K–12) school districts of America, this book presents statistical support for noteworthy and sometimes surprising conclusions about the functioning of democracy at this level. The study is important because it raises and answers theoretically valuable questions about democracy in the organization and functions of the public schools. It is ambitious because the data and analytical requirements upon which these questions and answers depend are substantial.
Multielement instrumental neutron activation analysis of biological tissue using a single comparator standard and data processing by computer.

Abstract A detailed description of a multielement instrumental neutron activation analysis approach to outine trace element measurements in biological samples is presented. The main new features of this method are the use of a single element, cobalt, as the comparator standard, and the use of a data smoothing computer technique employing a Fourier transform. A theoretical treatment of the single comparator method is given, along with practical experimental details. A brief description of the computer with special program emphasis on the data smoothing aspects follows. Some results of trace element measurements in biological tissue are then presented, and the paper is concluded by a discussion of the advantages and disadvantages of this approach.
The Control of Immune Response by Endocrine Factors and the Clinicial Significance of Such Regulation

The immune response has been shown to be under the control of a variety of factors including hormones from the pineal, pituitary, thymus, gonads, adrenals, and thyroid. Regulation of these substances by hormonal axes can account for the observed differences in immune responses between sexes as well as affect the onset, course and clinical outcome of disease processes. Fluctuation in hormonal levels resulting from changes in the light-dark cycle may also explain variation in immune response reported in man and experimental animal models. Because of the great volume of diverse publications dealing with hormones and the immune response, and the medical significance of their interactions, we have concisely summarized the pertinent material. While the hormonal regulation of immune function is already proving to be an important area for research, it is expected that within the next few years the interactions between endocrine, neural and immune systems will be even more widely studied.
Vegetation along hydrologic and edaphic gradients in a North Carolina coastal plain creek bottom and implications for restoration.

We described the vegetation of two alluvial swamp forest stands along Durham Creek in Beaufort County, North Carolina, USA in relation to elevation, hydrologic, and edaphic gradients. Over 3,000 sur- veyed elevations of individual plant microsites were used in conjunction with 26 years of stream gage data to examine individual species responses to annual and growing season flooding frequencies. Direct gradient analyses combined with plot ordinations derived from detrended correspondence analysis and canonical correspondence analysis suggested that differences in vegetation between the stands were primarily the result of variations in elevation, growing season flooding frequency, percent base saturation, exchangeable acidity, and soil physical properties. Although the stands were less than 4.5 km apart and without significant inter- mediate tributaries, growing season flooding frequency and duration were magnified in the lowest elevations of the downstream stand. An elevation difference of as little as 10 cm resulted in a 20% difference in the frequency of surface flooding during the growing season. Species distributions were significantly correlated with depth to mottling (r 2 5 0.75), flooding frequency (r 2 52 0.57), elevation (r 2 5 0.70), and several soil chemical properties. The two stands had very similar annual surface flooding regimes, but subtle differences in growing season flooding frequency, soil characteristics, and disturbance history have apparently resulted in dissimilar plant community composition and structure. These results suggest that the lack of quantitative data on vegetation-environment interactions occurring at the microtopographic scale (10 21 m) in alluvial swamp forests makes precise prediction, planning, or design of created or restored wetland composition and function a formidable challenge.
Genetic Information and Privacy Interests: The DNA Fingerprinting Act

The DNA Fingerprinting Act authorizes the collection of DNA from anyone convicted, charged, or arrested for a felony or crime of violence; and from any non-U.S. citizen who is merely detained by a federal agency. It further provides for the DNA samples to be entered into the CODIS system. The involuntary extraction of DNA without a warrant raises privacy concerns, particularly as regards the Fourth Amendment’s protection against unreasonable searches and seizures. Those concerns are legitimate, but the issue here is more a matter of political will than constitutional constraint. As such, the balance between individual privacy and government interest points to the reasonableness of the collection and use of DNA evidence.
Bayesian interpretation of the partial area under the ROC, with applications to spectrum sensing

The Receiver Operating Characteristic ROC is a fundamental concept for detection in spectrum sensing and other applications. The Area Under The Curve, AUC, or integrated ROC, is a detection metric, derived from the ROC, that has been recently applied signal processing problems in cognitive radio. We present a novel interpretation of the partial AUC, in which the a priori probability of the false alarm probability is introduced, which generalizes the classical PAUC concept. Further, we show that adaptive threshold detectors, often introduced for holding a constant false alarm rate, have identical average detection performance as the PAUC. This provides a new interpretation of both the PAUC and many CFAR tests. We apply the beta prior to obtain closed-form results. Finally, Monte Carlo estimation is discussed.
Symmetric and asymmetric period-1 motions in a periodically forced, time-delayed, hardening Duffing oscillator

In this paper, complex symmetric and asymmetric period-1 motions in a periodically forced, time-delayed, hardening Duffing oscillator are predicted through an implicit discrete map. The implicit discrete map is obtained by the discretization of a second-order differential equation of the time-delayed Duffing oscillator. Using the theory of nonlinear discrete systems, period-1 motions in the time-delayed Duffing oscillator are determined analytically from the fixed points of the mapping structures of discrete nodes under the computational accuracy of $$10^{-10}$$ , and the corresponding stability and bifurcation of period-1 motions are determined by eigenvalue analysis. From the discrete nodes of period-1 motions, the finite discrete Fourier series is employed to determine the frequency–amplitude characteristics of period-1 motions in the time-delayed, Duffing oscillator. The stable and unstable, symmetric and asymmetric period-1 motions are presented, and the corresponding stability and bifurcations are illustrated clearly. Presented are the quantity levels of harmonic amplitudes which indicate the accuracy of the semi-analytical solutions of period-1 motions in such a time-delayed oscillator. From the analytical prediction, numerical simulations of complex period-1 motions in the time-delayed, hardening Duffing oscillator are completed. The amplitude spectrums of period-1 motions in the time-delayed Duffing oscillator are given, and the approximate, analytical expressions of period-1 motions can be obtained. For small excitation frequency, discrete time step size should be reduced to keep the same computational accuracy of discrete nodes. This method can be applied to the time-varying time-delayed nonlinear dynamical systems and other nonlinear dynamical systems.
Adding Chemical Equilibrium to a Parallel, Unstructured Euler/Navier-Stokes Flow Solver

AVUS (Air Vehicles Unstructured Solver) is a parallel, unstructured flow solver developed by the Computational Science Branch of the Air Vehicles Directorate of AFRL (Air Force Research Laboratories). In this paper the procedure used to add equilibrium chemistry air to AVUS is discussed. To perform this task the Tannehill curve fits of Srinivasan et al. are used to determine the thermodynamic and transport properties of the air at various stages of disassociation and ionization. To verify the accuracy of the equilibrium air version of the AVUS code several comparisons are made to the published results of other researchers for both two and three-dimensional geometries. This is done for inviscid and viscous flows, subsonic and hypersonic flows, and different body geometries.
Preparation of Low Band Gap Fibrillar Structures by Solvent-Induced Crystallization

Solvent-induced crystallization of the low band gap polymer poly[N-9″-heptadecanyl-2,7-carbazole-alt-5,5-(4′,7′-di-2-thienyl-2′,1′,3′-benzothiadiazole)] (PCDTBT) was shown to give fibril-like structures of 40–60 nm width and ∼0.5 μm length. These structures, formed by heating and cooling PCDTBT in a marginal solvent for the polymer, were characterized by AFM, TEM, GI-WAXS, and steady state absorption and emission spectroscopy. The width of the PCDTBT structures suggests that the polymer chains are oriented perpendicular to the fiber axis, while the observed undulated structure, as revealed by AFM, suggests that the nanostructures may be composed of smaller crystalline units that associate preferentially on specific faces of the crystals. The spectroscopic signatures of the suspended PCDTBT fibrils resembled that of the polymer in solution, in contrast to features associated with the fibril formation of the well-known conjugated polymer poly(3-hexyl thiophene) (P3HT). The solution-based crystallization of ...
Development of a Super Sweet Corn Cultivar,Luyutian No.6

The selective breeding procedure of super sweet corn Luyutian No.6 is introduced. Its yield in regional test, quality is analyzed and evaluated, resistance identification and characteristic of its parents are given. This cultivar of maize has special flavor, good quality, high sugar content, good taste and wide adaptability. And its technologies of culti- vation and seed production are also introduced.
Increase in Postoperative Insulin Requirements Does Not Lead to Decreased Quality of Life after Total Pancreatectomy with Islet Cell Autotransplantation for Chronic Pancreatitis

Previous studies have shown that total pancreatectomy with islet cell autotransplantation improves quality of life in chronic pancreatitis. A significant number of these patients develop postoperative hyperglycemia and daily insulin requirements or increase in daily insulin requirements. Our study investigates whether increased insulin requirements postoperatively have a negative impact on quality of life. A prospectively collected database of 74 patients undergoing extensive pancreatectomy with islet autotransplantation for pancreatitis was reviewed. Data pertaining to daily requirements and quality of life (QOL), as measured by the SF-12 questionnaire, in the preoperative and postoperative period were reviewed. Approval from the Institutional Review Board for the evaluation of human subjects was obtained. Seventy-four patients underwent extensive pancreatectomy with islet autotransplantation for pancreatitis. The majority of these patients required new daily insulin or an increase in daily insulin requirements postoperatively. Mean preoperative HA1c in this group was 5.6 with an increase to 7.3 at 6 months postoperatively (P < 0.001), a mean of 8.1 at 12 months, and 8.9 at 2 years. Mean preoperative daily insulin requirements for this group were five units/day with average increase to 19 units/day at 6 months, 21 units/day at 12 months, and 26 units/day at 2 years. Preoperative QOL scores were a mean of 26 for the physical component and 36 for the mental health component. Postoperatively, physical component scores averaged 33 at 6 months (p < 0.001), 36 at 12 months, and 36 at 2 years; the mental health component scores averaged 42 at 6 months (p = 0.007), 41 at 12 months, and 41 at 2 years. There is no correlation between physical component score or mental component score QOL scores and daily insulin requirements (r = -0.016 and r = 0.039, respectively). Total pancreatectomy with islet cell autotransplantation is an effective surgery for end-stage chronic pancreatitis. Quality of life significantly improves in physical and mental health components regardless of a postoperative increase in daily insulin requirements.
Workup of abdominal pain or vomiting in the gastric band patient

While gastric band placement was a commonly performed operation for severe obesity during the decade after its approval by the FDA in 2001, it has become significantly less popular in recent years due to its inferior weight loss results compared to other bariatric operations. In addition, it is associated with more frequent weight regain, numerous major and minor complications, and the need for additional operations because of the presence of the band. General and bariatric surgeons and emergency departments will regularly see patients for band complications and this chapter is designed to guide in the evaluation and management of such issues.
Human Evolutionary History

We briefly review the relationships of modern humans and the great apes before considering the evidence for and against Ardipithecus ramidus, Ardipithecus kadabba, Orrorin tugenensis, and Sahelanthropus tchadensis being the earliest members of the hominin clade. We then describe each of the well-established hominin taxa recognized in a speciose interpretation of the hominin fossil record into five morphological grades, “archaic hominins,” “megadont and hypermegadont archaic hominins,” “transitional hominins,” “premodern Homo ,” and “anatomically modern Homo ” (the grade that includes modern humans). Within each grade we summarize the species and site samples in historical order. We also consider evidence for anagenesis and cladogenesis within the hominin clade. Finally, we summarize currently available estimates for endocranial volume and body mass, two variables particularly relevant for understanding the evolution of the hominin nervous system.
The Berkeley Contact Lens Extended Wear Study: part I: Study design and conduct

Abstract Objective The primary aim of the Berkeley Contact Lens Extended Wear Study (CLEWS) was to test the hypotheses that extended wear of rigid gas-permeable (RGP) contact lenses with greater oxygen permeability (Dk) reduces the incidence of contact lens–associated keratopathy (CLAK) and increases the survival rate in RGP extended wear (EW). In this article we describe the clinical trial design in detail, present the results of subject recruitment and retention, and provide the baseline demographic and ocular characteristics of the CLEWS subjects, whose data will be analyzed to address the study aims in a companion article. Design A randomized, concurrently controlled clinical trial. Intervention Subjects were fitted with day wear (DW) high-Dk RGP lenses and then adapted to EW. Subjects who adapted to EW were then randomly assigned to either high- or medium-Dk RGP lenses for 12 months of 6-nights/week EW. Main outcome measures Slit-lamp assessment and grading of 17 possible keratopathies, measurement of refractive error and corneal curvature, and symptoms. Follow-up data were collected every 3 months. Results From 545 subjects entering the DW adaptation phase, 201 adapted to EW and were randomly assigned to medium- or high-Dk lenses for 12 months of EW. The baseline characteristics of the two study groups were similar and did not differ from the 344 DW subjects who failed to adapt to EW. The distributions of oxygen transmissibility for the two study groups were disjoint, indicating that each group received distinctly different levels of hypoxia. Conclusions We show that CLEWS was appropriately designed to address the study hypotheses, was conducted with regard for the safety of the subjects, and adhered to rigorous protocols designed to control for bias and ensure the integrity of study data. We establish the internal validity of between-group statistical comparisons and characterize our study population to permit informed evaluation of the applicability of our results to the contact lens–wearing population in general.
A Free-Modular Algorithm for Minimal Design of Linear Multivariable Systems

Abstract Intuitively, the minimal design problem (MDP) for multivariable systems is to select from the set of dynamical systems satisfying a given dynamical constraint a system which can be realized with the smallest number of dynamical elements. In 1973, Wang and Davison gave an MDP algorithm; but an existence test was not in this algorithm. Building upon these results, Forney gave a three-step algorithm which solves MDP, including the question of existence. The present work reformulates MDP in terms of free polynomial modules and gives an improved two-step MDP Algorithm, providing a complete solution including existence and effectively eliminating the first of Forney's three steps.
Team-Based Health Information Exchange Use Increased Mammography Documentation and Referral in an Academic Primary Care Practice: An Interrupted Time Series

Few studies have examined the impact of health information exchanges (HIE) on quality in ambulatory settings. From September 29, 2014, to September 4, 2015, we conducted an interrupted time series analysis of query-based use of the state HIE as part of team-based care to improve mammography screening in an academic primary care practice. Women aged 50–74 years with a practice visit and who were eligible for mammography were included. We conducted non-parametric data analysis using LOESS, followed by ARIMA analysis. During the study period, there were 2020 visits among 904 eligible patients, including 648 visits among 485 patients during 16 baseline weeks, and 1372 visits by 755 patients during 33 intervention weeks. During the intervention period, 16.0% of eligible women who were not up to date in our EHR had a mammogram in the HIE. Of eligible women, the proportion who had a documented up-to-date mammogram at the time of their visit increased by 11.3%, from 73.4% at baseline to 84.7% (p < 0.0001), the proportion who had mammography addressed at the time of their visit increased by 42.7%, from 32.7% at baseline to 75.4% (p < 0.0001), and the proportion who were up to date at 8 weeks post-visit increased by 11.7%, from 76.3% at baseline to 88.0% (p < 0.0001). Query-based use of the state HIE as part of team-based care improved documentation of mammography and led to an increase in the proportion of eligible women who received counseling on mammography screening in one primary care practice. These results suggest that HIE use in primary care could lead to improved delivery of other preventive services.
Novel plasmonic polarimeter for biomedical imaging applications

Using polarized light in medical imaging is a valuable tool for diagnostic purposes since light traveling through scattering tissues such as skin, blood, or cartilage may be subject to changes in polarization. We present a new detection scheme and sensor that allows for directly measuring the polarization of light electronically using a plasmonic sensor. The sensor we fabricated consists of a plasmonic nano-grating that is embedded in a Wheatstone circuit. Using resistive losses induced by optically excited plasmons has shown promise as a CMOScompatible plasmonic light detector. Since the plasmonic response is sensitive to polarization with respect to the grating orientation, measuring the resistance change under incident light supplies a direct electronic measure of the polarization of light without polarization optics. Increased electron scattering introduced by plasmons in an applied current results in a measurable decrease in electrical conductance of a grating, allowing a purely electronic readout of a plasmonic excitation. Accordingly, because of its plasmonic nature, such a detector is dependent on both the wavelength and polarization of incident light with a response time limited by the surface plasmon lifetime.
Life Course: Developmental and Transitional Events

Older adults often face many complex life transitions, such as retirement, bereavement, and relocation. Though each older adult may cope with these transitions uniquely, such life transitions can often be disruptive and serve as psychosocial stressors. In this section, we will review the literature regarding retirement and its relationship to physical and mental health. We will also review the various courses of bereavement, as well as management of grief-related disorders.
SOIL AND OTHER SOURCES OF NITROUS OXIDE

ABSTRACT The soil serves as both a source and sink for nitrous oxide. The production of nitrous oxide tends to be increased by nitrogen fertilization, water logging, and conditions which contribute to low oxygen levels. Ambient atmospheric concentrations of nitrous oxide and soil concentration vary with time and location, with the mean tropospheric concentrations uniform up to altitudes of 12 km. Negative correlation with barometric pressure changes was observed immediately over fertilized soil but not unfertilized soil. Corona and arc discharges produce considerable quantities of nitrous oxide, suggesting that electrical storms and other ionizing phenomena are potential tropospheric sources.
Non-pathogenic Escherichia coli Enhance Stx2a Production of E. coli O157:H7 Through Both bamA -Dependent and Independent Mechanisms.

Intestinal colonization by the foodborne pathogen Escherichia coli O157:H7 leads to serious disease symptoms, including hemolytic uremic syndrome (HUS) and hemorrhagic colitis (HC). Synthesis of one or more Shiga toxins (Stx) is essential for HUS and HC development. The genes encoding Stx, including Stx2a, are found within a lambdoid prophage integrated in the E. coli O157:H7 chromosome. Enhanced Stx2a expression was reported when specific non-pathogenic E. coli strains were co-cultured with E. coli O157:H7, and it was hypothesized that this phenotype required the non-pathogenic E. coli to be sensitive to stx-converting phage infection. We tested this hypothesis by generating phage resistant non-pathogenic E. coli strains where bamA (an essential gene and Stx phage receptor) was replaced with an ortholog from other species. Such heterologous gene replacement abolished the ability of the laboratory strain E. coli C600 to enhance toxin production when co-cultured with E. coli O157:H7 strain PA2, which belongs to the hypervirulent clade 8. The extracellular loops of BamA (loop 4, 6, 7) were further shown to be important for infection by stx2a-converting phages. However, similar gene replacement in another commensal E. coli, designated 1.1954, revealed a bamA-independent mechanism for toxin amplification. Toxin enhancement by 1.1954 was not the result of phage infection through an alternative receptor (LamB or FadL), lysogen formation by stx2a-converting phages, or the production of a secreted molecule. Collectively, these data suggest that non-pathogenic E. coli can enhance toxin production through at least two mechanisms.
Engineering a second brain in a dish.

Abstract The utilization of human pluripotent stem cells holds great promise in elucidating principles of developmental biology and applications in personalized and regenerative medicine. Breakthroughs from the last decade have allowed the scientific community to better understand and successfully manipulate human pluripotent stem cells using distinct differentiation strategies into a variety of target tissues. This manipulation relies solely on our understanding of developmental processes occurring in model organisms. The in vitro translation of our developmental knowledge upon stem cells provides a new means to generate specific tissue to understand developmental and disease mechanisms, as well as physiological processes. The generation of an integrated human intestinal tissue is one such example. In this review, we highlight the biological motivation behind the generation of human intestinal organoids. We further describe the integration of an enteric nervous system within the organoid to generate a functional intestine. Forthcoming strategies to add additional complexities to the intestinal tissue so as to better understand how our “second brain” functions within the gut are also discussed. The organoid system offers a promising avenue to understand how the enteric nervous system works and patterns the human intestine during both physiology and disease.
Reactive Nitrogen Intermediates in Giant Cell Arteritis : Selective Nitration of Neocapillaries

Arterial wall damage in giant cell arteritis (GCA) is mediated by several different macrophage effector functions, including the production of metalloproteinases and lipid peroxidation. Tissue-invading macrophages also express nitric oxide synthase (NOS)-2, but it is not known whether nitric oxide-related mechanisms contribute to the disease process. Nitric oxide can form nitrating agents, including peroxynitrite, a nitric oxide congener formed in the presence of reactive oxygen intermediates. Protein nitration selectively targets tyrosine residues and can result in a gain, as well as a loss, of protein function. Nitrated tyrosine residues in GCA arteries were detected almost exclusively on endothelial cells of newly formed microcapillaries in the media, whereas microvessels in the adventitia and the intima were spared. Nitration correlated with endothelial NOS-3 expression and not with NOS-2-producing macrophages, which preferentially homed to the hyperplastic intima. The restriction of nitration to the media coincided with the production of reactive oxygen intermediates as demonstrated by the presence of the toxic aldehyde, 4-hydroxynonenal. Depletion of tissue-infiltrating macrophages in human temporal artery-SCID mouse chimeras disrupted nitrotyrosine generation, demonstrating a critical role of macrophages in the nitration process that targeted medial microvessels. Thus, protein nitration in GCA is highly compartmentalized, reflecting the production of reactive oxygen and reactive nitrogen intermediates in the inflamed arterial wall. Heterogeneity of microvessels in NOS-3 regulation may be an additional determinant contributing to this compartmentalization and could explain the preferential targeting of newly generated capillary beds.
Recent Research Contributions to Elementary School Mathematics.

In the first month of the Golden Jubilee Year, it seems appropriate to reflect upon selected pioneer researches on elementary school mathematics. This article presents thirty-four examples of research that touch the following eight topics: beginning instruction; content selection; role of drill and practice; basic operations; problem solving; readability and vocabulary; disability; history and summaries of research. Since most of the researches presented here are well known, the methods and results will be described only briefly; more important, they illustrate the tremendous zeal and insight with which elementary school mathematics, and the methods of teaching it, have been studied from the time of the initial professionalization of the subject matter for the elementary school ( 191520) to about the conclusion of World War II in 1945. This period corresponds roughly to the first twenty-five years of the National Council of Teachers of Mathematics.
Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex

Promoter-proximal pausing by RNA polymerase II (Pol II) is a key regulatory step in human immunodeficiency virus-1 (HIV-1) transcription and thus in the reversal of HIV latency. By binding to the nascent transactivating response region (TAR) RNA, HIV-1 Tat recruits the human super elongation complex (SEC) to the promoter and releases paused Pol II. Structural studies of TAR interactions have been largely focused on interactions between the TAR bulge and the arginine-rich motif (ARM) of Tat. Here, the crystal structure of the TAR loop in complex with Tat and the SEC core was determined at a 3.5-A resolution. The bound TAR loop is stabilized by cross-loop hydrogen bonds. It makes structure-specific contacts with the side chains of the Cyclin T1 Tat-TAR recognition motif (TRM) and the zinc-coordinating loop of Tat. The TAR loop phosphate backbone forms electrostatic and VDW interactions with positively charged side chains of the CycT1 TRM. Mutational analysis showed that these interactions contribute importantly to binding affinity. The Tat ARM was present in the crystallized construct; however, it was not visualized in the electron density, and the TAR bulge was not formed in the RNA construct used in crystallization. Binding assays showed that TAR bulge-Tat ARM interactions contribute less to TAR binding affinity than TAR loop interactions with the CycT1 TRM and Tat core. Thus, the TAR loop evolved to make high-affinity interactions with the TRM while Tat has three roles: scaffolding and stabilizing the TRM, making specific interactions through its zinc-coordinating loop, and making electrostatic interactions through its ARM.
Data collection without limits : Automated policing and the politics of framelessness

Predictive policing relies on the most ambitious form of information collection: the collection of everything about everyone, all the time. In this respect it anticipates the “becoming environmental” of surveillance associated with the so-called “internet of things”: the possibility that the entire lived environment could be fitted with an interactive overlay that generates information about users as they move through space and time. This chapter invokes the notion of framelessness to discuss the post-subjective framework for monitoring and policing associated with the rise of data driven pre-emption. It describes the emergence of a post-disciplinary form of policing – not least because disciplinary logics rely on processes of subjectification. If, for panoptic surveillance, being watched all the time was at once too much and not enough, it becomes crucial for post-panoptic regimes.
Numerical simulations of cell flow and trapping within microfluidic channels for stiffness based cell isolation

Analysis of rare cells in heterogenous mixtures is proven to be beneficial for regenerative medicine, cancer treatment and prenatal diagnostics. Scarcity of these cells, however, makes the isolation process extremely challenging. Efficiency in cell isolation is still low and therefore, novel cell isolation strategies with new biomarkers need exploration. In this study, we investigated the feasibility of using the mechanical stiffness difference to detect and isolate the rare cells from the surrounding cells without labelling them. Fluid and solid mechanics simulations have shown that cell isolation can be performed at high efficiency using stiffness-based isolation. Accuracy of the numerical simulations is established using microfluidic flow chamber experiments.
Towards a Theory of Mixing Graphs: A Characterization of Perfect Mixability (Extended Abstract)

We study the problem of fluid mixing in microfluidic chips represented by mixing graphs, that model a network of micro-mixers (vertices) connected by micro-pipes (edges). We address the following perfect mixability problem: given a collection C of droplets, is there a mixing graph that mixes C perfectly, producing only droplets whose concentration is the average concentration of C? We provide a complete characterization of such perfectly mixable sets and an efficient algorithm for testing perfect mixability. Further, we prove that any perfectly mixable set has a perfect-mixing graph of polynomial size, and that this graph can be computed in polynomial time.