cssi/SciSciGPT-SciSciNet huggingface dataset:
The ingredient co-occurrence network of packaged foods distributed in the United States

Abstract This work presents a novel, comprehensive ingredient co-occurrence network of foods in the United States from the Open Food Database. This network, which contains over 69,000 ingredients and 2 million ingredient co-occurrence relationships, provides a glimpse into the current use of common ingredients for food production and distribution in the United States. Understanding food intake behaviors from this data-driven perspective opens up new avenues for precision health and wellness, for example, in studies of obesity, eating disorders, food allergies, and nursing mothers. The results describe a co-occurrence network with a highly connected core of ingredients found in food distributed in the United States, including salt (4.86% of ingredients), sugar (3.63%), water (3.58%). Further analysis of the most densely connected core of ingredients reveals a majority are added nutrients (niacin, riboflavin) or derived from corn, soy, and wheat. Our results suggest a preference for a small group of ingredients that are used frequently in packaged foods and highlight semantic challenges for aggregating ingredients from food products in a systematic way. This novel approach to analysis of data from freely available food databases can be used to enhance existing methods for modeling food composition at the ingredient level.
THE IMPACT OF CARDIOTOXICITY AND TRASTUZUMAB INTERRUPTION ON BREAST CANCER OUTCOMES

Trastuzumab (T) improves outcomes in patients (pts) with HER2 (+) breast cancer (BCA) but is associated with risk of cardiotoxicity (CTOX). CTOX is the most common reason for early T interruption, but the impact of this practice on BCA outcomes is unknown. All pts with stage I-III HER2 (+) BCA
Using More Than 1 (Path)Way to Kill a Host Cell: Lessons From Clostridium perfringens Enterotoxin:

Clostridium perfringens enterotoxin (CPE) is responsible for the symptoms of common intestinal infections due to C. perfringens type F isolates. CPE is a pore-forming toxin that uses certain claudins as a receptor. Previous studies showed that, in enterocyte-like Caco-2 cells, low CPE concentrations cause caspase 3-mediated apoptosis but high CPE concentrations cause necrosis. The recent work published in mBio by Shrestha, Mehdizadeh Gohari, and McClane determined that RIP1 and RIP3 are involved in both CPE-mediated apoptosis and necrosis in Caco-2 cells. Furthermore, mixed lineage kinase-domain (MLKL) oligomerization was shown to be important for necrosis caused by CPE, identifying this necrosis as programmed necroptosis. In addition, calpain activation due to Ca2+ influx through the CPE pore was identified as a critical intermediate step for MLKL oligomerization and, thus, CPE-induced necroptosis. These findings may have applicability to understand the action of some other pore-forming toxins that induce necroptosis and may also be important for understanding CPE action in vivo.
Vertical shear pelvic ring injuries: do transsacral screws prevent fixation failure?

Objectives To determine the frequency of fixation failure after transsacral-transiliac (TS) screw fixation of vertical shear (VS) pelvic ring injuries (OTA/AO 61C1) and to describe the mechanism of failure of TS screws. Design Retrospective cohort study. Setting Level 1 academic trauma center. Patients/participants Twenty skeletally mature patients with unilateral, displaced, unequivocal VS injuries were identified between May 1, 2009 and April 31, 2016. Mean age was 31 years and mean follow-up was 14 months. Twelve had sacroiliac dislocations (61C1.2) and eight had vertical sacral fractures (61C1.3). Intervention Operative treatment with at least one TS screw. Main outcome measurements Radiographic failure, defined as a change of >1 cm of combined displacement of the posterior pelvis compared with the intraoperative position on inlet and outlet radiographs. Results Radiographic failure occurred in 4 of 8 (50%) vertical sacral fractures. Posterior fixation was comprised of a single TS screw in 3 of these 4 failures. The dominant mechanism of screw failure was bending. All of these failures occurred early in the postoperative period. No fixation failures occurred among the sacroiliac dislocations. There were no deep infections or nonunions. Conclusions This is the first study to describe the mechanism of failure of TS screws in a clinical setting after VS pelvic injuries. We caution surgeons from relying on single TS screw fixation for vertically unstable sacral fractures. Close radiographic monitoring in the first few weeks after surgery is advised. Level of evidence Level IV.
Site preference and magnetic properties of Zn-Sn-substituted strontium hexaferrite

The site preference and magnetic properties of Zn, Sn, and Zn-Sn substituted M-type strontium hexaferrite ( SrFe12O19) have been investigated using first-principles total-energy calculations based on density-functional theory. The site occupancy of substituted atoms was estimated by calculating the substitution energies of different configurations. The distribution of different configurations during the annealing process at high temperature was determined using the formation probabilities of configurations to calculate magnetic properties of substituted strontium hexaferrite. We found that the magnetization and magnetocrystalline anisotropy are closely related to the distributions of Zn-Sn ions on the five Fe sites. Our calculation shows that in SrFe11.5Zn0.5O19, Zn atoms prefer to occupy 4f1, 12k, and 2a sites with occupation probabilities of 78%, 19%, and 3%, respectively, while in SrFe11.5SnO19, Sn atoms occupy the 12k and 4f2 sites with occupation probabilities of 54% and 46%, respectively. We also found that in SrFe11Zn0.5Sn0.5O19, (Zn,Sn) atom pairs prefer to occupy the ( 4f1, 4f2), ( 4f1, 12k), and ( 12k, 12k) sites with occupation probabilities of 82%, 8%, and 6%, respectively. Our calculation shows that the increase of magnetization and the reduction of magnetic anisotropy in Zn-Sn substituted M-type strontium hexaferrite as observed experimentally are due to the occupation of (Zn,Sn) pairs at the ( 4f1, 4f2) sites.
NetDI: Methodology Elucidating the Role of Power and Dynamical Brain Network Features That Underpin Word Production.

Canonical language models describe eloquent function as the product of a series of cognitive processes, typically characterized by the independent activation profiles of focal brain regions. In contrast, more recent work has suggested that the interactions between these regions - the cortical networks of language - are critical for understanding speech production. We investigated the cortical basis of picture naming with human intracranial electrocorticography (ECoG) recordings and direct cortical stimulation (DCS), adjudicating between two competing hypotheses: Are task specific cognitive functions discretely computed within well-localized brain regions or rather by distributed networks? The time-resolution of ECoG allows direct comparison of intraregional activation measures (high-gamma power) with graph theoretic measures of interregional dynamics. We developed an analysis framework, “Network dynamics using Directed Information” (NetDI), using information and graph theoretic tools to reveal spatiotemporal dynamics at multiple scales: coarse, intermediate, and fine. Our analysis found novel relationships between the power profiles and network measures during the task. Furthermore, validation using DCS indicates that such network parameters combined with high-gamma power are more predictive than high-gamma power alone, for identifying critical language regions in the brain. NetDI reveals a high-dimensional space of network dynamics supporting cortical language function, and to account for disruptions to language function observed after neurosurgical resection, traumatic injury, and degenerative disease. Significance Statement This work quantifies the network phenomena of distributed cortical substrates supporting language. First, estimated causality among brain regions was assessed with Directed Information. Second, a graph theoretic framework extracted task related dynamics from the causal estimates. Finally, we validated these functionally defined networks against the gold standard for causal inference - behavioral disruption with direct cortical stimulation. We demonstrate that the network measures combined with power have greater predictive capability for identifying critical language regions than discrete, regional power analyses alone.
Deep learning combined with IAST to screen thermodynamically feasible MOFs for adsorption-based separation of multiple binary mixtures.

The structures of metal–organic frameworks (MOFs) can be tuned to reproducibly create adsorption properties that enable the use of these materials in fixed-adsorption beds for non-thermal separations. However, with millions of possible MOF structures, the challenge is to find the MOF with the best adsorption properties to separate a given mixture. Thus, computational, rather than experimental, screening is necessary to identify promising MOF structures that merit further examination, a process traditionally done using molecular simulation. However, even molecular simulation can become intractable when screening an expansive MOF database for their separation properties at more than a few composition, temperature, and pressure combinations. Here, we illustrate progress toward an alternative computational framework that can efficiently identify the highest-performing MOFs for separating various gas mixtures at a variety of conditions and at a fraction of the computational cost of molecular simulation. This framework uses a “multipurpose” multilayer perceptron (MLP) model that can predict single component adsorption of various small adsorbates, which, upon coupling with ideal adsorbed solution theory (IAST), can predict binary adsorption for mixtures such as Xe/Kr, CH4/CH6, N2/CH4, and Ar/Kr at multiple compositions and pressures. For this MLP+IAST framework to work with sufficient accuracy, we found it critical for the MLP to make accurate predictions at low pressures (0.01–0.1 bar). After training a model with this capability, we found that MOFs in the 95th and 90th percentiles of separation performance determined from MLP+IAST calculations were 65% and 87%, respectively, the same as MOFs in the simulation-predicted 95th percentile across several mixtures at diverse conditions (on average). After validating our MLP+IAST framework, we used a clustering algorithm to identify “privileged” MOFs that are high performing for multiple separations at multiple conditions. As an example, we focused on MOFs that were high performing for the industrially relevant separations 80/20 Xe/Kr at 1 bar and 80/20 N2/CH4 at 5 bars. Finally, we used the MOF free energies (calculated on our entire database) to identify privileged MOFs that were also likely synthetically accessible, at least from a thermodynamic perspective.
Natural killer T-cell lymphoma causing bilateral recurrent recalcitrant dacryocystitis.

A 35-year-old female with a history of chronic extensive rhinosinusitis, previously treated twice with functional endoscopic sinus surgery, presented with recurrent dacryocystitis despite prior dac...
CsoDIAq Software for Direct Infusion Shotgun Proteome Analysis (DISPA)

New mass spectrometry data collection methods require new computational tools. Direct Infusion Shotgun Proteome Analy-sis (DISPA) is a new paradigm for expedited mass spectrometry-based proteomics, but the original data analysis workflow was onerous. Here we introduce CsoDIAq, a user-friendly software package for the identification and quantification of pep-tides and proteins from DISPA data. In addition to establishing a complete and automated analysis workflow with a graph-ical user interface, CsoDIAq introduces algorithmic concepts to improve peptide identification speed and sensitivity. These include spectra pooling to reduce search time complexity, and a new spectrum-spectrum match score called match count and cosine (MaCC), which improves target discrimination in a target-decoy analysis. We further show that reanalysis after fragment mass tolerance correction increased the number of peptide identifications. Finally, we adapt CsoDIAq to standard LC-MS DIA, and show that it outperforms other spectrum-spectrum matching software.
What Are You Doing With Your Phone?: How Social Class Frames Parent-Teen Tensions around Teens’ Smartphone Use

Social class contexts shape parents’ guiding principles around teens’ smartphone use. These contexts can affect how parents coach and censor their teens’ smartphone use and can create tensions in the home. Through 174 interviews (87 parent-teen dyads), we find that upper-middle-class families generally adopt an orientation toward scaffolded achievements and working-class families tend to embrace an orientation toward empowered self-sufficiency. We further find that these class-based orientations contribute to parent-teen tensions. For upper-middle-class families, tensions arise when parents insist that teens should use smartphones to get help with academic and enrichment activities and teens disagree about whether their phone-related activities align with this goal. In contrast, we find that conflict can occur in working-class families when teens use their smartphones to get assistance and parents interpret such activity as teens being lazy or not self-sufficient. These findings highlight the role of social class contexts in shaping families’ orientations toward teens’ smartphone use and phone-related tensions.
Pervasive fold switching in a ubiquitous protein superfamily

Abstract Fold-switching proteins challenge the one-sequence-one-structure paradigm by adopting multiple stable folds. Nevertheless, it is uncertain whether fold switchers are naturally pervasive or rare exceptions to the well-established rule. To address this question, we developed a predictive method and applied it to the NusG superfamily of >15,000 transcription factors. We estimate that a substantial population (25%) of the proteins in this family switch folds. Circular dichroism and nuclear magnetic resonance spectroscopies of 10 sequence-diverse variants confirmed our predictions. Subsequently, we leveraged family-wide predictions to determine both conserved contacts and taxonomic distributions of fold-switching proteins. Our results indicate that fold switching is pervasive in the NusG superfamily and that the one-sequence-one-structure protein folding paradigm significantly biases protein structure prediction strategies.
Nitride memristors

We demonstrate a promising new material system for ionic resistive switches: nitride memristors. The switching material is an AlN film, deposited using atomic layer deposition (ALD), and the electrodes can be TiN, Pt or Al. A variety of materials characterizations were performed to determine the structure, composition and impurities of the AlN films.
Ureteral reconstruction and bypass: experience with ileal interposition, the Boari flap-psoas hitch and renal autotransplantation.

AbstractA total of 18 patients underwent an operation for extensive ureteral loss from 1980 to 1986. The indications included recurrent calculi, retroperitoneal fibrosis, surgical trauma and tumor. Of the patients 10 had construction of an ileal ureter (4 had bilateral reconstruction), 6 had creation of a psoas hitch with a Boari bladder tube and 2 were treated by autotransplantation. Mean duration of followup was 4.8 years. The procedure was successful in 17 patients. There were no apparent differences among the groups. Selection criteria and potential complications are discussed with regard to each technique. These procedures provide an excellent means for reconstruction of the urinary tract in patients who have failed other treatments. (J. Urol, 143: 20–23, 1990)
Susceptibility to prostate cancer: interaction between genotypes at the androgen receptor and prostate-specific antigen loci.

The androgen receptor (AR) regulates gene transcription by binding to androgen response elements in target gene promoters. The prostate-specific antigen ( PSA ) gene has a polymorphic androgen response element sequence with two alleles, A and G . We hypothesize that allelic differences in AR-driven PSA expression may influence prostate cancer risk. To test this hypothesis, we assayed PSA genotype for 57 prostate cancer cases and 156 controls from our previous pilot study in which prostate cancer risk was associated with the AR “ CAG - short ” genotype. Odds ratios (ORs) were estimated relating prostate cancer risk to AR and PSA genotypes, singly and in combination. Subjects with the PSA GG genotype were at significantly increased risk for advanced, but not for localized, prostate cancer (OR, 2.90; 95% confidence interval, 1.24–6.78). When cross-classifying subjects by AR and PSA genotypes, subjects with either a CAG-short allele (and not PSA GG ) or with the PSA GG genotype (and not CAG-short ) had a modest, statistically insignificant increase in prostate cancer risk overall. However, subjects with both a short CAG allele and PSA genotype GG had a more than 5-fold increase in prostate cancer risk (OR, 5.08; 95% confidence interval, 1.59–16.25). All of the ORs were substantially greater for advanced prostate cancer. Studies with larger numbers of advanced cases will be needed to confirm these results. These results indicate that polymorphism in the PSA gene promoter influences prostate cancer risk, and that the allelic variation in promoter activity may be androgen-dependent. Furthermore, these results support a multigenic etiology for prostate cancer.
A description of physical therapists' knowledge in managing musculoskeletal conditions.

Background Physical therapists increasingly provide direct access services to patients with musculoskeletal conditions, and growing evidence supports the cost-effectiveness of this mode of healthcare delivery. However, further evidence is needed to determine if physical therapists have the requisite knowledge necessary to manage musculoskeletal conditions. Therefore, the purpose of this study was to describe physical therapists' knowledge in managing musculoskeletal conditions.
Adam Smith and the Stages of Moral Development

The writer explores Adam Smith's Theory of Moral Sentiments, where Smith presents a rich and provocative account of morality. The writer offers an explication of Smith's moral psychology as a stage theory of moral development, with the intention of generating critical points on both mattes of detail and larger implications.
Effects of higher education on achievement for blacks and whites

This study assesses the impact of college on knowledge of vocabulary and mathematics. Unlike many previous studies, this one is able to control for precollege abilities in these academic areas, which presumably tend to select people into or out of college. The results indicate that college attendance has a strong impact on improved performance on these tests, and that these effects are similar for whites and blacks.
A market mechanism for electric power transmission

As competition is introduced into the electric power industry, access and pricing policy for transmission will play a pivotal role in shaping future market structure and performance. The externalities associated with the loop flow phenomenon in an electric power network constitute a significant barrier to the formation of efficient markets for electricity and transmission services. In this paper, we present a new approach to the design of an efficient market mechanism for transmission access that resolves these externalities. Under a trading rule that combines the Coasian and the Pigouvian principles to resolution of externalities, property rights are defined so that a competitive market could be established for transmission services and electricity to achieve a social optimum within a power pool. We characterize a dynamic trading process which is Lyapunov stable and always converges to a competitive equilibrium. Finally, we discuss some practical applicability and long-term investment issues.
Deformation and Fracture of Cu Alloy-Stainless Steel Layered Structures under Dynamic Loading

Abstract Fracture resistance of the current ITER first wall configuration, a copper alloy–stainless steel layered structure, is a major design issue. The question of dynamic crack propagation into and through the first wall structure is examined using dynamic finite element modeling (FEM). Several layered configurations that incorporate both strain and frictional energy dissipation during the fracture process are considered. With fixed overall specimen geometry, the energy required to extend a precrack is examined as a function of material properties, and the layer structure. It is found that the crack extension energies vary dramatically with the fracture strain of materials, and to a much lesser extent with the number of layers. In addition, it is found that crack propagation through the lower ductility copper alloy layer may be deflected at the stainless steel–copper interface and not result in total fracture of the structure. Although the total energy required is affected only to a small degree by the interface properties, the time to extend the precrack is strongly affected. By making proper selections of the interface and the layered material, crack propagation rates and the possibility of full fracture can be substantially reduced.
Impact of diabetes mellitus on outcomes of superficial femoral artery endoluminal interventions

Background Although aggressive endoluminal therapy for superficial femoral artery (SFA) occlusive disease is commonplace, the implications of diabetes mellitus (DM) on long-term outcomes in this population are unclear. We examined the consequences of endovascular treatment of the SFA in patients with and without DM. Methods A database of patients undergoing endovascular treatment of the SFA between 1986 and 2005 was maintained. Three groups were defined: nondiabetic patients, those with non-insulin-dependent DM (NIDDM), and those with insulin-dependent DM (IDDM). Intention-to-treat analysis was performed. Results were standardized to TransAtlantic Inter-Society Consensus (TASC) and Society for Vascular Surgery criteria. Time-dependent outcomes were assessed with Kaplan-Meier survival analyses. Factor analyses were performed using a Cox proportional hazard model for time-dependent variables. Data are presented as mean ± SD where appropriate. Results Endovascular treatment (ie, balloon angioplasty ± adjuvant stenting in 38%) was initiated in 525 limbs in 437 patients (68% male; average age, 66 ± 14 years) for claudication failing conservative therapy or chronic critical limb ischemia (CLI). Of these, 50% were nondiabetic, 26% had NIDDM, and 24% had IDDM. Analyses were separated by those presenting with claudication (61%) and those presenting with CLI (39%). Among patients presenting with claudication, those with IDDM had significantly lower assisted primary patency ( P P = .04). Patencies at 3 years for nondiabetic, NIDDM, and IDDM were 62%, 72%, and 54% (primary), and 81%, 86%, and 65% (assisted primary), respectively. Patency and restenosis rates were associated with lesion calcification, TASC D lesion categorization, and acute periprocedural occlusion. Among patients presenting with CLI, patency and restenosis rates were equivalent across all groups; however, limb salvage was significantly worse for both groups of diabetic patients compared with nondiabetic (NIDDM, P = .01; IDDM, P = .02). Reduction in limb salvage rates was associated with presence of tissue loss at presentation, end-stage renal disease, and progression of distal disease on follow-up. Conclusions Endoluminal therapy for SFA occlusive disease yields lower assisted patency rates and higher restenosis rates for those patients presenting with claudication who have more advanced diabetes (ie, IDDM). Among those patients presenting with CLI, particularly those with tissue loss, limb salvage rates are lowered for the diabetic groups (NIDDM and IDDM) despite equivalent patency and restenosis rates.
Semileptonic Weak Interactions in Nuclei: a Relativistic Analysis

We use a consistent relativistic formalism, with relativistic Hartree wave-functions and a covariant effective current operator with all the properties of the Standard Model, to study semileptonic weak processes in nuclei.Results are obtained for Beta - decay, mu-capture, charge-changing nu-reactions and neutral nu-scattering involving the isodoublet systems ^17F - ^17O and ^3H - ^3He.
What do wolves mean? Conflicting social constructions of Canis lupus in “bordertown”

Meanings are an indispensable part of all human societies, yet when social controversies arise, meanings often lose their shared, commonly understood characteristics. This is exhibited in the substantial variety of meanings imbued to wolves (Canis lupus) by social groups in communities bordering Yellowstone National Park, where wolves were reintroduced beginning in 1995. Residents of the region give a range of meanings to the wolves, including symbols of freedom and wildness, scientific conundrum, and vicious killer. Underlying this complex of meanings is a distinction between dichotomous pairs of concepts, “control/power”; and “self‐determination/freedom.”; Residents see their personal—and even the wolves'—volition (self‐determination and freedom) as being lost to a domineering (powerful and controlling) federal government. In the future, governmental agencies may be able to use an understanding of the multiplicity of meanings created by the social groups involved in environmental controversies to lessen...
Cervical pain syndromes: primary care diagnosis and management

This article discusses treatment of the most common musculoskeletal causes of cervical pain syndromes. A thorough history and physical exam can allow treatment of these disorders without use of unnecessary and costly testing in the current era of managed care.
Effect of morphology of ZnO nanostructures on their toxicity to marine algae

The influence of ZnO nanoparticle morphology on its toxicity for marine diatoms was evaluated. Four ZnO nanoparticle motifs, possessing distinctive sizes and shapes, were synthesized without adding surfactants. Diameters of ZnO spheres ranged from 6.3 nm to 15.7 nm, and lengths of rod-shaped particles were 242 nm to 862 nm. Their effects on the growth of the marine diatoms, Thalassiosira pseudonana, Chaetoceros gracilis, and Phaeodactylum tricornutum, were determined in laboratory cultures. Between 4.1 and 4.9% of the Zn from all types of nanoparticles dissolved within 72 h and was neither concentration dependent nor morphology dependent. Addition of all nanoparticles at all concentrations tested stopped growth of T. pseudonana and C. gracilis, whereas P. tricornutum was the least sensitive, with its growth rate inversely proportional to nanoparticle concentration. Bioaccumulation of Zn released from nanoparticles in T. pseudonana was sufficient to kill this diatom. The toxicity of rod-shaped particles to P. triocornutum was noted to be greater than that of the spheres. The overall results suggest that toxicity studies assessing the effects of nanoparticles on aquatic organisms need to consider both the dissolution of these particles and the cellular interaction of nanoparticle aggregates.
Optic Nerve Decompression May Improve the Progressive Form of Nonarteritic Ischemic Optic Neuropathy

• Optic nerve sheath decompression surgery improved visual function for 12 of 14 patients with progressive nonarteritic ischemic optic neuropathy (NAION). Visual recovery was maintained in all patients during a follow-up period of 6 to 18 months (average, 11 months). Seven patients had experienced a previous NAION in the eye that was not operated on that did not improve spontaneously. Surprisingly, 2 of these 7 eyes with long-standing decreased vision demonstrated some visual improvement after surgery on the contralateral, acutely affected eye. Spontaneous visual improvement did not occur in an age- and sex-matched control group of 12 patients with similar entry-level visual acuity and field loss. Only 1 of 3 patients with sudden, nonprogressive visual loss secondary to NAION improved after surgery. In a control group with nonprogressive NAION, 2 of 15 eyes (14 patients) demonstrated spontaneous improvement. Optic nerve sheath decompression improves visual loss due to progressive NAION, a disorder without any previously effective therapy. However, for acute, nonprogressive NAION, surgery for a small number of patients did not improve the natural history of the disease.
Anti-tumor necrosis factor α therapy and the risk of serious bacterial infections in elderly patients with rheumatoid arthritis

Objective To assess the association between the initiation of anti–tumor necrosis factor α (anti-TNFα) therapy and the risk of serious bacterial infections in routine care. Methods This was a cohort study of patients with rheumatoid arthritis (RA) in whom specific disease-modifying antirheumatic drugs (DMARDs) were initiated. Patients were Medicare beneficiaries ages 65 years and older (mean age 76.5 years) who were concurrently enrolled in the Pharmaceutical Assistance Contract for the Elderly provided by the state of Pennsylvania. A total of 15,597 RA patients in whom a DMARD was initiated between January 1, 1995 and December 31, 2003 were identified using linked data on all prescription drug dispensings, physician services, and hospitalizations. Initiation of anti-TNFα therapy, cytotoxic agents other than methotrexate (MTX), noncytotoxic agents, and glucocorticoids was compared with initiation of MTX. The main outcome measure was serious bacterial infections that required hospitalization. Results The incidence of serious bacterial infections was, on average, 2.2 per 100 patient-years in this population (95% confidence interval [95% CI] 2.0–2.4). Glucocorticoid use doubled the rate of serious bacterial infections as compared with MTX use, independent of previous DMARD use (rate ratio [RR] 2.1 [95% CI 1.5–3.1]), with a clear dose-response relationship for dosages >5 mg/day (for ≤5 mg/day, RR 1.34; for 6–9 mg/day, RR 1.53; for 10–19 mg/day, RR 2.97; and for ≥20 mg/day, RR 5.48 [P for trend < 0.0001]). Adjusted models showed no increase in the rate of serious infections among initiators of anti-TNFα therapy (RR 1.0 [95% CI 0.6–1.7]) or other DMARDs as compared with initiators of MTX. Conclusion In a large cohort of patients with RA, we found no increase in serious bacterial infections among users of anti-TNFα therapy compared with users of MTX. Glucocorticoid use was associated with a dose-dependent increase in such infections.
Scam feels the pinch.

The paper by Movileanu et al. 2001 in this issue of The Journal describes a test of the applicability of the substituted-cysteine-accessibility method (SCAM; Akabas et al. 1992; Akabas et al. 1994) to the problem of locating the narrowest region of a channel lumen. Movileanu et al. 2001 use unusually large sulfhydryl-directed reagents to probe the wide bore channel formed by Staphylococcal α-hemolysin. The structure of the membrane-associated form of this protein has been solved to high resolution (Song et al. 1996). It is a mushroom-shaped heptameric complex that inserts in the membrane of a susceptible cell with the wide cap on the extracellular side, or on the cis side of an artificial planar lipid membrane, and with the stem traversing the bilayer (see Figure 1 in Movileanu et al. 2001). The entrance to the pore at the extracellular or cis end is 30 A wide. The pore immediately narrows to ∼20 A, and then widens into a large vestibule 46 A across. The pore again narrows to ∼16 A, its major constriction, and then continues to its intracellular or trans end as an irregular cylinder, which is roughly 20 A wide. Bayley and co-workers (Movileanu et al. 2001) demonstrate that they can locate the narrowest constriction of the pore by applying SCAM with large enough reagents.
Genetically engineered crops and foods: back to the basics of technology diffusion

Abstract Genetically engineered crops and foods have been accepted in the marketplace at an impressive rate since their introduction in the mid-1990s. However, the future of these products, and the many agricultural and food products still under development, has become cloudy. To understand how the use of genetic engineering has arrived at this juncture and where the technology might go in the future, this article returns to a time-tested model from the past. Everett Rogers’ five factors of diffusion provide insight into the variety of influences—technical, ethical, political, economic, cultural, health, and environmental—that have encouraged and discouraged the global diffusion of genetically engineered crops and foods. The analysis sets the stage for a discussion of how the barriers to diffusion might be overcome in the future through new product development, increased study of health and environmental impacts, improved management of the global marketplace, labeling, and making important distinctions between genetic modification and genetic engineering.
Layered sensing with radio (LSWR)

An alternative approach to a Layered Sensing System-of-Systems methodology, denoted as LSWR (Layered Sensing With Radio), is outlined in this paper. This is a novel Broadcast-TV-Driven layered sensing technique that shows potential for finding embedded objects within, for example, buildings via leveraging and combining existing commercial satellite technologies with COTS (Commercial Off-the-Shelf) wireless network technologies and state-of-the-art wireless sensor mote technologies. Specifically, compact sensor mote technologies are employed in a cost-effective manner to interface with and control low-cost satellite radio/broadcast tuners. With this approach, initial concepts of this type are investigated via the analysis of compact custom sensor node technology (i.e. wireless sensor mote interfaced with satellite broadcast tuner) integrated onto a UGV (unmanned ground vehicle) robot arm for purposes developing prototype UGV robot systems with passive integrated RF sensors that support, for example, networked thru-wall embedded object detection. The primary category of commercial satellite signal considered for analysis within this paper is known as DVB (Digital Video Broadcast).
Enhancing Electrospray Ionization Efficiency of Peptides by Derivatization

With the advent of electrospray ionization mass spectrometry, the world was given a new way to look at complex peptide mixtures. Identification of proteins via their signature peptides requires ionization of a representative portion of the peptides derived from proteins by proteolysis. Unfortunately, matrix effects prohibited electrospray ionization of many peptides. This paper describes the development of a new labeling reagent that simultaneously adds a permanent positive charge to peptides and increases their hydrophobicity to enhance their ionization efficiency. The labeling agent is preactivated with N-hydroxysuccinimide to react with primary amines to form a peptide bond. In the most dramatic case, ionization efficiency of the peptide ADRDQYELLCLDNTRKPVDEYK increased 500-fold after derivatization as opposed to other peptides where ionization efficiency was impacted little. Ionization efficiency of peptides was enhanced roughly 10-fold in general by derivatization. Peptides of less than 500 Da experi...
Microbial Ecology of the Hive and Pollination Landscape: Bacterial Associates from Floral Nectar, the Alimentary Tract and Stored Food of Honey Bees (Apis mellifera)

Nearly all eukaryotes are host to beneficial or benign bacteria in their gut lumen, either vertically inherited, or acquired from the environment. While bacteria core to the honey bee gut are becoming evident, the influence of the hive and pollination environment on honey bee microbial health is largely unexplored. Here we compare bacteria from floral nectar in the immediate pollination environment, different segments of the honey bee (Apis mellifera) alimentary tract, and food stored in the hive (honey and packed pollen or “beebread”). We used cultivation and sequencing to explore bacterial communities in all sample types, coupled with culture-independent analysis of beebread. We compare our results from the alimentary tract with both culture-dependent and culture-independent analyses from previous studies. Culturing the foregut (crop), midgut and hindgut with standard media produced many identical or highly similar 16S rDNA sequences found with 16S rDNA clone libraries and next generation sequencing of 16S rDNA amplicons. Despite extensive culturing with identical media, our results do not support the core crop bacterial community hypothesized by recent studies. We cultured a wide variety of bacterial strains from 6 of 7 phylogenetic groups considered core to the honey bee hindgut. Our results reveal that many bacteria prevalent in beebread and the crop are also found in floral nectar, suggesting frequent horizontal transmission. From beebread we uncovered a variety of bacterial phylotypes, including many possible pathogens and food spoilage organisms, and potentially beneficial bacteria including Lactobacillus kunkeei, Acetobacteraceae and many different groups of Actinobacteria. Contributions of these bacteria to colony health may include general hygiene, fungal and pathogen inhibition and beebread preservation. Our results are important for understanding the contribution to pollinator health of both environmentally vectored and core microbiota, and the identification of factors that may affect bacterial detection and transmission, colony food storage and disease susceptibility.
Chapman and Alfvén: A rigorous mathematical physicist versus an inspirational experimental physicis

Modern magnetospheric physics owes its initial development to two great pioneers: Sydney Chapman and Hannes Alfven (Figure 1), who took very different and contrasting approaches to their research activities. This caused one of the most memorable controversies in space physics during the 20th century. The controversy was initiated formally by Alfven [1951] when he criticized a paper by D.F. Martyn entitled, “The Theory of Magnetic Storms and Auroras,” published in Nature in 1951. Alfven stated: “Dr. Martyns treatment is founded on Chapman-Ferraro's theory of magnetic storms. It is not my intention to review here the objections to this theory, objections which I believe to be fatal—nor is it worthwhile to discuss the curious super structure which Dr. Martyn tried to erect on this weak ground.” Alfven's objections will be described after briefly providing the background on which the Chapman-Ferraro theory was constructed. It may be mentioned at the outset that Chapman, together with T. G. Cowling, was well recognized by his publication of a classical treatise, “The Mathematical Theory of Non-Uniform Gases” in 1953; and also, with J. Bartels, of “Geomagnetism” in 1940, while Alfv´en established himself by the publication of an inspirational book,“Cosmical Electrodynamics” in 1950.
Sound Radiation from Ducts for the Case of Low Mach Number

A new method for rapidly solving duct end-plane impedance problems is presented. The method is based on deriving a new form of the Helmholtz integral formula expressing the normal derivative of the acoustic pressure at a boundary point. A set of integral expressions is obtained by satisfying the existing boundary conditions, and then solved using a general collocation method. The results obtained for the Levine-Schwinger problem agree well with the exact values. In the case of a duct flow having a temperature mismatch with the surroundings, the results show an increase in the magnitude of the reflection coefficient for the case of a cold core, and a decrease in its value for the case of hot core, as compared with the case of exhaust into a uniform medium. A phase change of between v/2 and TT is nearly always achieved, which indicates the tendency towards maintaining a constant pressure at the exit plane. The method can easily be extended to arbitrary duct shapes, as long as they are axisymmetric; and the method consumes relatively little computer time.
Mechanism of the light-state transition in photosynthesis: V. 77 K linear dichroism of Anacystis nidulans in State 1 and State 2

Abstract Linear-dichroism spectra of Anacystis nidulans at 77 K were determined for whole cells chemically fixed in light State 1 and light State 2. Whole cells were oriented by the squeezed gel technique using 5% gelatin 2.2 M sucrose gels. Peaks with positive dichroism were observed at 638 nm and 688 nm with shoulders at approx. 650 nm and 700 nm. The amplitude of the 650 nm shoulder was greater for cells in State 2 than those in State 1, and the State-2-minus-State 1 difference spectrum had a single peak at 656 nm. The linear dichroism spectrum of phycobilisomes isolated from A. nidulans showed peaks at 635 nm (phycocyanin) and 656 nm (allophycocyanin). The spectrum for thylakoid membranes free of phycobilisomes had one peak at 685 nm with a shoulder at 698 nm. We suggest that the change in dichroism at 656 nm between cells in State 1 and State 2 results from a change in orientation of the allophycocyanin core of the phycobilisome. This result is discussed in the context of our model for the light-state transition in phycobilisome-containing organisms.
Research on High School Economic Education

Attention is given to the ways in which high school student learning in economics has been measured and to research findings using those measures. Standardized test scores show no great difference between one method of instruction and another. There is a need for alternative measures.
Fredholm and regularity theory of Douglis–Nirenberg elliptic systems on $${\mathbb{R}^{N}}$$

We give a fairly complete exposition of the Fredholm properties of the Douglis–Nirenberg elliptic systems on $${\mathbb{R}^{N}}$$ in the classical (unweighted) L p Sobolev spaces and under “minimal” assumptions about the coefficients. These assumptions rule out the use of classical pseudodifferential operator theory, although it is indirectly of assistance in places. After generalizing a necessary and sufficient condition for Fredholmness, already known in special cases, various invariance properties are established (index, null space, etc.), with respect to p and the Douglis–Nirenberg numbers. Among other things, this requires getting around the problem that the L p spaces are not ordered by inclusion. In turn, with some work, invariance leads to a regularity theory more general than what can be obtained by the method of differential quotients.
Physical context for theoretical approaches to sediment transport magnitude-frequency analysis in alluvial channels

Theoretical approaches to magnitude-frequency analysis (MFA) of sediment transport in channels couple continuous flow probability density functions (PDFs) with power law flow-sediment transport relations (rating curves) to produce closed-form equations relating MFA metrics such as the effective discharge, Qeff, and fraction of sediment transported by discharges greater than Qeff, f+, to statistical moments of the flow PDF and rating curve parameters. These approaches have proven useful in understanding the theoretical drivers behind the magnitude and frequency of sediment transport. However, some of their basic assumptions and findings may not apply to natural rivers and streams with more complex flow-sediment transport relationships or management and design scenarios, which have finite time horizons. We use simple numerical experiments to test the validity of theoretical MFA approaches in predicting the magnitude and frequency of sediment transport. Median values of Qeff and f+ generated from repeated, synthetic, finite flow series diverge from those produced with theoretical approaches using the same underlying flow PDF. The closed-form relation for f+ is a monotonically increasing function of flow variance. However, using finite flow series, we find that f+ increases with flow variance to a threshold that increases with flow record length. By introducing a sediment entrainment threshold, we present a physical mechanism for the observed diverging relationship between Qeff and flow variance in fine and coarse-bed channels. Our work shows that through complex and threshold-driven relationships sediment transport mode, channel morphology, flow variance, and flow record length all interact to influence estimates of what flow frequencies are most responsible for transporting sediment in alluvial channels.
Strong Mechanoluminescence from UV-Irradiated Spinels of ZnGa2O4:Mn and MgGa2O4:Mn

The mechanoluminescence (ML) from spinels of MgAl2O4:Mn (MAO:Mn), MgGa2O4:Mn (MGO:Mn) and ZnGa2O4:Mn (ZGO:Mn) has been investigated. It was found that the MGO:Mn and ZGO:Mn gave a strong ML response and a long-lasting phosphorescence (LLP). On the contrary, MAO:Mn exhibited very weak ML and no LLP. The high ML intensity of MGO:Mn and ZGO:Mn is attributed to a large number of trapped carriers which has been clarified by the measurement of thermoluminescence. The carrier traps in MGO:Mn and ZGO:Mn are assumed to be produced by the point defects due to the partially inverse spinel structure and the oxygen vacancies generated by heat-treatment in a reducing atmosphere. It is suggested that the trapped electrons in oxygen vacancies can be excited by the application of friction, and the resultant recombination between the excited electrons and the trapped holes in the point defects gives rise to an energy which can be transferred to Mn2+ centers to produce the green emission according to the transition 4T1(4G)→6A1(6S).
To Share or Not to Share: The Place of Personal Disclosure in Scholarly Writing

The norms of scholarly discourse have traditionally excluded personal disclosures in conceptual articles, as if the subjective nature of such revelations would be inconsistent with the scientific/objective stature of these works. Based on the author's experience with a recent publication, based on recent studies of researcher projection and bias in case studies, and using a framework of organizational communication, it is suggested here that there is indeed a contribution such disclosures can make. It is not recommended that sharing on a personal level become a new norm, but rather that the choice to share be considered as viable in a scholarly context. Five specific benefits of such sharing are listed, including unearthing and revealing bias, demystifying the process of discovery, and avoiding the trap of defensive reasoning.
Superhydrophobic surfaces and emerging applications: Non-adhesion, energy, green engineering

Abstract This paper provides a review of superhydrophobicity and related phenomena (superoleophobicity, omniphobicity, self-cleaning) induced by surface micro- and nanostructuring. The classical approaches to superhydrophobicity using the Young, Wenzel, and Cassie–Baxter models for the contact angle (CA) are presented. After that, the issues that are beyond the Wenzel and Cassie–Baxter theories are discussed, such as multiscale effects, 1D vs. 2D interactions, the effects of contact line, size of roughness details, curvature, and CA hysteresis dependence on roughness. New potential applications of superhydrophobicity are reviewed, such as new ways of energy transition, antifouling, and environment-friendly manufacturing.