Miracle-dz/UniFAR-FTUs huggingface dataset:
Emergence of robust growth laws from optimal regulation of ribosome synthesis

Bacteria must constantly adapt their growth to changes in nutrient availability; yet despite large‐scale changes in protein expression associated with sensing, adaptation, and processing different environmental nutrients, simple growth laws connect the ribosome abundance and the growth rate. Here, we investigate the origin of these growth laws by analyzing the features of ribosomal regulation that coordinate proteome‐wide expression changes with cell growth in a variety of nutrient conditions in the model organism Escherichia coli. We identify supply‐driven feedforward activation of ribosomal protein synthesis as the key regulatory motif maximizing amino acid flux, and autonomously guiding a cell to achieve optimal growth in different environments. The growth laws emerge naturally from the robust regulatory strategy underlying growth rate control, irrespective of the details of the molecular implementation. The study highlights the interplay between phenomenological modeling and molecular mechanisms in uncovering fundamental operating constraints, with implications for endogenous and synthetic design of microorganisms.
A Combined Tree Ring and Vegetation Model Assessment of European Forest Growth Sensitivity to Interannual Climate Variability

The response of forest growth to climate variability varies along environmental gradients. A growth increase and decrease with warming is usually observed in cold‐humid and warm‐dry regions, respectively. However, it remains poorly known where the sign of these temperature effects switches. Here we introduce a newly developed European tree ring network that has been specifically collected to reconstruct forest aboveground biomass increment (ABI). We quantify, how the long‐term (1910–2009) interannual variability of ABI depends on local mean May–August temperature and test, if a dynamic global vegetation model ensemble reflects the resulting patterns. We find that sites at 8 °C mean May–August temperature increase ABI on average by 5.7 ± 1.3%, whereas sites at 20 °C decrease ABI by 3.0 ± 1.8% m−2 year−1 Δ°C−1. A threshold temperature between beneficial and detrimental effects of warming and the associated increase in water demand on tree growth emerged at 15.9 ± 1.4 °C mean May–August temperature. Because interannual variability increases proportionally with mean growth rate—that is, the coefficient of variation stays constant—we were able to validate these findings with a much larger tree ring data set that had been established following classic dendrochronological sampling schemes. While the observed climate sensitivity pattern is well reflected in the dynamic global vegetation model ensemble, there is a large spread of threshold temperatures between the individual models. Also, individual models disagree strongly on the magnitude of climate impact at the coldest and warmest locations, suggesting where model improvement is most needed to more accurately predict forest growth and effectively guide silvicultural practices.
Seismic imaging and monitoring in mines with ambient seismic noise correlations

This work focus on using passive noise-based seismic methods to image and monitor the rock mass in underground mines. The main results show that it is possible to gain benefit from the diffuse ambient seismic field in mines to 1/ image the rock mass and 2/ monitor its mechanical property changes over time. This work opens a way to improve safety in deep underground mines.
Marine subsidies change short‐term foraging activity and habitat utilization of terrestrial lizards

Abstract Resource pulses are brief periods of unusually high resource abundance. While population and community responses to resource pulses have been relatively well studied, how individual consumers respond to resource pulses has received less attention. Local consumers are often the first to respond to a resource pulse, and the form and timing of individual responses may influence how the effects of the pulse are transmitted throughout the community. Previous studies in Bahamian food webs have shown that detritivores associated with pulses of seaweed wrack provide an alternative prey source for lizards. When seaweed is abundant, lizards (Anolis sagrei) shift to consuming more marine‐derived prey and increase in density, which has important consequences for other components of the food web. We hypothesized that the diet shift requires individuals to alter their habitat use and foraging activity and that such responses may happen very rapidly. In this study, we used recorded video observations to investigate the immediate responses of lizards to an experimental seaweed pulse. We added seaweed to five treatment plots for comparison with five control plots. Immediately after seaweed addition, lizards decreased average perch height and increased movement rate, but these effects persisted for only 2 days. To explore the short‐term nature of the response, we used our field data to parametrize heuristic Markov chain models of perch height as a function of foraging state. These models suggest a “Synchronized‐satiation Hypothesis,” whereby lizards respond synchronously and feed quickly to satiation in the presence of a subsidy (causing an initial decrease in average perch height) and then return to the relative safety of higher perches. We suggest that the immediate responses of individual consumers to resource pulse events can provide insight into the mechanisms by which these consumers ultimately influence community‐level processes.
A decode-and-forward relaying scheme based on orthogonal superposition modulation

In this paper, we proposed a new scheme of cooperative relaying scheme base on orthogonal superposition modulation and soft demodulation which is similar with multiuser detection. The new scheme can be considered as a different way to achieve a similar purpose with superposition modulation [6]. We optimized the parameter in order to achieve the best performance. Simulation results show that our new scheme outperform the classical cooperation based on decode-and-forward by about 1-2 dB at the same complexity.
Regular Transformations of Infinite Strings

The theory of regular transformations of finite strings is quite mature with appealing properties. This class can be equivalently defined using both logic (Monadic second-order logic) and finite-state machines (two-way transducers, and more recently, streaming string transducers); is closed under operations such as sequential composition and regular choice; and problems such as functional equivalence and type checking, are decidable for this class. In this paper, we initiate a study of transformations of infinite strings. The MSO-based definition for regular string transformations generalizes naturally to infinite strings. We define an equivalent generalization of the machine model of streaming string transducers to infinite strings. A streaming string transducer is a deterministic machine that makes a single pass over the input string, and computes the output fragments using a finite set of string variables that are updated in a copyless manner at each step. We show how Muller acceptance condition for automata over infinite strings can be generalized to associate an infinite output string with an infinite execution. The proof that our model captures all MSO-definable transformations uses two-way transducers. Unlike the case of finite strings, MSO-equivalent definition of two-way transducers over infinite strings needs to make decisions based on omega-regular look-ahead. Simulating this look-ahead using multiple variables with copyless updates, is the main technical challenge in our constructions. Finally, we show that type checking and functional equivalence are decidable for MSO-definable transformations of infinite strings.
Strap-down Pedestrian Dead-Reckoning system

This paper presents a waist-worn Pedestrian Dead Reckoning (PDR) System that requires minimal end-user calibration. The PDR system is based on an Inertial Measurement Unit (IMU) comprising of a tri-axial accelerometer, a tri-axial magnetometer and a tri-axial gyroscope. We propose a novel heading estimation scheme using a quaternion-based extended Kalman filter (EKF) that estimates magnetic disturbances and corrects for them. Accelerometer measurements are used to detect step events and to estimate step lengths. Experimental results show that a relative distance error of about 3% to 8% can be obtained using our methods.
METABOLIC FACTORS AFFECTING FIBRILLATION IN DENERVATED MUSCLE

Introduction FIBRILLATION, the spontaneous rhythmical twitching in voluntary muscles following denervation, has been the subject of many observations since Schiff (1851) first described the phenomenon. Some workers have dealt with the time of onset and distribution of the activity, and others have concerned themselves with the unit in action and the frequency of the contractions. The electrical activity accompanying the twitches has also been investigated and a number of observers have been concerned with the chemical factors which influence fibrillation. Finally the relation of fibrillation activity to muscle atrophy following denervation has received considerable attention. In this paper we present the results of a study, by means of action potential records, of the relation between muscle fibrillation and metabolic activity. Different species of experimental animal have been used and observations have also been made from experimentally denervated muscles in man.
Long-term Change in Lightning Mortality and Its Relation to Annual Thunder Days in Japan

Long-term variations in annual lightning deaths in Japan were examined in relation to the number of thunder days, on the basis of death statistics for 1909 to 2014, and police data for 1968 to 2009. The number of lightning deaths was mostly 20 to 60 people without a remarkable trend before World War II, while it rose to over 100 just after the war, and then decreased during the latter half of the 20th century to less than 10 in recent decades. For the period before 1970, the number of annual lightning deaths was positively correlated with that of warm-season thunder days (averaged over 39 stations) with a correlation coefficient exceeding 0.5. The correlation became low and insignificant after the 1980s as lightning mortality decreased, although a high correlation of 0.6-0.8 was maintained between lightning damages and thunder days. There was also a positive correlation of 0.4-0.6 between lightning deaths and warm-season mean temperature until the 1980s, corresponding to a weak correlation between thunder days and temperature.
A Review of Prostate Cancer Genome-Wide Association Studies (GWAS)

Prostate cancer is the most common cancer in men in Europe and the United States. The genetic heritability of prostate cancer is contributed to by both rarely occurring genetic variants with higher penetrance and moderate to commonly occurring variants conferring lower risks. The number of identified variants belonging to the latter category has increased dramatically in the last 10 years with the development of the genome-wide association study (GWAS) and the collaboration of international consortia that have led to the sharing of large-scale genotyping data. Over 40 prostate cancer GWAS have been reported, with approximately 170 common variants now identified. Clinical utility of these variants could include strategies for population-based risk stratification to target prostate cancer screening to men with an increased genetic risk of disease development, while for those who develop prostate cancer, identifying genetic variants could allow treatment to be tailored based on a genetic profile in the early disease setting. Functional studies of identified variants are needed to fully understand underlying mechanisms of disease and identify novel targets for treatment. This review will outline the GWAS carried out in prostate cancer and the common variants identified so far, and how these may be utilized clinically in the screening for and management of prostate cancer. Cancer Epidemiol Biomarkers Prev; 27(8); 845–57. ©2018 AACR.
Pollen and seed flow patterns of Carapa guianensis Aublet. (Meliaceae) in two types of Amazonian forest

Various factors affect spatial genetic structure in plant populations, including adult density and primary and secondary seed dispersal mechanisms. We evaluated pollen and seed dispersal distances and spatial genetic structure of Carapa guianensis Aublet. (Meliaceae) in occasionally inundated and terra firme forest environments that differed in tree densities and secondary seed dispersal agents. We used parentage analysis to obtain contemporary gene flow estimates and assessed the spatial genetic structure of adults and juveniles. Despite the higher density of adults (diameter at breast height ≥ 25 cm) and spatial aggregation in occasionally inundated forest, the average pollen dispersal distance was similar in both types of forest (195 ± 106 m in terra firme and 175 ± 87 m in occasionally inundated plots). Higher seed flow rates (36.7% of juveniles were from outside the plot) and distances (155 ± 84 m) were found in terra firme compared to the occasionally inundated plot (25.4% and 114 ± 69 m). There was a weak spatial genetic structure in juveniles and in terra firme adults. These results indicate that inundation may not have had a significant role in seed dispersal in the occasionally inundated plot, probably because of the higher levels of seedling mortality.
Membrane Stretch Slows the Concerted Step prior to Opening in a Kv Channel

In the simplest model of channel mechanosensitivity, expanded states are favored by stretch. We showed previously that stretch accelerates voltage-dependent activation and slow inactivation in a Kv channel, but whether these transitions involve expansions is unknown. Thus, while voltage-gated channels are mechanosensitive, it is not clear whether the simplest model applies. For Kv pore opening steps, however, there is excellent evidence for concerted expansion motions. To ask how these motions respond to stretch, therefore, we have used a Kv1 mutant, Shaker ILT, in which the step immediately prior to opening is rate limiting for voltage-dependent current. Macroscopic currents were measured in oocyte patches before, during, and after stretch. Invariably, and directly counter to prediction for expansion-derived free energy, ILT current activation (which is limited by the concerted step prior to pore opening) slowed with stretch and the g(V) curve reversibly right shifted. In WTIR (wild type, inactivation removed), the g(V) (which reflects independent voltage sensor motions) is left shifted. Stretch-induced slowing of ILT activation was fully accounted for by a decreased basic forward rate, with no change of gating charge. We suggest that for the highly cooperative motions of ILT activation, stretch-induced disordering of the lipid channel interface may yield an entropy increase that dominates over any stretch facilitation of expanded states. Since tail current τ(V) reports on the opposite (closing) motions, ILT and WTIR τ(V)tail were determined, but the stretch responses were too complex to shed much light. Shaw is the Kv3 whose voltage sensor, introduced into Shaker, forms the chimera that ILT mimics. Since Shaw2 F335A activation was reportedly a first-order concerted transition, we thought its activation might, like ILT's, slow with stretch. However, Shaw2 F335A activation proved to be sigmoid shaped, so its rate-limiting transition was not a concerted pore-opening transition. Moreover, stretch, via an unidentified non–rate-limiting transition, augmented steady-state current in Shaw2 F335A. Since putative area expansion and compaction during ILT pore opening and closing were not the energetically consequential determinants of stretch modulation, models incorporating fine details of bilayer structural forces will probably be needed to explain how, for Kv channels, bilayer stretch slows some transitions while accelerating others.
Evaporative fractionation of zinc during the first nuclear detonation

Glass formed in the first nuclear detonation shows zinc loss by evaporation, indicating similar volatile loss during lunar formation. Volatile element and compound abundances vary widely in planets and were set during the earliest stages of solar system evolution. Experiments or natural analogs approximating these early conditions are limited. Using silicate glass formed from arkosic sands during the first nuclear detonation at the Trinity test site, New Mexico, we show that the isotopes of zinc were fractionated during evaporation. The green silicate glasses, termed “trinitite,” show +0.5 ± 0.1‰/atomic mass unit isotopic fractionation from ~200 m to within 10 m of ground zero of the detonation, corresponding to an α fractionation factor between 0.999 and 0.9995. These results confirm that Zn isotopic fractionation occurs through evaporation processes at high temperatures. Evidence for similar fractionations in lunar samples consequently implies a volatile-depleted bulk Moon, with evaporation occurring during a giant impact or in a magma ocean.
Efficacy of a synthetic zeolite against five species of stored-grain insects on concrete and wheat

A synthetic zeolite (Odor-Z-Way, sodium aluminum silicate) used for odor adsorption was tested for its ability to control adults of stored-grain insects on wheat and on concrete petri dishes used to simulate floors of empty bins. Insect species tested included unsexed adults of the lesser grain borer, Rhyzopertha dominica (F.); rice weevil, Sitophilus oryzae (L.); maize weevil, Sitophilus zeamais (Motschuslky); red flour beetle, Tribolium castaneum (Herbst), and sawtoothed grain beetle, Oryzaephilus surinamensis (L.). Two formulations were evaluated under laboratory conditions (28±10C and 65±1% r.h.): coarse zeolite (with 90% of particles having a mean diameter at or below 155 μm) and fine zeolite (with 90% of particles having a mean diameter at or below 47.0 μm). On concrete, arenas in 9-cm diameter Petri dishes were sprinkled with the synthetic zeolite to provide deposits of 0 (control), 5 and 10 g/m. Mortality was assessed at times ranging from 10 minutes to 24 hours followed by 48 hours recovery on wheat. Mortality in adults of the five species increased as the rate of application and the duration of exposure increased. Concrete Petri dishes sprinkled with the fine zeolite yielded percent mortality greater or equal to that observed with the coarse zeolitesprinkled Petri dishes. Bioassays on wheat were conducted using two dosage rates: 0.1 to 3.0 g/kg for R. dominica and 0.05 to 1.0 g/kg for the other insect species. Mortality was assessed 7 days postinfestation. A concentration of 0.75 g/kg of fine or coarse zeolite achieved 100% mortality in adults of S. zeamais, T. castaneum, and O. surinamensis. All adults of S. oryzae were killed using 0.50 g/kg of coarse or fine zeolite. Adults of R. dominica were the least susceptible: 2.50 g/kg of fine zeolite and 3.0 g/kg of coarse zeolite were required for 100% mortality. Mortality generally increased with the concentration of zeolite applied on wheat. Efficacy was not related to particle size. This is the first study showing the efficacy of a synthetic zeolite against adults of five species of stored-product insects on concrete and wheat. Synthetic zeolites can be a suitable alternative to currently used pesticides for treatment of empty bin floors and stored wheat for insect control.
Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design

MOTIVATION Accuracy in protein design requires a fine-grained rotamer search, multiple backbone conformations, and a detailed energy function, creating a burden in runtime and memory requirements. A design task may be split into manageable pieces in both three-dimensional space and in the rotamer search space to produce small, fast jobs that are easily distributed. However, these jobs must overlap, presenting a problem in resolving conflicting solutions in the overlap regions. RESULTS Piecemeal design, in which the design space is split into overlapping regions and rotamer search spaces, accelerates the design process whether jobs are run in series or in parallel. Large jobs that cannot fit in memory were made possible by splitting. Accepting the consensus amino acid selection in conflict regions led to non-optimal choices. Instead, conflicts were resolved using a second pass, in which the split regions were re-combined and designed as one, producing results that were closer to optimal with a minimal increase in runtime over the consensus strategy. Splitting the search space at the rotamer level instead of at the amino acid level further improved the efficiency by reducing the search space in the second pass. AVAILABILITY AND IMPLEMENTATION Programs for splitting protein design expressions are available at www.bioinfo. rpi.edu/tools/piecemeal.html CONTACT: bystrc@rpi.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Correlation of synovial fluid HMGB-1 levels with radiographic severity of knee osteoarthritis.

PURPOSE This study measured high-mobility group box 1 (HMGB-1) levels in serum and synovial fluid (SF) in patients with primary knee osteoarthritis (OA) and correlated these levels with radiographic disease severity. METHODS Seventy-eight OA patients and 30 controls were enrolled in this study. All OA patients were scored according to the Kellgren-Lawrence (KL) grading system. HMGB-1 levels were measured by enzyme-linked immunosorbent assay (ELISA). RESULTS SF HMGB-1 levels were significantly higher in knee OA patients, compared with controls (P < 0.01). Moreover, SF HMGB-1 levels were positively associated with KL scores (P < 0.01). Multinomial logistic regression demonstrated that the SF HMGB-1 level was an independent factor for radiographic severity of OA (P=0.002); however, serum HMGB-1 levels did not differ significantly between OA patients and controls and did not correlate with KL scores (P > 0.05). CONCLUSION These results demonstrate that HMGB-1 levels in SF of knee OA patients are independently associated with radiographic disease severity.
Pronoun Language Model and Grammatical Heuristics for Aiding Pronoun Prediction

The cross-lingual pronoun prediction task at WMT 2016 requires to restore the missing target pronouns from source text and target lemmatized and POS-tagged translations. We study the beneﬁts for this task of a speciﬁc Pronoun Language Model (PLM), which captures the likelihood of a pronoun given the gender and number of the nouns or pronouns preceding it, on the target-side only. Experimenting with the English-to-French subtask, we select the best candidate pronoun by applying the PLM and additional heuristics based on French grammar rules to the target-side texts provided in the subtask. Although the PLM helps to outperform a random baseline, it still scores far lower than sys-tem using both source and target texts.
Multiple Equivalent Scale Scan: An Enhancing Technique for Malware Detection

Malware is a set of unwanted software that spreads itself over the Internet without boundaries. These software can cause various damages to the infected system, or just annoy users while use the computer system. Thus, many methods have been proposed and implemented. However, the performance and efficiency of the detecting software are relied on the detection algorithm and the number of files to be scanned. Moreover, efficiency of the popular signature technique is also based on the size of the signature file that is used during the scan process. This paper proposed a multiple equivalent scale scan technique that eliminates the effect from the number of the scan files, and enhances the available scan algorithm to perform its task in a short period of time. The result of this method, comparing with the original ClamWin freeware, is two time faster. Therefore, implementing this technique with any available scan mechanism will also speed up the scan time.