Miracle-dz/UniFAR-FTUs huggingface dataset:
The medial and lateral bellies of gastrocnemius: A cadaveric and ultrasound investigation

It is commonly reported that the medial belly (MG) of the gastrocnemius muscle extends further distally than the lateral belly (LG). This observation is made in several standard anatomy texts with no explanation or quantitative data. In this study, the medial and lateral bellies of gastrocnemius in 45 embalmed cadavers were measured. The observed difference in length of the two bellies was found to be highly significant (mean difference in length = 1.74 cm, P < 0.001). In 8 out of 84 legs examined (9.5%), however, the MG was found to be shorter than the LG (three right legs, five left legs, bilateral in two individuals). Surprisingly, there was no correlation between the difference in muscle belly length in any individual and ipsilateral leg length or total body length, suggesting that the difference in belly length may be unrelated to biomechanical function. An ultrasound investigation into the activity pattern of the two bellies was carried out on five volunteers. Muscle activity was monitored during passive and active movements of the ankle and knee joints at different leg positions. During knee flexion and ankle plantarflexion, the LG contracted first in four of the five subjects, followed by the MG, then a period of either LG predomination or equal contraction. The fifth subject, who showed a reversed pattern of activity, had previously suffered an inversion injury of the ankle. We suggest that the initial activation of the LG may help to stabilize the ankle during plantarflexion. We found no evidence that gastrocnemius acts as a shunt muscle during distraction of the knee. Clin. Anat. 21:66–74, 2008. © 2007 Wiley‐Liss, Inc.
An Autonomous In Vivo Dual Selection Protocol for Boolean Genetic Circuits

Success in synthetic biology depends on the efficient construction of robust genetic circuitry. However, even the direct engineering of the simplest genetic elements (switches, logic gates) is a challenge and involves intense lab work. As the complexity of biological circuits grows, it becomes more complicated and less fruitful to rely on the rational design paradigm, because it demands many time-consuming trial-and-error cycles. One of the reasons is the context-dependent behavior of small assembly parts (like BioBricks), which in a complex environment often interact in an unpredictable way. Therefore, the idea of evolutionary engineering (artificial directed in vivo evolution) based on screening and selection of randomized combinatorial genetic circuit libraries became popular. In this article we build on the so-called dual selection technique. We propose a plasmid-based framework using toxin-antitoxin pairs together with the relaxase conjugative protein, enabling an efficient autonomous in vivo evolutionary selection of simple Boolean circuits in bacteria (E. coli was chosen for demonstration). Unlike previously reported protocols, both on and off selection steps can run simultaneously in various cells in the same environment without human intervention; and good circuits not only survive the selection process but are also horizontally transferred by conjugation to the neighbor cells to accelerate the convergence rate of the selection process. Our directed evolution strategy combines a new dual selection method with fluorescence-based screening to increase the robustness of the technique against mutations. As there are more orthogonal toxin-antitoxin pairs in E. coli, the approach is likely to be scalable to more complex functions. In silico experiments based on empirical data confirm the high search and selection capability of the protocol.
Work Ability Trajectories and Retirement Pathways

Objective: To determine whether older workers who follow different work ability (WA) trajectories tend to follow different retirement pathways. Methods: Nationally representative data on Americans born between 1943 and 1948. Latent class growth modeling to estimate trajectories of work ability between ages 53–54 and 65–66. Multinomial log-linear models to assess the association between WA trajectories and retirement pathways. Results: Three WA trajectories were identified: high (74%), declining (17%), and low (9%). Low WA leads more often to an early-gradual retirement. Declining WA leads to both early-gradual and early-crisp retirements. Conclusions: Workers with low and declining WA are more at risk of unemployment, disability, and inactivity prior to retirement; workers with declining WA are also likely to make a direct transition to early retirement. Future changes to social security should consider inter-individual variation over time in WA.
Design of Moore finite state machine with coding space stretching

The proposed method is targeted on reduction of hardware amount in logic circuit of Moore finite-state machine implemented with programmable logic arrays (PLA). The method is based on using more than minimal amount of variables in codes of FSM internal states. The method includes two stages of state encoding. The second stage is connected with recoding of states inside each class of pseudoequivalent states.
Valuing Equal Protection in Aviation Security Screening

The growing number of anti‐terrorism policies has elevated public concerns about discrimination. Within the context of airport security screening, the current study examines how American travelers value the principle of equal protection by quantifying the “equity premium” that they are willing to sacrifice to avoid screening procedures that result in differential treatments. In addition, we applied the notion of procedural justice to explore the effect of alternative selective screening procedures on the value of equal protection. Two‐hundred and twenty‐two respondents were randomly assigned to one of three selective screening procedures: (1) randomly, (2) using behavioral indicators, or (3) based on demographic characteristics. They were asked to choose between airlines using either an equal or a discriminatory screening procedure. While the former requires all passengers to be screened in the same manner, the latter mandates all passengers undergo a quick primary screening and, in addition, some passengers are selected for a secondary screening based on a predetermined selection criterion. Equity premiums were quantified in terms of monetary cost, wait time, convenience, and safety compromise. Results show that equity premiums varied greatly across respondents, with many indicating little willingness to sacrifice to avoid inequitable screening, and a smaller minority willing to sacrifice anything to avoid the discriminatory screening. The selective screening manipulation was effective in that equity premiums were greater under selection by demographic characteristics compared to the other two procedures.
Ovary and Ovulation: Contralateral selection of dominant follicle favours pre-embryo development

: Ovulation was studied using vaginosonography in a total of 410 natural cycles of 123 women undergoing infertility treatment [267 intrauterine insemination (IUI) cycles of 103 women and 143 in-vitro fertilization (IVF) cycles of 50 women]. None of the women received ovarian stimulation. Each follicle was measured daily from 14 mm in diameter until formation of corpus luteum or oocyte retrieval. Contralateral ovulation as compared with the preceding cycle occurred in 57% of the 410 cycles. Contralateral ovulations occurred in 72% of cycles with a follicular phase 14 days, ovulations occurred at random. The length of follicular phase in contralateral ovulation cycles (15.2 +/- 3.2 days) was significantly (P < 0.05) shorter than that of ipsilateral ovulation cycles (15.8 +/- 2.8). During the 57% contralateral ovulations in 143 IVF cycles, the rates of oocyte retrieval (89%), fertilization (69%), cleavage (90%) and embryo transfer (56%) were significantly higher than those of ipsilateral ovulations (69, 51, 64 and 23% respectively). The pregnancy rate of contralateral ovulations (9%) was also higher, though not significantly, than that of ipsilateral ovulations (3%), although the pregnancy rates per transfer were similar (16 and 14% respectively). The total pregnancy rate of both IUI and IVF was higher in contralateral than in ipsilateral ovulation cycles (8.1 and 4.0% respectively). The dominant follicles in contralateral ovulation cycles showed significantly higher oestradiol/androstenedione ratio (P < 0.025) and oestradiol/testosterone + androstenedione ratio (P < 0.025) and lower androstenedione (P < 0.05) than those of ipsilateral ovulation cycles. There was no significant difference in oestradiol, progesterone and testosterone. These results indicate that the dominant follicles in contralateral ovulation cycles are healthier than those of ipsilateral ones. Local intra-ovarian factors, e.g. from the corpus luteum, may negatively affect the health of the dominant follicle and the enclosed oocyte. Therefore contralateral selection of the dominant follicle in the succeeding cycle may favour pre-embryo development. The chance of conceiving during a natural cycle may be affected by the site of ovulation in the preceding cycle.
Cooperative Effect of the Attenuation Determinants Derived from Poliovirus Sabin 1 Strain Is Essential for Attenuation of Enterovirus 71 in the NOD/SCID Mouse Infection Model

ABSTRACT Enterovirus 71 (EV71) is a causative agent of hand, foot, and mouth disease and is also associated with serious neurological disorders. An attenuated EV71 strain [EV71(S1-3′)] has been established in the cynomolgus monkey infection model; this strain contains the attenuation determinants derived from the type 1 poliovirus vaccine strain, Sabin 1 [PV1(Sabin)], in the 5′ nontranslated region (NTR), 3D polymerase, and 3′ NTR. In this study, we analyzed the effect of the attenuation determinants of PV1(Sabin) on EV71 infection in a NOD/SCID mouse infection model. We isolated a mouse-adapted EV71 strain [EV71(NOD/SCID)] that causes paralysis of the hind limbs in 3- to 4-week-old NOD/SCID mice by adaptation of the virulent EV71(Nagoya) strain in the brains of NOD/SCID mice. A single mutation at nucleotide 2876 that caused an amino acid change in capsid protein VP1 (change of the glycine at position 145 to glutamic acid) was essential for the mouse-adapted phenotype in NOD/SCID mice. Next, we introduced attenuation determinants derived from PV1(Sabin) along with the mouse adaptation mutation into the EV71(Nagoya) genome. In 4-week-old mice, the determinants in the 3D polymerase and 3′ NTR, which are the major temperature-sensitive determinants, had a strong effect on attenuation. In contrast, the effect of individual determinants was weak in 3-week-old NOD/SCID mice, and all the determinants were required for substantial attenuation. These results suggest that a cooperative effect of the attenuation determinants of PV1(Sabin) is essential for attenuated neurovirulence of EV71.
Proteomics of rat liver Golgi complex: Minor proteins are identified through sequential fractionation

The discovery of novel proteins resident to the Golgi complex will fuel our future studies of Golgi structure/function and provide justification for proteomic analysis of this organelle. Our approach to Golgi proteomics was to first isolate and characterize the intact organelle free of proteins in transit by use of tissue pretreated with cycloheximide. Then the stacked Golgi fraction was fractionated into biochemically defined subfractions: Triton X‐114 insoluble, aqueous, and detergent phases. The aqueous and detergent phases were further fractionated by anion‐exchange column chromatography. In addition, radiolabeled cytosol was incubated with stacked Golgi fractions containing proteins in transit, and the proteins bound to the Golgi stacks in an energy‐dependent manner were characterized. All fractions were analyzed by two‐dimensional (2‐D) gel electrophoresis and identification numbers were given to 588 unique 2‐D spots. Tandem mass spectrometry was used to analyze 93 of the most abundant 2‐D spots taken from preparative Triton X‐114 insoluble, aqueous and detergent phase 2‐D gels. Fifty‐one known and 22 unknown proteins were identified. This study represents the first installment in the mammalian Golgi proteome database. Our data suggest that cell fractionation followed by biochemical dissection of specific classes of molecules provides a significant advantage for the identification of low abundance proteins in organelles.
Submodule Voltage Estimation Scheme in Modular Multilevel Converters with Reduced Voltage Sensors Based on Kalman Filter Approach

This paper presents a new voltage estimation method for the submodule (SM) capacitor in a modular multilevel converter (MMC). The proposed method employs a Kalman filter algorithm to estimate the SM voltages of the converter. Compared with sensor-based methods, this scheme requires only one voltage sensor to achieve the voltage-balancing of the converter. This sensor is connected to the total arm voltage; the proposed algorithm also requires the switching patterns of each upper SM switch, which are provided by the controller used without the need for extra sensors. The substantial reduction in the number of voltage sensors improves the system reliability and decreases its cost and complexity. Extensive simulation and experimental analyses carried out to validate the proposed estimation scheme under different conditions include steady-state analyses, the effect of variations in capacitance and inductance, the impact of low carrier and effective switching frequency on the accuracy of the estimation, step changes to the load, and range changes in dc voltage. The results obtained are experimentally verified using a single-phase MMC.
A Multipurpose Toolkit to Enable Advanced Genome Engineering in Plants[OPEN]

An integrated reagent toolkit and streamlined protocols work across diverse plant species to enable sophisticated genome edits. We report a comprehensive toolkit that enables targeted, specific modification of monocot and dicot genomes using a variety of genome engineering approaches. Our reagents, based on transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, are systematized for fast, modular cloning and accommodate diverse regulatory sequences to drive reagent expression. Vectors are optimized to create either single or multiple gene knockouts and large chromosomal deletions. Moreover, integration of geminivirus-based vectors enables precise gene editing through homologous recombination. Regulation of transcription is also possible. A Web-based tool streamlines vector selection and construction. One advantage of our platform is the use of the Csy-type (CRISPR system yersinia) ribonuclease 4 (Csy4) and tRNA processing enzymes to simultaneously express multiple guide RNAs (gRNAs). For example, we demonstrate targeted deletions in up to six genes by expressing 12 gRNAs from a single transcript. Csy4 and tRNA expression systems are almost twice as effective in inducing mutations as gRNAs expressed from individual RNA polymerase III promoters. Mutagenesis can be further enhanced 2.5-fold by incorporating the Trex2 exonuclease. Finally, we demonstrate that Cas9 nickases induce gene targeting at frequencies comparable to native Cas9 when they are delivered on geminivirus replicons. The reagents have been successfully validated in tomato (Solanum lycopersicum), tobacco (Nicotiana tabacum), Medicago truncatula, wheat (Triticum aestivum), and barley (Hordeum vulgare).
FtsH protease is required for induction of inorganic carbon acquisition complexes in Synechocystis sp. PCC 6803

Cyanobacteria possess a complex CO2‐concentrating mechanism (CCM), which is induced by low inorganic carbon conditions. To investigate the involvement of proteases in the processes of induction and degradation of the CCM complexes, we studied the FtsH2 (ΔSlr0228) and Deg‐G (ΔSlr1204/ΔSll1679/ΔSll1427) protease mutants of Synechocystis sp. PCC 6803. WT and protease mutant cells were grown under high CO2 and then shifted to low CO2, followed by a proteome analysis of the membrane protein complexes. Interestingly, in the FtsH2 protease mutant, inducible CCM complexes were not detected upon shift to low CO2, whereas the Deg‐G mutant behaved like WT. Also the transcripts of the inducible CCM genes and their regulator ndhR failed to accumulate upon shift of FtsH2 mutant cells from high to low CO2, indicating that the regulation by the FtsH2 protease is upstream of NdhR. Moreover, functional photosynthesis was shown a prerequisite for induction of CCM in WT at low CO2, possibly via generation of oxidative stress, which was shown here to enhance the expression of inducible CCM genes even at high CO2 conditions. Once synthesized, the CCM complexes were not subject to proteolytic degradation, even when dispensable upon a shift of cells to high CO2.
The Mushroom Body of Adult Drosophila Characterized by GAL4 Drivers

Abstract: The mushroom body is required for a variety of behaviors of Drosophila melanogaster. Different types of intrinsic and extrinsic mushroom body neurons might underlie its functional diversity. There have been many GAL4 driver lines identified that prominently label the mushroom body intrinsic neurons, which are known as “Kenyon cells. ” Under one constant experimental condition, we analyzed and compared the the expression patterns of 25 GAL4 drivers labeling the mushroom body. As an internet resource, we established a digital catalog indexing representative confocal data of them. Further more, we counted the number of GAL4-positive Kenyon cells in each line. We found that approximately 2,000 Kenyon cells can be genetically labeled in total. Three major Kenyon cell subtypes, the γ, α′/β′, and α/β neurons, respectively, contribute to 33, 18, and 49% of 2,000 Kenyon cells. Taken together, this study lays groundwork for functional dissection of the mushroom body.
Low-power and high-performance 2.4 GHz RF transmitter for biomedical application

A high performance and low power 2.4 GHz radio frequency (RF) transmitter for biomedical application is presented. The design utilizes LC voltage control oscillator (VCO), ASK modulator, and an inverse Class-D (D−1) power amplifier (PA). The ASK modulates the carrier signal generated by a low phase noise LC-VCO, then the modulated signal is amplified by the inverse Class-D−1 PA. The proposed RF transmitter achieves −11.14-dBm output power with 3.88% efficiency. It also supports 130-Mb/s data rate and consumes 1.98-mW. The design has been implemented in a 0. 13μm CMOS process technology and fully integrated on-chip.
Genome Sequence of Halanaerobium saccharolyticum subsp. saccharolyticum Strain DSM 6643T, a Halophilic Hydrogen-Producing Bacterium

ABSTRACT Halanaerobium saccharolyticum is a halophilic anaerobic fermentative bacterium capable of producing hydrogen, a potential future energy carrier molecule. The high-quality draft genome of H. saccharolyticum subsp. saccharolyticum strain DSM 6643T consists of 24 contigs for 2,873,865 bp with a G+C content of 32.3%.
The BioCreative VI Precision Medicine Track corpus Selection , annotation and curation of protein-protein interactions affected by mutations in scientific literature

The Precision Medicine Track in BioCreative VI aims to bring together the biomedical text mining community for a novel challenge: mining the biomedical literature in search of information of value to precision medicine initiatives such as mutations disrupting/affecting protein-protein interactions (PPI). The Precision Medicine track is organized into two tasks: 1) the triage task – focusing on selection of relevant PubMed articles describing PPI affected by mutations, and 2) the relation extraction task – focusing on extracting the interacting gene pairs for the interactions that are affected by the presence of a mutation. To support this track with an effective training dataset and limited curator time, the track organizers used a two-staged approach. First, for the creation of the training dataset, the organizers and curators worked on leveraging the information from expertly curated and publicly available PPI databases, augmenting it with a set of articles selected via publicly available state-of-the-art text mining tools. 4,082 PubMed articles were thus carefully reviewed, annotated and released for system development. They contained 1,729 articles labelled positive for curation, out of which, 597 contained 752 curated relations. The second stage pertained to the creation of the testing dataset, which consisted of 1,464 PubMed articles, previously not curated in any of the known PPI databases. These articles were highly likely to describe PPI and sequence variants according to several text mining tests. Each article in the testing dataset was annotated by at least two curators, for relevance relation extraction. Five BioGRID annotators participated and reviewed more than 600 articles each. The testing set contained 730 articles labelled positive for curation, out of which, 688 articles contained 930 curated relations. We detail here the data collection, manual review and annotation process. We give a report on the precision medicine track corpus characteristics. This analysis will provide useful information to developers and researchers for comparing and developing innovative text mining approaches for the https://thebiogrid.org/ BioCreative VI challenge and other Precision Medicine related applications. Keywords—corpus creation, manual annotation, protein-protein interaction, mutation, relation extraction, information extraction.
Increasing returns to scale, technological catch-up and research intensity: endogenising the Verdoorn coefficient

This paper examines the importance of output growth and research intensity for productivity growth. Two hypotheses are tested. First, the paper investigates the impact of the two variables on productivity growth when simultaneously considered, assessing whether the basic Kaldorian and Schumpeterian models can be combined. Second, it examines whether research intensity impacts on the magnitude of returns to scale, assessing if countries with higher research intensity benefit from higher returns to scale. The tests reported in the paper provide strong evidence of the importance of demand growth for productivity growth, and on the existence of increasing returns to scale in manufacturing, while also recognizing the relevance of research intensity for productivity growth. Most importantly, the test results suggest that research intensity has a more relevant impact on the magnitude of returns to scale than on productivity growth directly.
Distributed estimation of LMS adaptive consensus filter for aggregation over sensor networks

This paper introduces adaptive consensus's improvement on data aggregation algorithm in WSN. In this algorithm, each node uses the average of each related sensors as a reference signal for the adaptive filter, and modifies the weighted matrix of the consensus filter according to the algorithm of the LMS adaptive filter. The simulation results demonstrate that the proposed algorithm can make better performance in multi-hop consensus, accelerate the convergence of the nodes' estimation.