Miracle-dz/UniFAR-FTUs huggingface dataset:
Non‐native protein aggregation kinetics

Experimental kinetics of non‐native protein aggregation are of practical importance in that they help dictate viable processing, formulation, and storage conditions for biotechnology products, and appear to play a role in determining the onset of a number of diseases. Fundamentally, aggregation kinetics provide insights into the identity of key intermediates in the process, and quantitative tests of available models of aggregation. Although aggregation kinetics often display seemingly disparate behaviors across different proteins and sample conditions, this review illustrates how many of these can be understood within a general framework that treats aggregation as a multi‐stage process, and how most available kinetic models of aggregation can be grouped hierarchically in terms of which stage(s) they include. This provides an aid for workers seeking a mechanistic interpretation of in vitro aggregation kinetics, for discriminating among competing models, and in designing experiments to assess in vitro protein stability. Limitations and the utility of purely kinetic approaches to studying aggregation, clarifications of common misperceptions regarding experimental aggregation kinetics, and some outstanding challenges in the field are briefly discussed. Biotechnol. Bioeng. 2007;98: 927–938. © 2007 Wiley Periodicals, Inc.
Levels of nerve growth factor and its mRNA in the central nervous system of the rat correlate with cholinergic innervation.

The levels of nerve growth factor (NGF) and its mRNA in the rat central nervous system were determined by two‐site enzyme immunoassay and quantitative Northern blots, respectively. Relatively high NGF levels (0.4‐1.4 ng NGF/g wet weight) were found both in the regions innervated by the magnocellular cholinergic neurons of the basal forebrain (hippocampus, olfactory bulb, neocortex) and in the regions containing the cell bodies of these neurons (septum, nucleus of the diagonal band of Broca, nucleus basalis of Meynert). Comparatively low, but significant NGF levels (0.07‐0.21 ng NGF/g wet weight) were found in various other brain regions. mRNANGF was found in the hippocampus and cortex but not in the septum. This suggests that magnocellular cholinergic neurons of the basal forebrain are supplied with NGF via retrograde axonal transport from their fields of innervation. These results, taken together with those of previous studies showing that these neurons are responsive to NGF, support the concept that NGF acts as trophic factor for magnocellular cholinergic neurons.
Patient counseling practices in U.S. pharmacies: effects of having pharmacists hand the medication to the patient and state regulations on pharmacist counseling.

OBJECTIVES To determine the amount and type of oral counseling given to shoppers posing as new patients with new prescriptions and to determine how state regulations, pharmacy and pharmacist characteristics, and environmental factors affect oral counseling practices. DESIGN Cross-sectional, observational, correlational study. SETTING 41 states and the District of Columbia between January 28 and March 31, 2008. PARTICIPANTS 365 community pharmacy staff members had interactions with shopper-patients. INTERVENTION Shoppers presented new prescriptions in community pharmacies and recorded observations related to oral communication with pharmacy staff. MAIN OUTCOME MEASURES Oral provision of medication information and risk information to shoppers by pharmacy staff, as well as questions asked of shoppers by pharmacy staff. RESULTS Some form of oral communication related to a medication was reported in 68% of encounters. At least one informational item for either medication was provided for approximately 42% of encounters. At least one risk information item was provided in 22% of encounters. Logistic regression findings indicated that the strongest predictor of oral counseling, either providing information or asking questions, was the pharmacist being the pharmacy staff member who handed the medication to the patient, controlling for all other variables in the models. In addition, having strict state regulations specifying that pharmacists must counsel all patients receiving new prescriptions predicted whether patients received counseling. A more private area for prescription pick up also was a significant predictor. CONCLUSION The importance of the direct encounter between the pharmacist and patient and strict state regulations mandating that pharmacists counsel patients with new prescriptions were highlighted by these findings.
The Relationship of Fracture Mechanism between High Temperature Tensile Mechanical Properties and Particle Erosion Resistance of Selective Laser Melting Ti-6Al-4V Alloy

In this study, selective laser melting (SLM) Ti-6Al-4V is subjected to heat treatment for 4 h at 400 °C, 600 °C, and 800 °C, followed by air cooling. After heat treatment at 400 °C and 600 °C, the ductility was lower (strength increased). This was could be for two reasons: (1) high temperature tensile properties, and (2) particle erosion wear induced phase transformation. Finally, the particle erosion rates of as-SLM Ti-6Al-4V and heat treatment for 4 h at 800 °C (labeled 800-AC) were investigated and compared; the lamellar α + β phases in 800-AC are difficult to destroy with erosion particles, resulting in the erosion resistance of 800-AC being higher than that of the martensitic α’ needles in the as-SLM Ti-6Al-4V at all impact angles (even the hardness of the 800-AC specimen was lower). The as-SLM Ti-6Al-4V alloy needs heat treatment to have better wear resistance.
Mutualism versus Independence: Strategies of Mixed-Species Oral Biofilms In Vitro Using Saliva as the Sole Nutrient Source

ABSTRACT During initial dental plaque formation, the ability of a species to grow when others cannot would be advantageous, and enhanced growth through interspecies and intergeneric cooperation could be critical. These characteristics were investigated in three coaggregating early colonizers of the tooth surface (Streptococcus gordoniiDL1, Streptococcus oralis 34, and Actinomyces naeslundii T14V). Area coverage and cell cluster size measurements showed that attachment of A. naeslundii and of S. gordonii to glass flowcells was enhanced by a salivary conditioning film, whereas attachment of S. oralis was hindered. Growth experiments using saliva as the sole carbon and nitrogen source showed that A. naeslundii was unable to grow either in planktonic culture or as a biofilm, whereas S. gordonii grew under both conditions. S. oralis grew planktonically, but to a much lower maximum cell density than did S. gordonii;S. oralis did not grow reproducibly as a biofilm. Thus, only S. gordonii possessed all traits advantageous for growth as a solitary and independent resident of the tooth. Two-species biofilm experiments analyzed by laser confocal microscopy showed that neither S. oralis nor A. naeslundii grew when coaggregated pairwise with S. gordonii. However, both S. oralis and A. naeslundii showed luxuriant, interdigitated growth when paired together in coaggregated microcolonies. Thus, the S. oralis-A. naeslundiipair formed a mutualistic relationship, potentially contact dependent, that allows each to grow where neither could survive alone. S. gordonii, in contrast, neither was hindered by nor benefited from the presence of either of the other strains. The formation of mutually beneficial interactions within the developing biofilm may be essential for certain initial colonizers to be retained during early plaque development, whereas other initial colonizers may be unaffected by neighboring cells on the substratum.
Post–Vertebral Augmentation Back Pain: Evaluation and Management

The causes of persistent pain following vertebral augmentation were investigated by these authors. They evaluated 124 patients and those with pain underwent fluoroscopy at 3 weeks, 3 months, and 12 months. Pain was present in 23% of patients and in most cases arose from the sacroiliac and/or lumbar facet joints. It was immediately relieved in 59% of those who had a local injection of steroid/anesthetics. Forty-one percent had relief after additional injections and 34% eventually required neurolysis for pain control. Thus, pain after vertebral augmentation commonly arises from sites distal to the initial procedure. BACKGROUND AND PURPOSE: Vertebral augmentation is an established treatment for painful osteoporotic vertebral fractures of the spine. Nevertheless, patients may continue to have significant back pain afterward. The purpose of this study was to assess the source of persistent or recurrent back pain following vertebral augmentation. MATERIALS AND METHODS: Our institutional review board approved this study. We evaluated 124 consecutive patients who underwent vertebral augmentation for painful osteoporotic vertebral fractures. All patients were evaluated after 3 weeks, 3 months, and 1 year following their procedure. Patients with any type of back pain after their procedure were examined under fluoroscopy. RESULTS: Thirty-four of 124 (27%) patients were men, and 90/124 (73%) were women. Persistent or recurrent back pain, not due to a new fracture or a failed procedure, was present in 29/124 (23%) patients. The source of pain was most often attributed to the sacroiliac and/or lumbar facet joints (25/29 or 86%). Seventeen of 29 (59%) patients experienced immediate relief after facet joint injection of a mixture of steroid and local anesthetic agents. The remaining 12 (41%) had relief after additional injections. Ten (34%) patients ultimately required radio-frequency neurolysis for long-term relief. CONCLUSIONS: Back pain after vertebral augmentation may not be due to a failed procedure but rather to an old or a new pain generator, such as an irritated sacroiliac or lumbar facet joint. This is of importance not only for further pain management of these patients but also for designing trials to compare the efficacy of vertebral augmentation to other treatments.
A New Technique for the Analysis of Energy Coupling and Exchange in General Antenna Systems

This paper provides a deeper insight into the nature of electromagnetic interactions by studying practical settings of strong and weak mutual coupling involving typical antenna elements coupled through the near field. We develop new techniques capable of analyzing the dynamic structure of generic antenna-antenna interactions by describing how energy exchange is divided between propagating and nonpropagating parts in a way reflecting the geometrical shapes and interelement distances of the coupled antennas. The proposed method is implemented through a special method-of-moment (MoM) numerical model and is used to give information about how energy is localized between antennas or electromagnetic objects, which is directly related to the physics of complex systems and the problem of energy storage, transfer, and manipulations. The work utilizes some recent developments in which a spectral near-field theory and the antenna current Green's function formalism were proposed to analyze and describe general electromagnetic systems. The present formulation is developed in conjunction with the special MoM implementation to generate various numerical illustrations and new field energy density pictures combined with analysis of the physics of near-field coupling as revealed through the new results. The technique realized here can be easily integrated into existing full-wave solvers such as MoM to provide systematic pictures of near-field interactions and coupling with more comprehensive and detailed information compared with conventional port parameters such as the S-matrix. The method is suitable for applications such as near-field detection, energy transfer, and near-field communications, besides its fundamental importance for mutual coupling in antenna arrays in general.
Clustering Induces Redistribution of Syndecan-4 Core Protein into Raft Membrane Domains*

Syndecan-4 is a heparan sulfate-carrying core protein that has been directly implicated in fibroblast growth factor 2 (FGF2) signaling. Recent studies have suggested that many signaling proteins localize to the raft compartment of the plasma cell membrane. To establish whether syndecan-4 is present in the raft compartment, we have studied the distribution of the core protein and an Fc receptor (FcR)-syndecan-4 chimera prior to and following clustering with FGF2 or antibodies. Whereas unclustered syndecan-4 was present predominantly in the non-raft membrane compartment, clustering induced extensive syndecan-4 redistribution to the rafts as demonstrated by the sucrose gradient centrifugation and life confocal microscopy. Although syndecan-4 and caveolin-1 moved in tandem, syndecan-4 was not present in caveolae, a major subset of raft compartments. We conclude that syndecan-4 clustering induces its redistribution to the non-caveolae raft compartment. This process may play an important role in syndecan-4-mediation of FGF2 signaling.
Controlling for false positives: interpreting MBL Etest and MBL combined disc test for the detection of metallo-beta-lactamases.

48: 3729–35. 4. Abouzeed YM, Baucheron S, Cloeckaert A. ramR mutations involved in efflux-mediated multidrug resistance in Salmonella enterica serovar Typhimurium. Antimicrob Agents Chemother 2008; 52: 2428–34. 5. Bailey AM, Paulsen IT, Piddock LJV. RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB, which is inhibited by chlorpromazine. Antimicrob Agents Chemother 2008; 52: 3604–11. 6. Chollet R, Chevalier J, Bollet C et al. RamA is an alternate activator of the multidrug resistance cascade in Enterobacter aerogenes. Antimicrob Agents Chemother 2004; 48: 2518–23. 7. Schneiders T, Amyes SGB, Levy SB. Role of AcrR and RamA in fluoroquinolone resistance in clinical Klebsiella pneumoniae isolates from Singapore. Antimicrob Agents Chemother 2003; 47: 2831–7. 8. Zheng J, Cui S, Meng J. Effect of transcriptional activators RamA and SoxS on expression of multidrug efflux pumps AcrAB and AcrEF in fluoroquinolone-resistant Salmonella Typhimurium. J Antimicrob Chemother 2009; 63: 95–102. 9. Andrews JM. BSAC standardized disc susceptibility testing method (version 7). J Antimicrob Chemother 2008; 62: 256–78. 10. http://www.bsac. org.uk/_db/_documents/version_7_1_february_ 2008.pdf (14 May 2009, date last accessed).
Candidate nsSNPs that can affect the functions and interactions of cell cycle proteins

Nonsynonymous single nucleotide polymorphisms (nsSNPs) alter the encoded amino acid sequence, and are thus likely to affect the function of the proteins, and represent potential disease‐modifiers. There is an enormous number of nsSNPs in the human population, and the major challenge lies in distinguishing the functionally significant and potentially disease‐related ones from the rest. In this study, we analyzed the genetic variations that can alter the functions and the interactions of a group of cell cycle proteins (n = 60) and the proteins interacting with them (n = 26) using computational tools. As a result, we extracted 249 nsSNPs from 77 cell cycle proteins and their interaction partners from public SNP databases. Only 31 (12.4%) of the nsSNPs were validated. The majority (64.5%) of the validated SNPs were rare (minor allele frequencies < 5%). Evolutionary conservation analysis using the SIFT tool suggested that 16.1% of the validated nsSNPs may disrupt the protein function. In addition, 58% of the validated nsSNPs were located in functional protein domains/motifs, which together with the evolutionary conservation analysis enabled us to infer possible biological consequences of the nsSNPs in our set. Our study strongly suggests the presence of naturally occurring genetic variations in the cell cycle proteins that may affect their interactions and functions with possible roles in complex human diseases, such as cancer. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Partial life‐cycle and acute toxicity of perfluoroalkyl acids to freshwater mussels

Freshwater mussels are among the most sensitive aquatic organisms to many contaminants and have complex life‐cycles that include several distinct life stages with unique contaminant exposure pathways. Standard acute (24–96 h) and chronic (28 d) toxicity tests with free larva (glochidia) and juvenile mussels are effective at generating data on contaminant effects at two discrete life stages but do not incorporate effects on brooded glochidia. We developed a novel partial life‐cycle assay that incorporates exposures to brooding adult female mussels and used this method in combination with acute toxicity tests to assess adverse effects of perfluoroctanesulfonic acid (PFOS) and perfluoroctanoic acid (PFOA) on freshwater mussels. Fatmucket (Lampsilis siliquoidea) were exposed to PFOS at two life stages: brooding glochidia (in marsupia) for 36 d and free glochidia in water for 24 h. In standard acute tests with glochidia (24–48 h exposures) and juveniles (48–96 h exposures) of fatmucket and black sandshell (Ligumia recta), glochidia were 8 to 25 times more sensitive than juveniles. Perfluoroctanesulfonic acid significantly reduced the duration of glochidia viability and reduced probability of metamorphosis at concentrations 3,000 times lower than the most sensitive acute endpoint (24‐h EC50). The partial life‐cycle test is adaptable to a variety of endpoints and research objectives and is useful for identifying adverse effects at contaminant concentrations below those required for an acute lethal response. Environ. Toxicol. Chem. 2012; 31: 1611–1620. © 2012 SETAC
Comparison of activities of fluoroquinolones in murine macrophages infected with Mycobacterium tuberculosis

In this study the compounds levofloxacin and sparfloxacin, as well as three experimental compounds (AMQ2, AMQ4, and AMQ5), were compared with isoniazid and rifabutin in terms of their capacity to inhibit the intracellular growth of the drug-susceptible Mycobacterium tuberculosis strain Erdman and the isoniazid-resistant katG gene-negative strain 24 within monolayers of mouse bone marrow-derived macrophages. Both levofloxacin and sparfloxacin, as well as compound AMQ4, had substantial activity in this physiologically relevant model, further confirming the potential usefulness of this class of compounds in the therapy of tuberculosis.
Will Coal save Japan and the World?

The central dogma is critically evaluated in the anthropogenic global warming (AGW) theory of the IPCC, claiming the Planck response is 1.2K when CO2 is doubled. The first basis of it is one dimensional model studies with the fixed lapse rate assumption of 6.5K/km. It is failed from the lack of the parameter sensitivity analysis of the lapse rate for CO2 doubling. The second basis is the Planck response calculation by Cess in 1976 having a mathematical error. Therefore, the AGW theory is collapsed along with the canonical climate sensitivity of 3 K utilizing the radiative forcing of 3.7W/m2 for CO2 doubling. The surface climate sensitivity is 0.14–0.17K in this study with the surface radiative forcing of l.lW/m2. Since the CO2 issue is removed, coal will be the energy for the future of many nations in terms of the amount of resource and production cost.
Young obese women with polycystic ovary syndrome have evidence of early coronary atherosclerosis.

CONTEXT Polycystic ovary syndrome (PCOS) is associated with comorbidities that may contribute to increased risk of cardiovascular disease. PCOS is associated with increased risk of metabolic syndrome, dyslipidemia, and diabetes, but it remains unclear whether traditional cardiovascular (CV) risk factors can help predict coronary artery disease in this population. OBJECTIVE The objectives of the study were to detect early-onset subclinical coronary atherosclerosis (using coronary artery calcium as a marker) in young women with PCOS, compared with age- and body mass index-matched controls, and to compare traditional CV risk factors and inflammatory markers in the two groups. DESIGN This was a prospective case-control study. SETTING The study was conducted at a university hospital. SUBJECTS Twenty-four obese (body mass index >or= 30 kg/m2) PCOS subjects and 24 obese controls participated. OUTCOME MEASURES Coronary artery calcium, inflammatory markers (high-sensitivity C-reactive protein, IL-6, TNFalpha, adiponectin, leptin), fasting blood tests (glucose, lipids, insulin), and dual-energy x-ray absorptiometry scan for body fat distribution were measured. RESULTS Coronary artery calcium was detected in eight of 24 PCOS subjects (33%) and two of 24 controls (8%) (odds ratio 5.5, 95% confidence interval 1.03, 29.45, P < 0.03). Traditional CV risk factors did not differ significantly between the two groups, nor did markers of inflammation or adiposity, body fat distribution, or metabolic parameters with the exception of significantly lower quantitative insulin sensitivity check index (marker for insulin resistance) in the PCOS group (P < 0.05). CONCLUSIONS Young, obese women with PCOS have a high prevalence of early asymptomatic coronary atherosclerosis, compared with obese controls. This increased risk is independent of traditional CV risk factors and novel markers of inflammation. These findings underscore the need to screen and aggressively counsel and treat these women to prevent symptomatic CV disease.
Momentary Patterns of Covariation Between Specific Affects and Interpersonal Behavior: Linking Relationship Science and Personality Assessment

Relationships are among the most salient factors affecting happiness and wellbeing for individuals and families. Relationship science has identified the study of dyadic behavioral patterns between couple members during conflict as an important window in to relational functioning with both short-term and long-term consequences. Several methods have been developed for the momentary assessment of behavior during interpersonal transactions. Among these, the most popular is the Specific Affect Coding System (SPAFF), which organizes social behavior into a set of discrete behavioral constructs. This study examines the interpersonal meaning of the SPAFF codes through the lens of interpersonal theory, which uses the fundamental dimensions of Dominance and Affiliation to organize interpersonal behavior. A sample of 67 couples completed a conflict task, which was video recorded and coded using SPAFF and a method for rating momentary interpersonal behavior, the Continuous Assessment of Interpersonal Dynamics (CAID). Actor partner interdependence models in a multilevel structural equation modeling framework were used to study the covariation of SPAFF codes and CAID ratings. Results showed that a number of SPAFF codes had clear interpersonal signatures, but many did not. Additionally, actor and partner effects for the same codes were strongly consistent with interpersonal theory’s principle of complementarity. Thus, findings reveal points of convergence and divergence in the 2 systems and provide support for central tenets of interpersonal theory. Future directions based on these initial findings are discussed.