Miracle-dz/UniFAR-FTUs huggingface dataset:
NR2A‐containing NMDA receptors are required for L‐LTP induction and depotentiation in CA1 region of hippocampal slices

Long‐term potentiation (LTP) is a well‐characterized form of synaptic plasticity that fulfills many of the criteria for the neural correlate of memory. LTP reversal (or depotentiation, DP) is thought to correlate with prevention or elimination of memory storage. LTP during and immediately after induction can be easily reversed by afferent stimulation, when applied within the optimal time window. The aim of the present study was to determine whether later‐phase LTP (L‐LTP) could be reversed by special patterned stimulation applied at 2 h after LTP induction, as well as to characterize the receptor mechanisms underlying this reversal. Field excitatory postsynaptic potentials evoked by Schaffer collateral stimulation were recorded from the CA1 subfield of adult rat hippocampal slices. Results demonstrated that stable LTP, which was induced by six theta‐burst stimulations, was mediated by NR2A‐containing N‐methyl‐d‐aspartate receptors (NMDARs). This L‐LTP was partially reversed by high‐intensity paired‐pulse low‐frequency stimulation (HI‐PP‐LFS) and was inhibited by Zn2+ (30 nm), a voltage‐independent NR2A‐NMDAR antagonist. However, NR2B‐NMDAR antagonists (Ro 25‐6981, 1 μm) displayed no effect on L‐LTP reversal. L‐LTP partial reversal was also induced by HI‐PP‐LFS, when the protein synthesis inhibitors anisomycin (25 μm) and cycloheximide (60 μm) were applied following LTP induction. These results suggested that NR2A‐containing NMDARs are required for L‐LTP induction and DP in the hippocampal CA1 area of adult rats. Moreover, HI‐PP‐LFS was an effective stimulation pattern to induce DP.
Methods for Pretreatment of Lignocellulosic Biomass for Efficient Hydrolysis and Biofuel Production

Biofuels produced from various lignocellulosic materials, such as wood, agricultural, or forest residues, have the potential to be a valuable substitute for, or complement to, gasoline. Many physicochemical structural and compositional factors hinder the hydrolysis of cellulose present in biomass to sugars and other organic compounds that can later be converted to fuels. The goal of pretreatment is to make the cellulose accessible to hydrolysis for conversion to fuels. Various pretreatment techniques change the physical and chemical structure of the lignocellulosic biomass and improve hydrolysis rates. During the past few years a large number of pretreatment methods have been developed, including alkali treatment, ammonia explosion, and others. Many methods have been shown to result in high sugar yields, above 90% of the theoretical yield for lignocellulosic biomasses such as woods, grasses, corn, and so on. In this review, we discuss the various pretreatment process methods and the recent literature that.
Evidence in the auroral record for secular solar variability

The historial record of aurorae is continuous and usefully dense for at least the 2000 years. Revival of interest in the secular variability in solar activity motivates a review of the auroral record. The existence of secular variations in the auroral occurrence frequency has been known since the early 1700's, including the existence of a significant attenuation of auroral activity during the Maunder Minimum. Investigation of secular variations prior to the Maunder Minimum is now possible based on six auroral catalogs that have been published within the last 20 years. The catalogs cover the time period from the fifth century B.C. to the seventeenth century A.D. and combine both oriental and European obsertions. Features corresponding to the previously recognized Medieval Minimum, Medieval Maximum, and the Spoerer Minimum are clearly evident in both oriental and European records. The global synchronicity of anomalies in the auroral occurrence frequency is used to argue that they are caused by changes in the level or state of solar activity. The combined catalogs provide a sufficient number of events in the Middle Ages to resolve a quasi-80-year periodicity in the recorded auroral occurrence frequency. Also in the unusually rich intervals of the Middle Ages, clear quasi-10-yearmore » periodicities appear in the recorded occurrence frequency wave from. These are most reasonably interpreted as manifestations of the 11-year solar cycle and indicate that the solar cycle was then operative. « less
Cluster-Randomized Studies.

BACKGROUND Cluster-randomized trials (CRT) are needed to compare interventions that are allocated to entire groups of subjects, rather than to individuals. Publications about CRT have become steadily more common over the past decade. Readers of such publications should be able to categorize and interpret the findings of CRT correctly while considering the methodological requirements applicable to this type of study. METHODS This review is based on a selection of pertinent literature and on the authors' expertise. CRT-specific methodological aspects of the planning, performance, and interpretation of studies are discussed. RESULTS Readers of publications on CRT should check whether due consideration has been given to correlations within and between the clusters during the planning of the study. These correlations enable the determination whether persons within a cluster resemble each other more closely, or respond more similarly to the study intervention, than persons drawn from different clusters. It should also be checked whether the randomization for the study has been carried out with such methods as stratification and covariate-adjusted randomization. CRT can be analyzed on either the individual or the cluster level. The rationale for the choice of a clusterrandomized design should be explained, and intracluster correlation coefficients (ICC) should be reported as an aid to the planning of future studies. Particular requirements are also described in an extended version of the CONSORT guidelines that has been developed specifically for CRT. CONCLUSION Readers of publications on CRT should be aware of the special requirements mentioned above with respect to the design, performance, and analysis of this type of study as opposed to individually randomized studies. If no special techniques are applied in the design, performance, and analysis of a CRT, or if the assumptions underlying each of these steps have not been properly checked, then the findings of the study may well be misleading.
Reducing Parental Demand for Antibiotics by Promoting Communication Skills

Abstract Antibiotic-resistant strains of bacteria are continuing to emerge as high rates of antibiotic use persist. Children are among the highest users of antibiotics, with parents influencing physician decision-making regarding antibiotic prescription. An intervention based on Social Cognitive Theory (SCT) to reduce parents' expectations for antibiotics in favor of communication with the physician was tested. A randomized factorial design study was conducted testing a communication skills intervention against an information-based intervention, a combined intervention and a control condition. Parents receiving the communication skills intervention reported higher efficacy to communicate with the physician (p = 0.021). Interaction between the communication skills and information interventions was observed for specific treatment expectations prior to the visit (p = 0.049). The communication skills intervention was protective against antibiotic prescribing (p = 0.042). Satisfaction was positively associated with parents' efficacy to communicate (p = 0.002) and when an antibiotic was not prescribed (p = 0.005). Interventions using information to reduce antibiotic use may be based on the false assumption that such approaches are sufficient for motivating appropriate health practices. Using demonstrated behavior change approaches to promote communication behaviors by parents might result in the dual benefits of reducing unwarranted antibiotic use and improving satisfaction with the clinic visit.
Two Yeast PUF Proteins Negatively Regulate a Single mRNA*

mRNA stability and translation are regulated by protein repressors that bind 3′-untranslated regions. PUF proteins provide a paradigm for these regulatory molecules: like other repressors, they inhibit translation, enhance mRNA decay, and promote poly(A) removal. Here we show that a single mRNA in Saccharomyces cerevisiae, encoding the HO endonuclease, is regulated by two distinct PUF proteins, Puf4p and Mpt5p. These proteins bind to adjacent sites and can co-occupy the mRNA. Both proteins are required for full repression and deadenylation in vivo; their removal dramatically stabilizes the mRNA. The two proteins act through overlapping but non-identical mechanisms: repression by Puf4p is dependent on deadenylation, whereas repression by Mpt5p can occur through additional mechanisms. Combinatorial action of the two regulatory proteins may allow responses to specific environmental cues and be common in 3′-untranslated region-mediated control.
Effects of Laser Power on Track Profile and Structure Formation during Selective Laser Melting of CoCrMo Alloy

A strong research effort has continued to determine how selective laser melting (SLM) process parameters relate to the amount of defects present in SLM products. However, how these parameters affect the track profiles which should geometrically affect the amount of lack of fusion (LOF) during SLM has not been studied. This study is needed as severe LOF should be a severe quality and property issue. In this work, how laser power (P) and thus energy, as other build rate related parameters are kept unchanged, affects the size of SLM tracks and the formation of LOF during SLM of CoCrMo alloy has been studied. Through examining the track profiles, track sizes have been geometrically demonstrated to insufficiently overlay and overlap for LOF free when the recommended condition (P = 180W) was used. A further contributing factor for LOF is the irregularity of track shape. Increasing P increased the sizes and improved the stability of the melt and the shape regularity of the tracks, reducing the amount of LOF. It will be shown that there is a rapid decay in the amount of LOF as P increases from 180 W, predominantly as the result of geometrical effect of the track profile on track coverage.
Proteomic identification of novel targets regulated by the mammalian target of rapamycin pathway during oligodendrocyte differentiation

Previous work from our laboratory demonstrated that the mammalian target of rapamycin (mTOR) is active during and required for oligodendrocyte progenitor cell (OPC) differentiation. Here, we applied an iTRAQ mass spectrometry‐based proteomic approach to identify novel targets of the mTOR pathway during OPC differentiation. Among the 978 proteins identified in this study, 328 (34%) exhibited a greater than 20% change (P < 0.05) in control versus rapamycin‐treated cultures following 4 days of differentiation in vitro. Interestingly, 197 (20%) proteins were elevated in rapamycin‐treated cultures, while 131 (13%) proteins were downregulated by rapamycin. In support of our previous data, inhibiting mTOR caused a dramatic reduction in the expression of myelin proteins. mTOR also was required for the induction of proteins involved in cholesterol and fatty acid synthesis, as well as the expression of many cytoskeletal proteins, cell signaling components, and nuclear/transcriptional regulators. Of particular interest was the identification of several critical mediators of oligodendrocyte differentiation. Specifically, mTOR activity controls the developmentally programmed upregulation of the prodifferentiation factors Fyn and Quaking, whereas the expression of the differentiation repressor Gpr17 was elevated by mTOR inhibition. These data reveal a distinct signature of mTOR‐regulated protein expression during OPC differentiation. © 2011 Wiley‐Liss, Inc.
Integrating one-dimensional and three-dimensional maps of genomes

Genomes exist in vivo as complex physical structures, and their functional output (i.e. the gene expression profile of a cell) is related to their spatial organization inside the nucleus as well as to local chromatin status. Chromatin modifications and chromosome conformation are distinct in different tissues and cell types, which corresponds closely with the diversity in gene-expression patterns found in different tissues of the body. The biological processes and mechanisms driving these general correlations are currently the topic of intense study. An emerging theme is that genome compartmentalization – both along the linear length of chromosomes, and in three dimensions by the spatial colocalization of chromatin domains and genomic loci from across the genome – is a crucial parameter in regulating genome expression. In this Commentary, we propose that a full understanding of genome regulation requires integrating three different types of data: first, one-dimensional data regarding the state of local chromatin – such as patterns of protein binding along chromosomes; second, three-dimensional data that describe the population-averaged folding of chromatin inside cells and; third, single-cell observations of three-dimensional spatial colocalization of genetic loci and trans factors that reveal information about their dynamics and frequency of colocalization.
Reliability and validity of the Pittsburgh Sleep Quality Index and the Epworth Sleepiness Scale in older men.

BACKGROUND The Pittsburgh Sleep Quality Index (PSQI) and the Epworth Sleepiness Scale (ESS) are commonly used to quantify sleep and excessive daytime sleepiness in older adults. These measures, however, have not been comprehensively evaluated for their psychometrics in older men. We determined the internal consistency reliability and construct validity of the PSQI and ESS in a sample of older men. METHODS Participants were 3,059 men (mean age = 76.4 years) in the Osteoporotic Fractures in Men Study (MrOS) who completed the two questionnaires, wrist actigraphy, and a range of additional psychosocial and health measures. RESULTS Internal consistency was adequate for the PSQI (Cronbach's α =.69) and the ESS (α = .70) total scores. PSQI daytime dysfunction and sleep medications components were weakly associated with the total score, but their removal did not notably improve internal consistency. PSQI and ESS totals were associated with each other and with theoretically related variables (ie, actigraphic variables, depressive symptoms, mobility/instrumental activities of daily living, health-related quality of life) in expected directions. The PSQI differentiated participants reporting no sleep disorder from those reporting particular disorders more reliably than the ESS. CONCLUSIONS In general, we found evidence of the internal consistency reliability and construct validity of the PSQI and ESS in older men. Despite low correlation with the PSQI global score, the PSQI daytime dysfunction and sleep medications components do not appreciably reduce the PSQI total score's reliability or validity in older men.
Prospective uncertainty: The range of possible futures in physical prediction

Recent research has suggested that people make physical predictions based on extrapolation from a noisy representation of the world, which gives rise to a probabilistic distribution over possible future worlds. But can people use the uncertainty of their predictions to inform their decisions, or can people access only a single possible future? Here we demonstrate that confidence-sensitive decisions about the future track the amount of uncertainty expected from probabilistic forward extrapolations. Participants were asked to make predictions about where a ball would go and indicate an expected range around that prediction. This range was well correlated with two measures of uncertainty: variability in predictions across participants and the amount of uncertainty expected by a model of physical prediction. This suggests that people form a probabilistic distribution over possible futures in the course of physical prediction and base their decisions about the future on this range.
Purification of Intracellular Bacterial Communities during Experimental Urinary Tract Infection Reveals an Abundant and Viable Bacterial Reservoir

ABSTRACT Urinary tract infections (UTIs) are a major infection of humans, particularly affecting women. Recurrent UTIs can cause significant discomfort and expose patients to high levels of antibiotic use, which in turn contributes to the development of higher antibiotic resistance rates. Most UTIs are caused by uropathogenic Escherichia coli, which is able to form intracellular collections (termed intracellular bacterial communities [IBCs]) within the epithelial cells lining the bladder lumen. IBCs are seen in both infected mice and humans and are a potential cause of recurrent UTI. Genetic and molecular studies of IBCs have been hampered both by the low number of bacteria in IBCs relative to the number extracellular bacteria and by population bottlenecks that occur during IBC formation. We now report the development of a simple and rapid technique for isolating pure IBCs from experimentally infected mice. We verified the specificity and purity of the isolated IBCs via microscopy, gene expression, and culture-based methods. Our results further demonstrated that our isolation technique practically enables specific molecular studies of IBCs. In the first such direct measurement, we determined that a single epithelial cell containing an early IBC typically contains 103 viable bacteria. Our isolation technique complements recent progress in low-input, single-cell genomics to enable future genomic studies of the formation of IBCs and their activation pathways during recurrent UTI, which may lead to novel strategies to eliminate them from the bladder.
Agent-based modelling as scientific method: a case study analysing primate social behaviour

A scientific methodology in general should provide two things: first, a means of explanation and, second, a mechanism for improving that explanation. Agent-based modelling (ABM) is a method that facilitates exploring the collective effects of individual action selection. The explanatory force of the model is the extent to which an observed meta-level phenomenon can be accounted for by the behaviour of its micro-level actors. This article demonstrates that this methodology can be applied to the biological sciences; agent-based models, like any other scientific hypotheses, can be tested, critiqued, generalized or specified. We review the state of the art for ABM as a methodology for biology and then present a case study based on the most widely published agent-based model in the biological sciences: Hemelrijk's DomWorld, a model of primate social behaviour. Our analysis shows some significant discrepancies between this model and the behaviour of the macaques, the genus used for our analysis. We also demonstrate that the model is not fragile: its other results are still valid and can be extended to compensate for these problems. This robustness is a standard advantage of experiment-based artificial intelligence modelling techniques over analytic modelling.
Body Shape and Coloration of Silkworm Larvae Are Influenced by a Novel Cuticular Protein

Body shape and color patterns of insect larvae are fundamental traits for survival. Typically, transcription factors or members of signaling pathways. The genetic basis of body shape and coloration patterns on caterpillars is often assumed to be regulated separately, but it is possible that common molecules affect both types of trait simultaneously. Here we examine the genetic basis of a spontaneous cuticle defect in silkworm, where larvae exhibit a bamboo-like body shape and decreased pigmentation. We performed linkage mapping and mutation screening to determine the gene product that affects body shape and coloration simultaneously. In these mutant larvae we identified a null mutation in BmorCPH24, a gene encoding a cuticular protein with low complexity sequence. Spatiotemporal expression analyses showed that BmorCPH24 is expressed in the larval epidermis postecdysis. RNAi-mediated knockdown and CRISPR/Cas9-mediated knockout of BmorCPH24 produced the abnormal body shape and the inhibited pigment typical of the mutant phenotype. In addition, our results showed that BmorCPH24 may be involved in the synthesis of endocuticle and its disruption-induced apoptosis of epidermal cells that accompanied the reduced expression of R&R-type larval cuticle protein genes and pigmentation gene Wnt1. Strikingly, BmorCPH24, a fast-evolving gene, has evolved a new function responsible for the assembly of silkworm larval cuticle and has evolved to be an indispensable factor maintaining the larval body shape and its coloration pattern. This is the first study to identify a molecule whose pleiotropic function affects the development of body shape and color patterns in insect larvae.
Lipid and Carbohydrate Metabolism in Caenorhabditis elegans

Lipid and carbohydrate metabolism are highly conserved processes that affect nearly all aspects of organismal biology. Caenorhabditis elegans eat bacteria, which consist of lipids, carbohydrates, and proteins that are broken down during digestion into fatty acids, simple sugars, and amino acid precursors. With these nutrients, C. elegans synthesizes a wide range of metabolites that are required for development and behavior. In this review, we outline lipid and carbohydrate structures as well as biosynthesis and breakdown pathways that have been characterized in C. elegans. We bring attention to functional studies using mutant strains that reveal physiological roles for specific lipids and carbohydrates during development, aging, and adaptation to changing environmental conditions.
Interactions between deformation and fluids in the frontal thrust region of the NanTroSEIZE transect offshore the Kii Peninsula, Japan: Results from IODP Expedition 316 Sites C0006 and C0007

Integrated Ocean Drilling Program (IODP) Expedition 316 Sites C0006 and C0007 examined the deformation front of the Nankai accretionary prism offshore the Kii Peninsula, Japan. In the drilling area, the frontal thrust shows unusual behavior as compared to other regions of the Nankai Trough. Drilling results, integrated with observations from seismic reflection profiles, suggest that the frontal thrust has been active since ∼0.78–0.436 Ma and accommodated ∼13 to 34% of the estimated plate convergence during that time. The remainder has likely been distributed among out‐of‐sequence thrusts further landward and/or accommodated through diffuse shortening. Unlike results of previous drilling on the Nankai margin, porosity data provide no indication of undercompaction beneath thrust faults. Furthermore, pore water geochemistry data lack clear indicators of fluid flow from depth. These differences may be related to coarser material with higher permeability or more complex patterns of faulting that could potentially provide more avenues for fluid escape. In turn, fluid pressures may affect deformation. Well‐drained, sand‐rich material under the frontal thrust could have increased fault strength and helped to maintain a large taper angle near the toe. Recent resumption of normal frontal imbrication is inferred from seismic reflection data. Associated décollement propagation into weaker sediments at depth may help explain evidence for recent slope failures within the frontal thrust region. This evidence consists of seafloor bathymetry, normal faults documented in cores, and low porosities in near surface sediments that suggest removal of overlying material. Overall, results provide insight into the complex interactions between incoming materials, deformation, and fluids in the frontal thrust region.