Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth and cortical microtubule dynamics in shoot organs under microgravity and hypergravity conditions

ABSTRACT The body shape of plants varied in proportion to the logarithm of the magnitude of gravity in the range from microgravity to hypergravity to resist the gravitational force. Here we discuss the roles of cortical microtubule and 65 kDa microtubule-associated protein-1 (MAP65-1) in gravity-induced modification of growth anisotropy. Microgravity stimulated elongation growth and suppressed lateral expansion in shoot organs, such as hypocotyls and epicotyls. On the other hand, hypergravity inhibited elongation growth and promoted lateral expansion in shoot organs. The number of cells with transverse microtubules was increased by microgravity, but decreased by hypergravity. Furthermore, the levels of MAP65-1, which is involved in the maintenance of the transverse microtubule orientation, were increased by microgravity, but decreased by hypergravity. Therefore, the regulation of orientation of cortical microtubules via changes in the levels of MAP65-1 may contribute to the modification of the body shape of plants to resist the gravitational force.
Towards Automatic Methods to Detect Errors in Transcriptions of Speech Recordings

This work explores different methods to detect errors in transcriptions of speech recordings. We artificially corrupt well transcribed speech transcriptions with three types of errors: substitution, insertion and deletion on TIMIT phonemic transcriptions and WSJ word transcriptions. First, we use Bayesian model selection method by comparing the log-likelihoods from alignment and phone recognizer, a final score is computed to make decision. In this method, we consider two models, Bayesian Hidden Markov Model (HMM) and a Variational Auto-Encoder (VAE) combined with a HMM. Alternately, we build a biased ASR system with language models trained on individual transcriptions, detection decision is based on Levenshtein distance (LD) between transcription and oracle path from decoded lattice. We evaluate the methods of detecting errors in corrupted TIMIT transcription, the best result (either using model selection with VAE model or biased ASR) achieves 7% equal error rate on the Detection Error Tradeoff (DET) curve; we also evaluate the methods of detecting errors in corrupted WSJ transcriptions, and the best result (using biased ASR) achieves 3% equal error rate.
Population structure in artificial selection: studies with Drosophila melanogaster.

The effect of sub-dividing a population during selection was studied by selecting downwards for sternopleural bristles in Drosophila melanogaster. The four structures used all involved the selection of 40 individuals out of 200 measured in each sex. The alternatives were: (i) large generations, (ii) lines the all generations, (iii) the ' single cycle' large crosses between selected small lines at either the sixth or twelth (iv) the' repeated cycle' structure in which the best five small lines were mixed at the sixth generation of selection to produce a new set of small lines on which the procedure was repeated for a total of three cycles. Of the first two methods, the large line had a higher final response than did any of the small lines. The latter, selected with an intensity of 5 out of 25 in each sex, had lower average final response than had a similar group of lines selected from the same base population with the lower intensity of 10/25. The results showed no clear effect of the sub-division of the population, followed by selection between lines, though they were in general agreement with theoretical expectations. Several second chromosome recessive lethals were found at high frequencies in different selected lines. One of these, found in eight of the lines, had an effect on bristles in the heterozygote of about 1-5 phenotypic standard deviations. The evidence strongly suggests a pleiotropic effect on bristle score.
Studies of isolated global brain ischaemia: I. A new large animal model of global brain ischaemia and its baseline perfusion studies.

OBJECTIVES Neurological injury after global brain ischaemia (i.e. sudden death) remains problematic, despite improving cardiac survival. Unfortunately, sudden death models introduce unwanted variables for studying the brain because of multiple organ injury. To circumvent this, a new minimally invasive large animal model of isolated global brain ischaemia, together with baseline perfusion studies is described. METHODS The model employs neck and small (3-4 inches) supra-sternal incisions to block inflow from carotid and vertebral arteries for 30 min of normothermic ischaemia. Neurological changes after 24 h in six pigs was compared with six Sham pigs assessing neurological deficit score (NDS, 0 = normal, 500 = brain death), brain oedema and cerebral infarction by 2,3,5-triphenyltetrazolium chloride (TTC) stain. Six other pigs had baseline perfusion characteristics in this new model evaluated at carotid flows of 750, 550 and 450 cc/min, with cerebral perfusion pressure, cerebral oximeter saturation [IN Vivo Optical Spectroscopy (INVOS)] and transcranial O(2) uptake measurements. RESULTS The model never altered cardiac or pulmonary function, and six Sham pigs had normal (NDS = 0) neurological recovery without brain injury. Conversely, 24 h analysis showed that 30 min of global normothermic brain ischaemia caused multiple post-reperfusion seizures (P < 0.001 versus Sham), raised NDS (231 ± 16; P < 0.001 versus Sham) in four of six survivors and caused marked post-brain oedema (P < 0.001 versus Sham) and extensive cerebral infarctions (TTC stain; P < 0.001 versus Sham). Baseline perfusion showed 750 cc/min flow rate produced normal INVOS levels and O(2) consumption at mean 90-100 mmHg carotid pressure. Carotid pressure and INVOS fell at mid- and low-flow rates. Although INVOS did not change, 450 cc/min flow lowered global O(2) consumption, which further decreased after transient ischaemia (30 s) and 5 min of reperfusion. CONCLUSIONS This new isolated global brain model consistently caused anatomic, biochemical and functional neurological damage in pigs after 30 min of ischaemia. Flows of 750 cc/min maintained normal mean systemic arterial (90-100 mmHg) pressure, INVOS levels and O(2) consumption. Cerebral pressure and INVOS fell in mid- and low-flow studies. A disparity existed between INVOS oxygen saturation and global O(2) consumption at lower flow rates of 450 cc/min following transient ischaemia, indicating that surface oxygen saturation measurement does not reflect global brain O(2) consumption.
Human in the Loop Simulation Measures of Pilot Response Delay in a Self-Separation Concept of Operations

A human-in-the-loop (HITL) simulation experiment was conducted by the National Aeronautics and Space Administration (NASA) to assess airline transport pilots’ performance and reported acceptance of the use of procedures relying on airborne separation assistance and trajectory management tools. This study was part of a larger effort involving two NASA centers that includes multiple HITL experiments planned over the next few years to evaluate the use of automated separation assurance (SA) tools by both air traffic controllers and pilots. This paper presents results of measured pilot response delay that subject pilots incurred when interacting with cockpit tools for SA and discusses possible implications for future concept and procedures design.
Introduction and expression of the 400 kilobase amyloid precursor protein gene in transgenic mice [corrected].

Overexpression of the gene encoding the beta-amyloid precursor protein (APP) may have a key role in the pathogenesis of both Alzheimer's disease (AD) and Down Syndrome (DS). We have therefore introduced a 650 kilobase (kb) yeast artificial chromosome (YAC) that contains the entire, unrearranged 400 kb human APP gene into mouse embryonic stem (ES) cells by lipid-mediated transfection. ES lines were generated that contain a stably integrated, unrearranged human APP gene. Moreover, we demonstrate germ line transmission of the APP YAC in transgenic mice and expression of human APP mRNA and protein at levels comparable to endogenous APP. This transgenic strategy may prove invaluable for the development of mouse models for AD and DS.
Marooned magic numbers - An adaptive congestion control architecture

TCP and other Internet transport protocols rely on series of hard-coded initial values for their connection state, particularly for the congestion control parameters. For example, recently the initial value of congestion window has been under much debate, as there is a desire to make TCP more efficient for common use cases, while not endangering its performance on scenarios with limited network bandwidth. Our take on this discussion is that there is no clear single set of initial values that would work for all cases. Earlier research has proposed sharing connection and congestion control state among multiple connections over time, but that approach is limited to sharing connections to a particular host, which is not sufficient, because services are often distributed across multiple hosts, and opening multiple connections to the same host is a rather rare use case. We aim to solve this problem by proposing the Pathlet Transport Architecture that models the network paths as a series of pathlets, and uses those as the basis of initializing and maintaining the various transport parameters, particularly those related to congestion control. We analyze our initial instantiation of the PTA architecture using ns-3 simulations for TCP congestion control parameters, and show how it improves the communication performance in various different network scenarios, where single common set of magic values would fail.
Detection of corrosion on 304 stainless steel by acoustic emission measurement

Purpose - The purpose of this paper is to report an investigation of the acoustic emission (AE) characteristics of the corrosion process of 304 stainless steel in acidic NaCl solution. Design/methodology/approach - The corrosion behavior of a specimen with constant load in acidic NaCl solution was studied, and the AE signal characteristics of the corrosion process were analyzed. Stress corrosion cracking of the specimen was detected using the AE and electrochemical noise (EN) techniques, and the acquired data were compared. Findings - The results indicated that AE technology is very sensitive to the AE signals generated by 304 nitrogen controlled stainless steel in acidic NaCl solution. The characteristics of AE signals at different stages of the corrosion process are significantly different. Additionally, the AE test result is confirmed by the EN test results. Originality/value - The characteristics of AE signals at different stages of the corrosion process are gained for the first time, which is an important guide by which to distinguishing different stages of corrosion.
Two Drosophila beta tubulin isoforms are not functionally equivalent

We have tested the functional capacity of different beta tubulin isoforms in vivo by expressing beta 3-tubulin either in place of or in addition to beta 2-tubulin in the male germ line of Drosophila melanogaster. The testes-specific isoform, beta 2, is conserved relative to major metazoan beta tubulins, while the developmentally regulated isoform, beta 3, is considerably divergent in sequence. beta 3-tubulin is normally expressed in discrete subsets of cells at specific times during development, but is not expressed in the male germ line. beta 2-Tubulin is normally expressed only in the postmitotic germ cells of the testis, and is required for all microtubule-based functions in these cells. The normal functions of beta 2-tubulin include assembly of meiotic spindles, axonemes, and at least two classes of cytoplasmic microtubules, including those associated with the differentiating mitochondrial derivatives. A hybrid gene was constructed in which 5' sequences from the beta 2 gene were joined to protein coding and 3' sequences of the beta 3 gene. Drosophila transformed with the hybrid gene express beta 3-tubulin in the postmitotic male germ cells. When expressed in the absence of the normal testis isoform, beta 3-tubulin supports assembly of one class of functional cytoplasmic microtubules. In such males the microtubules associated with the membranes of the mitochondrial derivatives are assembled and normal mitochondrial derivative elongation occurs, but axoneme assembly and other microtubule-mediated processes, including meiosis and nuclear shaping, do not occur. These data show that beta 3 tubulin can support only a subset of the multiple functions normally performed by beta 2, and also suggest that the microtubules associated with the mitochondrial derivatives mediate their elongation. When beta 3 is coexpressed in the male germ line with beta 2, at any level, spindles and all classes of cytoplasmic microtubules are assembled and function normally. However, when beta 3-tubulin exceeds 20% of the total testis beta tubulin pool, it acts in a dominant way to disrupt normal axoneme assembly. In the axonemes assembled in such males, the doublet tubules acquire some of the morphological characteristics of the singlet microtubules of the central pair and accessory tubules. These data therefore unambiguously demonstrate that the Drosophila beta tubulin isoforms beta 2 and beta 3 are not equivalent in intrinsic functional capacity, and furthermore show that assembly of the doublet tubules of the axoneme imposes different constraints on beta tubulin function than does assembly of singlet microtubules.
Automatic Generation and Recommendation for API Mashups

Until today, finding the most suitable APIs to use in an application was burdensome, requiring manual and time-consuming searches across a diverse set of websites, in particular regarding how multiple APIs could be combined and worked together (i.e. API mashups). In this paper, we propose a new method to automatically generate API mashups through real-world data collection, text mining and natural language processing (NLP ) techniques. The generated API mashups are further ranked and recommended to developers based on a quantitative indicator of whether the given API mashup is plausible. To evaluate the overall accuracy of the proposed method, we use the generated API mashups to train several machine learning and deep learning models, and then use an independent mashup dataset collected from Github projects for testing. The experimental results show that our proposed method is feasible and accurate for automatic API mashup generation and recommendation.
The Narrator: NLG for digital storytelling

An aqueous completion or workover fluid for oil or gas wells having at least two solid components. One component is a hydroxy containing aluminum compound represented by the formula AlO(OH). xH2O. The second component is a fluid loss control agent which can be either a cross-linked polyvinyl alcohol or a cross-linked hydroxyalkyl cellulose reaction product. An acid soluble weighting agent can be added for wells having higher down hole pressures. Examples of the weighting agents include iron carbonates, iron oxides, calcium carbonates, dolomite, sodium or calcium chloride, zinc bromide and calcium bromide. After use, the fluid can be displaced from the well with acid, e.g. 15% HCl, and the cake previously deposited on the bore-hole wall is dissolved by the acid so that no damaging residue remains.
Adrenalectomy Improves the Long-Term Risk of End-Stage Renal Disease and Mortality of Primary Aldosteronism

Abstract Objective Primary aldosteronism (PA) is a common cause of secondary hypertension, and the long-term effect of excess aldosterone on kidney function is unknown. Patients and Methods We used a longitudinal population database from the Taiwan National Health Insurance system and applied a validated algorithm to identify patients with PA diagnosed between 1997 and 2009. Results There were 2699 patients with PA recruited, of whom 761 patients with an aldosterone-producing adenoma (APA) were identified. The incidence rate of end-stage renal disease (ESRD) was 3% in patients with PA after targeted treatments and 5.2 years of follow-up, which was comparable to the rate in controls with essential hypertension (EH). However, after taking mortality as a competing risk, we found a significantly lower incidence of ESRD when comparing patients with PA vs EH [subdistribution hazard ratio (sHR), 0.38; P = 0.007] and patients with APA vs EH (sHR 0.55; P = 0.021) after adrenalectomy; however, we did not see similar results in groups with mineralocorticoid receptor antagonist (MRA)‒treated PA vs EH. There was also a significantly lower incidence of mortality in groups with PA and APA who underwent adrenalectomy than among EH controls (P < 0.001). Conclusion Regarding incident ESRD, patients with PA were comparable to their EH counterparts after treatment. After adrenalectomy, patients with APA had better long-term outcomes regarding progression to ESRD and mortality than hypertensive controls, but MRA treatments did not significantly affect outcome.
Chapels in the Bazaar ? Latent Social Structure in OSS

Commercial software project managers design project organizational structure carefully, mindful of available skills, division of labour, geographical boundaries, etc. These organizational “cathedrals” are to be contrasted with the “bazaarlike” nature of Open Source Software (OSS) Projects, which have no pre-designed organizational structure. Any structure that exists is dynamic, self-organizing, latent, and usually not explicitly stated. However, in large, complex, successful, OSS projects, we expect that sub-communities will form organically within the “bazaar” of developer teams. Studying these sub-communities, and their behavior can shed light on how successful OSS projects self-organize. This phenomenon could even hold important lessons for how commercial software teams might be organized. Building on wellestablished techniques for detecting community structure in complex networks, we extract and evaluate latent subcommunities from the email social network of several projects: Apache HTTPD, Python, PostgresSQL, Perl, and Apache ANT. We then validate them with software development activity history. Our results show that subcommunities do indeed form within these projects. We find, in other words, that “chapels” (if not cathedrals) spontaneously arise within the bazaar as OSS systems and the teams evolve. We also find that these subgroups manifest most strongly in technical discussions, and are significantly connected with collaboration behaviour.
Impact of Local-Oscillator Imperfections on Nonregenerative TDD and FDD Relaying

In this work we investigate the impact of imperfect local oscillators (LOs) at the relays in nonregenerative two-hop networks. Due to the specific traffic pattern of multihop networks, hardware imperfections at the relays have a different impact on the system than hardware imperfections at the sources and destinations. Based on the assumption that one LO generates all oscillations in each node, we consider baseband sampling time as well as sampling frequency offsets, RF frequency and phase offsets, timing errors, and phase noise. In the presence of these imperfections, time division duplex (TDD) and frequency division duplex (FDD) relays introduce errors to their forwarded signals. We identify these errors for both types of relays and use Monte-Carlo simulations to compare the performance of a multiuser network employing either TDD or FDD relays with imperfect LOs.
Efficient Synchronization for Distributed Embedded Multiprocessors

In multiprocessor systems, low-latency synchronization is extremely important to effectively exploit fine-grain data parallelism and improve overall performance. This brief presents an efficient synchronization for embedded distributed multiprocessors. The proposed solution works in a completely decentralized request-response manner via explicit message exchange among the processing elements. Scalable lock and barrier synchronization algorithms, which are derived from the inherent distributed characteristics of the underlying architecture, are proposed to enable fair, orderly, and contention-free synchronization. We implement the proposed synchronization model in a distributed 32-core architecture with a commercial cycle-accurate SystemC simulation platform. Experimental results that show our proposed approach achieves ultralow synchronization latency and almost ideal scalability when the core count scales.
A Taxonomy of Schedulers – Operating Systems, Clusters and Big Data Frameworks

This review analyzes deployed and actively used workload schedulers’ solutions and presents a taxonomy in which those systems are divided into several hierarchical groups based on their architecture and design. While other taxonomies do exist, this review has focused on the key design factors that affect the throughput and scalability of a given solution, as well as the incremental improvements which bettered such an architecture. This review gives special attention to Google’s Borg, which is one of the most advanced and published systems of this kind.
Thermostable Aldolase from Thermus aquaticus HUDSON FREEZE

Data are presented on the purification and properties of the thermostable fructose1, 6-diphosphate aldolase of Thermus aquaticus, a nonsporulating, extreme thermophile. The enzyme shows little activity at temperatures below 60 C and optimal activity at about 95 C. The enzyme was purified 43-fold by diethylaminoethyl cellulose column chromatography and Sephadex G-200 gel filtration. The enzyme is activated by high concentrations of NH4+ and low concentrations of Fe2+ and Co2+ and is strongly inhibited by ethylenediaminetetraacetic acid (EDTA). The activation by Fe2+ and Co2+ and the inhibition by EDTA are both reversed by dialysis. The enzyme is greatly activated by cysteine and less so by other sulfhydryl compounds. Activation by cysteine is reversible by dialysis. The purified enzyme had a molecular weight as determined by Sephadex G-200 gel filtration of 140,000; after incubation of enzyme with cysteine, another molecular species was also found with a molecular weight of 70,000. The purified enzyme is stable at low protein concentrations to 97 C but is rapidly inactivated at 105 C. In cysteine the enzyme is more heat labile; heat inactivation in the presence of cysteine is prevented by substrate, although, in the absence of cysteine, substrate partially labilizes the enzyme to heat. The temperature optimum for enzyme activity is several degrees lower in the presence of cysteine than in its absence, and the Km is threefold lower. It is concluded that the T. aquaticus enzyme resembles some other aldolases of Rutter's class II, except for its extreme heat stability. The T. aquaticus enzyme is compared with that of Bacillus stearothermophilus, a moderate thermophile. Although the T. aquaticus enzyme is considerably more heat stable, the enzymes from the two thermophiles have many similarities. New data are presented which show that the B. stearothermophilus aldolase is metal ion-dependent, in disagreement with earlier
Multi-Covering Radius for Rank Metric Codes

The results of this paper are concerned with the multi-covering radius, a generalization of covering radius, of Rank Distance (RD) codes. This leads to greater understanding of RD codes and their distance properties. Results on multi-covering radii of RD codes under various constructions are given by varying the parameters. Some bounds are established. A relationship between multi-covering radii of an RD code and that of its ambient space is also found. The classical sphere bound is generalized.