Miracle-dz/UniFAR-FTUs huggingface dataset:
A Molecular Perspective on Ecological Differentiation and Biogeography of Cyclotrichiid Ciliates

ABSTRACT. Cyclotrichiids are of ecological and evolutionary interest by virtue of their importance in red tide formation, their highly divergent small subunit (SSU) ribosomal RNA (rRNA) genes, kleptoplastidy, and utility as indicators of eutrophication. However, only seven strains have had their SSU rRNA genes sequenced and their environmental diversity and distribution are largely unknown. We probed 67 globally dispersed freshwater column/sediment and soil DNA samples (eDNAs) and constructed 24 environmental gene libraries using polymerase chain reaction primers specific to an uncharacterised cyclotrichiid subgroup. We reveal a novel, globally ubiquitous freshwater clade comprising 25 genetically distinct SSU ribosomal DNA (rDNA) sequences (SSU‐types). Some identical SSU‐types were detected at globally widely distributed sites. The SSU‐types form four distinct phylogenetic clusters according to marine or non‐marine provenance, suggesting at least one major marine–freshwater evolutionary transition within the cyclotrichiids. We used the same primers to sample intensively 18 sampling points in 13 closely situated lakes, each characterised by 14 environmental variables, and showed that molecular detection or non‐detection of cyclotrichiids was most significantly influenced by levels of total phosphorus, dissolved organic carbon, and chlorophyll a. Within the subset of lakes in which cyclotrichiids were detected, closely related SSU‐types differed in their ecological preferences to pH, total phosphorus, and sample depth.
Evidence for expectancy as a mediator of avoidance and anxiety in a laboratory model of human avoidance learning

A laboratory model was developed to study human avoidance learning. Participants could avoid an electric shock signalled by a 5-s conditioned stimulus (CS) by pressing one of a set of response buttons. Self-reported shock expectancy and skin conductance were recorded during a subsequent 10-s interval before shock. Shock expectancy declined when the correct avoidance response was learned and returned when the response was unavailable. Learning transferred to another shock CS. Parallel effects were observed on skin conductance once performance anxiety was controlled by requiring responding on all trials. Learning was faster when the Pavlovian contingencies were trained before introduction of the instrumental response. The results support a cognitive model of anxiety in which performance of an avoidance response reduces expectancy of an aversive outcome and thereby reduces anxiety.
Niching foundations: basin identification on fixed-property generated landscapes

The performance of niching based or related evolutionary algorithms clearly depends on problem properties as e.g. the number of local optima of a problem. We assume there must be more such properties currently not taken into account and, following from practical experience, suggest two more, namely basin size contrast (BSC), the size relation of the largest and the smallest basin, and global to local optima contrast (GLC), the height relation of the global and an average local optimum. We investigate the effect of these problem properties on the performance of different basin identification methods (as subtasks of niching algorithms), namely nearest-better clustering, detect-multimodal, and Jarvis-Patrick clustering, individually, or in combinations. Employing an existing problem generator that enables complete control and knowledge of basins, instances are generated and validated according to predefined property values and the basin identification performance data is modeled in order to detect similarities that may be interpreted as effects of the stated properties. We also give recommendations concerning usage of basin identification methods in different situations. Our approach is strongly related to the recently suggested general idea of exploratory landscape analysis (ELA).
Differentiation of Rickettsiae by groEL Gene Analysis

ABSTRACT The nucleotide sequences (534 to 546 bp) of the groEL gene, which encodes the 60-kDa heat shock protein GroEL, from 15 rickettsial strains were determined and compared. In the phylogenetic tree created by the unweighted pair group method with arithmetic averages and the neighbor-joining method, rickettsial strains could be distinguished from Ehrlichia strains. Five spotted fever group strains, four typhus group strains, and six scrub typhus group (STG) strains were differentiated as distinct entities. Unlike gltA and ompA gene analyses, differentiation between members of the genus Rickettsia and the STG rickettsiae by groEL gene analysis was possible. In comparison with 16S rRNA gene analysis, the groEL gene has a higher degree of divergence among the rickettsiae. We therefore successfully developed rapid differentiation methods, PCR-restriction fragment length polymorphism analysis and a species-specific PCR, based on the groEL gene sequences. Four Korean isolates were identified by these methods and groEL gene analysis. The results suggest that the groEL gene is useful for the identification and characterization of rickettsiae.
"Tuning in" to mollusk shell nacre- and prismatic-associated protein terminal sequences. Implications for biomineralization and the construction of high performance inorganic-organic composites.

The field of biomineralization has expanded over the past decade, and there is now a growing database of information on the molecular participants in nucleation and crystal growth processes in organisms. In particular, we now know that proteins play key roles in nucleation and crystal growth of inorganic solids in Nature. Using biomineralization proteins as inspiration, the material science and nanotechnology fields have now embarked upon the use of phage and bacterial polypeptide screening and expression systems directedagainstbiologicalandartificial inorganicmaterials. This has led to the development of polypeptide sequence libraries which can selective bind, interact, and assemble inorganic solids, as well as regulate the nucleation of these inorganic solids in solution.
A growth model for RNA secondary structures

A hierarchical model for the growth of planar arch structures for RNA secondary structures is presented, and shown to be equivalent to a tree-growth model. Both models can be solved analytically, giving access to scaling functions for large molecules, and corrections to scaling, checked by numerical simulations of up to 6500 bases. The equivalence of both models should be helpful in understanding more general tree-growth processes.
Alignment Tolerant Slim Optical Interconnect for On-Board Interconnections

A four-channel slim optical interconnect is proposed and realized, featuring relaxed structural tolerance along with passive alignment. A compact micro-optic beam coupler in plastic, in which a prism and lens are integrated with a plastic optical fiber (POF) guide in a single body, is commonly incorporated in the transmitter (Tx) and receiver (Rx). A pair of finely controlled reference holes is created in a printed circuit board (PCB), onto which a vertical cavity surface emitting laser (VCSEL) and photodetector (PD) are mounted. The optical coupling for VCSEL-to-POF and POF-to-PD was meticulously performed via the pick-and-place scheme in a cost effective manner, through the mediation of the beam coupler in conjunction with the reference holes. For the manufactured slim interconnect, the effective thicknesses of the Tx and Rx modules were only 1.43 mm. The achieved 3-dB alignment tolerances were 28 and 46 μm for the VCSEL and PD, respectively. The proposed optical interconnect was finally demonstrated to deliver high speed video data at 5.4 Gb/s with high fidelity.
Breaking The One-Third Bit Error Rate Barrier Of Quantum Key Distribution

To push up the error tolerance rate of quantum key distribution, I propose a prepare-and-measure quantum key distribution scheme using $N$-dimensional quantum particles as information carriers where $N$ is a prime power. Remarkably, this prepare-and-measure scheme can distribute a provably secure key against all attacks allowed by the laws of quantum physics for at least one-third bit error rate whenever $N$ is even and $N\geq 16$. Since one-third bit error rate is the maximum limit for any qubit-based key distribution scheme to handle securely, the scheme reported here demonstrates the advantage of using high dimensional quantum particles as information carriers at high eavesdropping rate.
An integrated floorplanning with an efficient buffer planning algorithm

Previous works on buffer planning are mainly based on fixed die placement. It is necessary to reduce the complexity of computing the feasible buffer insertion sites to integrate the buffer planning with the floorplanning process. In this paper, we give an efficient buffer planning algorithm with linear complexity by computing all the feasible buffer insertion sites in a 2-step method. By partitioning all the dead spaces into blocks while doing the packing, the buffer allocation can be handled as an integral part in the floorplanning process. Our method is based on a simulated annealing approach which is divided into two phases: timing optimization phase and buffer insertion phase. Since there is more freedom for floorplan optimization, the floorplanning algorithm integrated with buffer planning can result in better time performance and chip area.
Impact of health and maternal investment on survival of endangered Steller sea lion pups Principal Investigator :

There is increasing interest in assessing the health of individuals and populations of pinnipeds found in the North Pacific, primarily due to population declines leading to conservation concerns. The western population of Steller sea lions (SSL; Eumetopias jubatus) has declined by more than 80% since the 1970’s (Loughlin, 1998) and is listed as endangered under the Endangered Species Act (ESA). During three breeding seasons (2005, 2007, and 2008) 76 pups (32 female, 43 male, 1 unknown) ranging in age from 5 to 38 days old were measured, weighed, blood collected and permanently marked with hot-iron branding. This study assessed the “health” of SSL pups by quantifying hormones associated with fat mass (leptin), energy and water metabolism (cortisol and aldosterone), and growth and metabolism (thyroxine and triiodothyronine) as well as circulating total and differential leukocyte counts and in vitro proliferation of peripheral blood mononuclear cells (PBMC). We hypothesized that age or maternal investment, as quantified by body mass or condition, would influence leukocyte counts, PBMC proliferation, and hormone concentrations in SSL pups. Further, given the inherent requirements of disturbance and animal handling necessary for sampling free ranging pinnipeds, the impact of these activities and the short term effect of hot-iron branding on endocrine and immune profiles were also assessed. Total white blood cell (WBC) counts, neutrophil counts and T cell proliferation decreased with increasing age in SSL pups, and no relationship between body condition index and circulating concentration of hormones quantified was detected. Circulating monocytes counts and concentrations of cortisol, thyroxine, and triiodothyronine were influenced by the rookery disturbance. However, the variation attributed to the disturbance was low and did not alter total or differential WBC counts or in vitro proliferation of PBMC. These findings are presented in three studies outlined in the present report. The aims of these studies were to 1) assess the postnatal changes in circulating immune components and in vitro PBMC proliferation; 2) quantify circulating concentrations of cortisol, aldosterone, total and free thyroxine (T4), total triiodothyronine (T3), and leptin, and to determine if these hormones were associated with body condition or age; 3) given the inherent requirements of disturbance and animal handling necessary for sampling pinnipeds, the impact of these activities on endocrine and immune profiles was assessed, and 4) to determine if these hormones and immune parameters were affected by hot-iron branding.
Monocyte Chemoattractant Protein-1 (CCL-2) Integrates Mechanical and Endocrine Signals That Mediate Term and Preterm Labor1

Recent evidence suggests that leukocytes infiltrate uterine tissues at or around the time of parturition, implicating inflammation as a key mechanism of human labor. MCP-1 (also known as C-C chemokine motif ligand 2, CCL-2) is a proinflammatory cytokine that is up-regulated in human myometrium during labor. Myometrium was collected from pregnant rats across gestation and at labor. Total RNA and proteins were subjected to real-time PCR and ELISA, respectively. Ccl-2 gene and protein expression was significantly up-regulated in the gravid rat myometrium before and during labor, which might suggest that it is regulated positively by mechanical stretch of the uterus imposed by the growing fetus and negatively by physiological withdrawal of progesterone (P4). We confirmed in vivo that: 1) administration of P4 receptor antagonist RU486 induced an increase in Ccl-2 mRNA and preterm labor, whereas 2) artificial maintenance of elevated P4 levels at late gestation caused a significant decrease in gene expression and blocked labor; 3) Ccl-2 was elevated specifically in the gravid horn of unilaterally pregnant rats suggesting that mechanical strain imposed by the growing fetus controls its expression in the myometrium; 4) in vitro static mechanical stretch of primary rat myometrial smooth muscle cells (25% elongation) induced a release of Ccl-2 protein, which was repressed by pretreatment with P4 (1 μM); and 5) stretch enhanced their monocyte chemoattractant activity. These data indicate that Ccl-2 protein serves to integrate mechanical and endocrine signals contributing to uterine inflammation and the induction of labor and thus may represent a novel target for therapeutic prevention of preterm labor in humans.
Vascular endothelial growth factor receptor-1 (VEGFR-1) expression in human corneal fibroblast decreased with age

Purpose Mechanisms by which fibroblast networks between stromal lamellae are laid in the corneal stroma are far from clear. We have investigated the role of vascular endothelial growth factor receptors (VEGFRs) by in vitro studies in the human corneal network formation obtained from donors whose ages ranged from 19 to 89 years. Methods Corneal fibroblasts were prepared from cornea donations. The functional properties of these cells to form networks were analyzed using a semi solid matrix (substratum) of Matrigel™. The presence of VEGF receptor-1 (VEGFR-1) and the functionality in these fibroblasts were investigated using immunofluorescence, molecular analysis (gene microarray, reverse transcription polymerase chain reaction [RT–PCR] and VEGFR siRNA transfections), and cell culture. Results Corneal fibroblasts from 61 donors were classified into two groups according to whether they formed (82%) a reticulum on Matrigel™ or not (18%). By RT–PCR and immunofluorescence analysis, we showed that corneal fibroblasts expressed VEGFR-1 (mRNA and protein). Further, cell culture analysis revealed that only the network (reticulum) forming corneal fibroblast expressed VEGFR-1 in contrast to non network-forming fibroblasts. Use of inhibitors such as VEGFR-1 siRNA transfection or neutralizing antibody (Avastin™) indicated that VEGFR-1 was essential to the formation of the corneal network in vitro. Conclusions The cell reticulum formation seemed to be directly related to the expression of VEGFR-1 in the corneal fibroblast, and this expression decreased with age. The decrease in VEGFR-1 expression is probably related to the diminution of autocrine functions, which may alter the overall tissular homeostasis. This may culminate in the gradual development of poor vision, which is observed in certain pathologies and in aging individuals.
Why most interventions to improve physician prescribing do not seem to work.

It is well established that the quality of physician prescribing is suboptimal. [1][1] , [2][2] , [3][3] , [4][4] , [5][5] Elderly patients are at risk of potentially inappropriate prescribing because of their need for polypharmacy, increased susceptibility to adverse reactions, greater comorbidity
Role of Sodium-Calcium Exchanger in Modulating the Action Potential of Ventricular Myocytes From Normal and Failing Hearts

Abstract— Increased Na+-Ca2+ exchange (NCX) activity in heart failure and hypertrophy may compensate for depressed sarcoplasmic reticular Ca2+ uptake, provide inotropic support through reverse-mode Ca2+ entry, and/or deplete intracellular Ca2+ stores. NCX is electrogenic and depends on Na+ and Ca2+ transmembrane gradients, making it difficult to predict its effect on the action potential (AP). Here, we examine the effect of [Na+]i on the AP in myocytes from normal and pacing-induced failing canine hearts and estimate the direction of the NCX driving force using simultaneously recorded APs and Ca2+ transients. AP duration shortened with increasing [Na+]i and was correlated with a shift in the reversal point of the NCX driving force. At [Na+]i ≥10 mmol/L, outward NCX current during the plateau facilitated repolarization, whereas at 5 mmol/L [Na+]i, NCX had a depolarizing effect, confirmed by partially inhibiting NCX with exchange inhibitory peptide. Exchange inhibitory peptide shortened the AP duration at 5 mmol/L [Na+]i and prolonged it at [Na+]i ≥10 mmol/L. With K+ currents blocked, total membrane current was outward during the late plateau of an AP clamp at 10 mmol/L [Na+]i and became inward close to the predicted reversal point for the NCX driving force. The results were reproduced using a computer model. These results indicate that NCX plays an important role in shaping the AP of the canine myocyte, helping it to repolarize at high [Na+]i, especially in the failing heart, but contributing a depolarizing, potentially arrhythmogenic, influence at low [Na+]i.
The functional significance of primate mandibular form

A stress analysis of the primate mandible suggests that vertically deep jaws in the molar region are usually an adaptation to counter increased sagittal bending stress about the balancing‐side mandibular corpus during unilateral mastication. This increased bending stress about the balancing side is caused by an increase in the amount of balancing‐side muscle force. Furthermore, this increased muscle force will also cause an increase in dorsoventral shear stress along the mandibular symphysis. Since increased symphyseal stress can be countered by symphyseal fusion and as increased bending stress can be countered by a deeper jaw, deep jaws and symphyseal fusion are often part of the same functional pattern. In some primates (e.g., Cercocebus albigena), deep jaws are an adaptation to counter bending in the sagittal plane during powerful incisor biting, rather than during unilateral mastication.
The Use of Flagella and Motility for Plant Colonization and Fitness by Different Strains of the Foodborne Pathogen Listeria monocytogenes

The role of flagella and motility in the attachment of the foodborne pathogen Listeria monocytogenes to various surfaces is mixed with some systems requiring flagella for an interaction and others needing only motility for cells to get to the surface. In nature this bacterium is a saprophyte and contaminated produce is an avenue for infection. Previous studies have documented the ability of this organism to attach to and colonize plant tissue. Motility mutants were generated in three wild type strains of L. monocytogenes by deleting either flaA, the gene encoding flagellin, or motAB, genes encoding part of the flagellar motor, and tested for both the ability to colonize sprouts and for the fitness of that colonization. The motAB mutants were not affected in the colonization of alfalfa, radish, and broccoli sprouts; however, some of the flaA mutants showed reduced colonization ability. The best colonizing wild type strain was reduced in colonization on all three sprout types as a result of a flaA deletion. A mutant in another background was only affected on alfalfa. The third, a poor alfalfa colonizer was not affected in colonization ability by any of the deletions. Fitness of colonization was measured in experiments of competition between mixtures of mutant and parent strains on sprouts. Here the flaA and motAB mutants of the three strain backgrounds were impaired in fitness of colonization of alfalfa and radish sprouts, and one strain background showed reduced fitness of both mutant types on broccoli sprouts. Together these data indicate a role for flagella for some strains to physically colonize some plants, while the fitness of that colonization is positively affected by motility in almost all cases.
On the semantics of qualitative attributes in knowledge elicitation

In this work we propose a new discretization method for quantitative domains. We give an overview of the methods in the literature and we introduce a new one that returns better results. As the need for a discretization method appeared in the definition of a procedure for evaluating the semantics of linguistic labels defined in a previous paper, we also give in this paper an overview of this semantics and of its analysis. ©1999 John Wiley & Sons, Inc.
Repeatable Folding Task by Humanoid Robot Worker Using Deep Learning

We propose a practical state-of-the-art method to develop a machine-learning-based humanoid robot that can work as a production line worker. The proposed approach provides an intuitive way to collect data and exhibits the following characteristics: task performing capability, task reiteration ability, generalizability, and easy applicability. The proposed approach utilizes a real-time user interface with a monitor and provides a first-person perspective using a head-mounted display. Through this interface, teleoperation is used for collecting task operating data, especially for tasks that are difficult to be applied with a conventional method. A two-phase deep learning model is also utilized in the proposed approach. A deep convolutional autoencoder extracts images features and reconstructs images, and a fully connected deep time delay neural network learns the dynamics of a robot task process from the extracted image features and motion angle signals. The “Nextage Open” humanoid robot is used as an experimental platform to evaluate the proposed model. The object folding task utilizing with 35 trained and 5 untrained sensory motor sequences for test. Testing the trained model with online generation demonstrates a 77.8% success rate for the object folding task.