Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of thermal stratification on microbial community diversity and structure in a temperate reservoir

Miyun reservoir is a typical temperate deep reservoir located in the northeast of Beijing, China. In order to explore the effect of thermal stratification on microbial community diversity, structure and its influencing environmental factors, stratified sampling at three sites was conducted during the summer period. Field observations indicate that the water temperature and dissolved oxygen concentrations dropped to 11.9 °C and 1.57 mg/L, respectively, leading to the development of anoxia in the hypolimnetic layer. The Illumina Miseq sequencing results showed that microbial communities from different thermal stratification showed obvious differences, the highest microbial diversity and richness in the hypolimnion samples. RDA ordination analysis suggested that the microbial communities in the epilimnion and metalimnion were mainly affected by water temperature, pH and dissolved oxygen, while total nitrogen was the key environmental factor which shaped the microbial structure in hypolimnion.
ASSER: An Efficient, Reliable, and Cost-Effective Storage Scheme for Object-Based Cloud Storage Systems

High reliability, efficient I/O performance and flexible consistency provided with low storage cost are all desirable properties of cloud storage systems. Due to the inherent conflicts, however, simultaneously achieving optimum on all these properties is impractical. N-way Replication and Erasure Coding, two extensively-applied storage schemes with high reliability, adopt opposite and unbalanced strategies on the tradeoff among these properties, thus considerably restraining their effectiveness on wide range of workloads. To address the aforementioned obstacle, we propose a novel storage scheme called ASSER, an ASSembling chain of Erasure coding and Replication. ASSER stores each object in two parts: a full copy and a certain amount of erasure-coded segments. We establish dedicated read/write protocols for ASSER leveraging the unique structural advantages. On the basis of elementary protocols, we implement sequential and PRAM (Pipeline-RAM) consistency to make ASSER feasible for various services with different performance/consistency requirements. Evaluation results demonstrate that under the same fault tolerance and consistency level, ASSER outperforms N-way replication and pure erasure coding in I/O throughput under diverse system and workload configurations with superior performance stability. More importantly, ASSER delivers stably efficient I/O performance at much lower storage cost than the other comparatives.
Paul Nurse and Pierre Thuriaux on wee Mutants and Cell Cycle Control

[Figure][1] In 1974, Paul Nurse was searching for fission yeast mutants that were larger than normal when he instead found one that was smaller. This unexpected wee mutant (named for its discovery in Scotland) led Nurse to identify a critical regulator of the cell cycle, and helped him win a
ALPINE PLANT DISTRIBUTION AND THERMIC VEGETATION INDICATOR ONGLORIA SUMMITS IN THE CENTRAL GREATER CAUCASUS

The distribution of plant species within alpine areas is often directly related to climate or climate-influenced ecological factors. Responding to observed changes in plant species, cover and composition on the GLORIA summits in the Central Caucasus, an extensive setup of 1m x 1m permanent plots was established at the treeline-alpine zones and nival ecotone (between 2240 and 3024 m a.s.l.) on the main watershed range of the Central Greater Caucasus nearby the Cross Pass, Kazbegi region, Georgia. Recording was repeated in a representative selection of 64 quadrates in 2008. The local climatic factors - average soil T°C and growing degree days (GDD) did not show significant increasing trends. For detection of climate warming we used two indices: thermic vegetation indicator S and thermophilization indicator D. They were varying along altitudinal and exposition gradients. The thermic vegetation indicator decrease in all monitoring summits. The abundance rank of the dominant and endemic species did not change during monitoring period.
Palmitoylated Peptides from the Cysteine-rich Domain of SNAP-23 Cause Membrane Fusion Depending on Peptide Length, Position of Cysteines, and Extent of Palmitoylation*

Synaptosome-associated proteins SNAP-23/25, members of a family of proteins essential for exocytosis, have a highly conserved central cysteine-rich domain that plays an important role in membrane targeting. More than one cysteine in this domain is modified by palmitic acid through a thioester linkage. In an effort to address the biological significance of acylation of this domain, we have generated synthetic peptides corresponding to the cysteine-rich region of SNAP-23 and covalently modified the cysteines with palmitic acid. The interaction of acylated and nonacylated peptides with lipid vesicles and natural membranes has been investigated. Our results indicate that palmitoylation is essential for membrane association. The palmitoylated peptides were able to fuse both model and natural membranes. The extent of fusion depended on the length of the peptides and the number and positions of covalently linked palmitic acids. Peptide-mediated fusion was suppressed by lysolipid and involved both outer and inner leaflets of the lipid bilayer, which is characteristic of natural membrane fusion. Our results suggest an important role for the cysteine-rich palmitoylated domain of SNAP-23 in promoting membrane fusion in cells.
How fish power predation fast-starts

Short-horned sculpin (Myoxocephalus scorpius L.) were acclimated for 6­8 weeks to either 5 °C or 15 °C (12 h dark: 12 h light). Fast-starts elicited by prey capture were filmed from above in silhouette using a high-speed video camera (200 frames s-1). Outlines of the body in successive frames were digitised and changes in strain for the dorsal fast muscle calculated from a knowledge of backbone curvature and the geometrical arrangement of fibres. For 15 °C-acclimated fish at 15 °C, muscle strain amplitude (peak-to-peak) during the first tail-beat was approximately 0.16 at 0.32L, 0.19 at 0.52L and 0.15 at 0.77L, where L is the total length of the fish. Fast muscle fibres were isolated and subjected to the strains calculated for the first tail-beat of the fast-start (abstracted cycle). Preparations were electrically stimulated at various times after the initiation of the fast-start using an in vivo value of duty cycle (27 %). Prior to shortening, muscle fibres at 0.52L and 0.77L were subjected to a pre-stretch of 0.055l0 and 0.085l0 respectively (where l0 is resting muscle length). The net work per cycle was calculated from plots of fibre length and tensile stress. For realistic values of stimulus onset, the average power output per abstracted cycle was similar at different points along the body and was in the range 24­31 W kg-1 wet muscle mass. During shortening, the instantaneous power output reached 175­265 W kg-1 wet muscle mass in middle and caudal myotomes. At the most posterior position examined, the muscle fibres produced significant tensile stresses whilst being stretched, resulting in an initially negative power output. The fibres half-way down the trunk produced their maximum power at around the same time that caudal muscle fibres generated significant tensile stress. Fast muscle fibres at 0.37­0.66L produced 76 % of the total work done during the first tail-beat compared with only 14 % for fibres at 0.67­0.86L, largely reflecting differences in muscle mass. The effect of temperature acclimation on muscle power was determined using the strain fluctuations calculated for 0.52L. For 5 °C-acclimated fish, the average power per cycle (± s.e.m.; W kg-1 wet muscle mass) was 21.8±3.4 at 5 °C, falling to 6.3±1.8 at 15 °C. Following acclimation to 15 °C, average power per cycle increased to 23.8±2.8 W kg-1 wet muscle mass at 15 °C. The results indicate near-perfect compensation of muscle performance with temperature acclimation.
Association of an HLA-DQ allele with clinical tuberculosis.

CONTEXT Although tuberculosis (TB) is the leading worldwide cause of death due to an infectious disease, the extent to which progressive clinical disease is associated with genetic host factors remains undefined. OBJECTIVE To determine the distribution of HLA antigens and the frequency of 2 alleles of the tumor necrosis factor alpha (TNF-alpha) gene in unrelated individuals with clinical TB (cases) compared with individuals with no history of clinical TB (controls) in a population with a high prevalence of TB exposure. DESIGN A 2-stage, case-control molecular typing study conducted in 1995-1996. SETTING Three district hospitals in Svay Rieng Province in rural Cambodia. PATIENTS A total of 78 patients with clinical TB and 49 controls were included in the first stage and 48 patients with TB and 39 controls from the same area and socioeconomic status were included in the second stage. MAIN OUTCOME MEASURES Presence of HLA class I and class II alleles determined by sequence-specific oligonucleotide probe hybridization and presence of 2 TNF-alpha alleles determined by restriction fragment length polymorphism analysis. RESULTS In the first stage, 7 DQB1*0503 alleles were detected among 156 alleles derived from patients with TB, whereas no DQB1*0503 alleles were found among the 98 alleles derived from controls (P=.04). There was no detectable difference in the distribution of the 2 TNF-alpha alleles in patients with TB compared with controls. In the second stage, we tested for the presence of a single variable, the DQB1*0503 allele, and found 9 DQB1*0503 alleles among 96 alleles derived from patients with TB and no DQB1*0503 alleles among 78 alleles in controls (P=.005). CONCLUSIONS The HLA-DQB1*0503 allele is significantly associated with susceptibility to TB in Cambodian patients and, to our knowledge, is the first identified gene associated with development of clinical TB.
Directionality assessment of adaptive binaural beamforming with noise suppression in hearing aids

In this work we present a new method for assessment of directionality in modern hearing aids, which has the benefit of simulating both a target source and an interfering source at the same time using speech signals. We show the benefits and the limitations of the method and present measurements for different microphone modes of different manufacturers. Furthermore, a sequential index based on these measurements is introduced.
Engines, Accelerators, and Brakes on Functional Spinal Cord Repair a

Abstract: It is proposed that four essential goals should be met for functional repair after traumatic injury of the adult spinal cord. These include protecting neural tissue after injury and limiting secondary cell damage; replacing lost tissue with transplanted cell “bridges”; blocking the expression of intrinsic factors within the adult CNS that inhibit neural repair; and providing appropriate sensorimotor activity to enhance plasticity within surviving circuits, as well as consolidate any anatomical repair/regeneration. Included is a brief discussion on the approaches and limitations in the evaluation of functional spinal cord repair.
Timing of levothyroxine administration affects serum thyrotropin concentration.

CONTEXT Patients treated with levothyroxine typically ingest it in a fasting state to prevent food impairing its absorption. The serum thyrotropin concentration is the therapeutic index of levothyroxine action. OBJECTIVE The study objective was to determine the effect of the timing of levothyroxine administration in relationship to food on serum thyrotropin levels. DESIGN Participants were randomized to one of six sequences, each consisting of three 8-wk regimens in a three-period crossover design. These regimens were in a fasting state, at bedtime, and with breakfast. The concentrations of TSH, free T(4), and total T(3) during each of the three timing regimens were documented. The primary outcome was the difference between serum TSH concentrations under fasting conditions compared with concentrations during the other 8-wk regimens. SETTING The study was conducted in an academic medical center. PARTICIPANTS Study participants were receiving levothyroxine for treatment of hypothyroidism or thyroid cancer. RESULTS Sixty-five patients completed the study. The mean thyrotropin concentration was 1.06 +/- 1.23 mIU/liter when levothyroxine was administered in the fasting state. When levothyroxine was taken with breakfast, the serum thyrotropin concentration was significantly higher (2.93 +/- 3.29 mIU/liter). When levothyroxine was taken at bedtime, the serum TSH concentration was also significantly higher (2.19 +/- 2.66 mIU/liter). CONCLUSION Nonfasting regimens of levothyroxine administration are associated with higher and more variable serum TSH concentrations. If a specific serum TSH goal is desired, thereby avoiding iatrogenic subclinical thyroid disease, then fasting ingestion of levothyroxine ensures that TSH concentrations remain within the narrowest target range.
Phase transitions and universal dynamics in confined films.

We describe molecular dynamics simulations of fluid films confined between two solid walls. The films consist of spherical molecules, or flexible linear chains with up to twenty monomers. When the wall separation is only a few molecular diameters, crystalline or glassy order is induced across the film. The onset of the glassy phase is characterized by rapidly increasing relaxation times. These manifest themselves through changes in the diffusion constant and in the response to shear. The viscosity exhibits the same power-law scaling with shear rate that was observed in recent experiments
Blockade of Receptor-Activated Gi Signaling in Osteoblasts In Vivo Leads to Site-Specific Increases in Cortical and Cancellous Bone Formation

Osteoblasts play a critical role in the maintenance of bone mass through bone formation and regulation of bone resorption. Targeted expression of a constitutively active engineered Gi‐coupled G protein–coupled receptor (GPCR) to osteoblasts in vivo leads to severe osteopenia. However, little is known about the role of endogenous receptor‐mediated Gi signaling in regulating osteoblast function. In this study, we investigated the skeletal effects of blocking Gi‐coupled signaling in osteoblasts in vivo. This was accomplished by transgenic expression of the catalytic subunit of pertussis toxin (PTX) under control of the collagen Iα 2.3‐kb promoter. These mice, designated Col1(2.3)+/PTX+, showed increased cortical thickness at the femoral midshaft at 12 weeks of age. This correlated with increased periosteal bone formation associated with expanded mineralizing surface observed in 8‐week‐old mice of both genders. The cancellous bone phenotype of the Col1(2.3)+/PTX+ mice was sexually dimorphic, with increases in fractional bone volume at the distal femur seen only in females. Similarly, while cancellous bone‐formation rates were unchanged in males, they could not be quantified for female Col1(2.3)+/PTX+ mice owing to the disorganized nature of the labeling pattern, which was consistent with rapid formation of woven bone. Alterations in osteoclast activity did not appear to participate in the phenotype. These data demonstrate that Gi‐coupled signaling by GPCRs endogenous to osteoblasts plays a complex role in the regulation of bone formation in a manner that is dependent on both gender and the anatomic site within bone. © 2011 American Society for Bone and Mineral Research.
Unusual presentation of Kallmannn syndrome with contiguous gene deletion in three siblings of a family

We report the case of 3 brothers aged 34, 24, and 22 years, unmarried, who presented to our endocrinology clinic with absence of secondary sexual characters. There was no such history in other siblings, but their maternal uncle had similar complaints. On examination, all 3 had pre-pubertal appearance, voice, and genitalia along with anosmia and bimanual synkinesia. Cryptorchidism was noticed in 2 while third person had small hypoplastic testes. It was also noted that all 3 patients had icthyosis mainly involving trunk, back, and limbs. The hormonal assays were consistent with isolated hypogonadotrophic hypogonadism. IQ testing revealed mental retardation in the 2 patients. Ultrasound showed ectopic right kidney in one patient, atrophic right kidney in the second patient while the third patient had normal kidneys. MRI brain of all the patients showed poorly visualized olfactory tract and bulb. Kallmann syndrome (KS) was diagnosed based on hormonal evaluation and MRI results. Of the four types of KS: Synkinesia, renal anomaly, and X-linked pedigree pattern in our patients pointed towards X-linked type 1 KS as the possible cause. But, icthyosis and mental retardation are not usual presentation of type 1 KS. They are usually seen as a result of contiguous gene deletion of KAL1, steroid sulfatase (STS), and mental retardation (MRX) gene on X chromosome. Hence, the possible gene defect in our cases is inherited defect in contiguous gene deletion. The contiguous gene deletion as the cause of KS in 3 patients of same family is very rare and worth reporting. Also, the significance of phenotype-genotypic association in Kallmann syndrome is discussed
Clinical features of spinal and bulbar muscular atrophy

Spinal and bulbar muscular atrophy is an X-linked motor neuron disease caused by a CAG repeat expansion in the androgen receptor gene. To characterize the natural history and define outcome measures for clinical trials, we assessed the clinical history, laboratory findings and muscle strength and function in 57 patients with genetically confirmed disease. We also administered self-assessment questionnaires for activities of daily living, quality of life and erectile function. We found an average delay of over 5 years from onset of weakness to diagnosis. Muscle strength and function correlated directly with serum testosterone levels and inversely with CAG repeat length, age and duration of weakness. Motor unit number estimation was decreased by about half compared to healthy controls. Sensory nerve action potentials were reduced in nearly all subjects. Quantitative muscle assessment and timed 2 min walk may be useful as meaningful indicators of disease status. The direct correlation of testosterone levels with muscle strength indicates that androgens may have a positive effect on muscle function in spinal and bulbar muscular atrophy patients, in addition to the toxic effects described in animal models.
Unobservable Directions of VINS Under Special Motions

In this paper, we study the unobservable directions of vision-aided inertial navigation systems (VINS) under special motion profiles. It is well-known that the VINS has four unobservable directions, corresponding to the global translation and the rotation around gravity, under the assumption of generic 3D motions. Here we study the case when the motion is constrained to be of either constant local acceleration or no rotation, as commonly found with ground vehicles. We show and prove the additional unobservable directions due to these special motions analytically, as well as the corresponding physical meanings of these new directions. 1 Vision-aided Inertial Navigation System (VINS) First, we provide a brief review of the VINS. The VINS estimates the following state vector: x = [ IqTG b T g v I b T a GpTI | f 1 · · · f N ]T (1) where IqG is the unit quaternion that represents the orientation of the global frame {G} in the IMU frame {I} at time t. GvI and GpI are the the velocity and position of {I} in {G}, respectively, and the gyroscope and accelerometer biases are denoted by bg and ba, respectively. Finally, the positions of point features in {G} are denoted by Gfj , j = 1, . , N . The IMU provides measurements of the rotational velocity, ωm, and the linear acceleration, am, as: ωm(t) = ω(t) + bg(t) + ng(t) (2) am(t) = C( IqG(t))( a(t)− g) + ba(t) + na(t) where the noise terms, ng(t) and na(t) are modelled as zero-mean, white Gaussian noise processes, C( IqG(t)) denotes the rotational matrix associated with the quaternion IqG at time t, while the gravitational acceleration, g, is considered a known constant. The IMU’s rotational velocity ω(t) and linear acceleration a(t), in (2), can be used to derive the continuous-time system equations: Iq̇G(t) = 1 2 Ω(ωm(t)− bg(t)− ng(t))IqG(t) ḃg(t) = nwg(t) Gv̇I(t) = C( IqG(t)) T (am(t)− ba(t)− na(t)) + g ḃa(t) = nwa(t) GṗI(t) = GvI(t) Gḟj(t) = 0, j = 1, . , N (3)
Human Choice Strategy Varies with Anatomical Projections from Ventromedial Prefrontal Cortex to Medial Striatum

Two distinct systems, goal-directed and habitual, support decision making. It has recently been hypothesized that this distinction may arise from two computational mechanisms, model-based and model-free reinforcement learning, neuronally implemented in frontostriatal circuits involved in learning and behavioral control. Here, we test whether the relative strength of anatomical connectivity within frontostriatal circuits accounts for variation in human individuals' reliance on model-based and model-free control. This hypothesis was tested by combining diffusion tensor imaging with a multistep decision task known to distinguish model-based and model-free control in humans. We found large interindividual differences in the degree of model-based control, and those differences are predicted by the structural integrity of white-matter tracts from the ventromedial prefrontal cortex to the medial striatum. Furthermore, an analysis based on masking out of bottom-up tracts suggests that this effect is driven by top-down influences from ventromedial prefrontal cortex to medial striatum. Our findings indicate that individuals with stronger afferences from the ventromedial prefrontal cortex to the medial striatum are more likely to rely on a model-based strategy to control their instrumental actions. These findings suggest a mechanism for instrumental action control through which medial striatum determines, at least partly, the relative contribution of model-based and model-free systems during decision-making according to top-down model-based information from the ventromedial prefrontal cortex. These findings have important implications for understanding the neural circuitry that might be susceptible to pathological computational processes in impulsive/compulsive psychiatric disorders. SIGNIFICANCE STATEMENT Scholars from several disciplines have long been interested in the neural mechanisms of decision-making. An influential suggestion has structured decision-making into a flexible but expensive model-based system, and a more rapid but also more rigid model-free system. Here, we show that anatomical properties of the connections between frontal and striatal regions predict the use of a model-based system when individuals make decisions. Individuals with stronger top-down connectivity from the ventromedial prefrontal cortex to the medial striatum were more likely to rely on a model-based strategy during decision-making, suggesting that the ventromedial prefrontal cortex biases a striatal balance between model-based and model-free control. These findings qualify the neural implementation of decision-making computations and open the way for understanding decision-making pathologies.
A Diagonal-Augmented quasi-Newton method with application to factorization machines

We present a novel quasi-Newton method for convex optimization, in which the Hessian estimates are based not only on the gradients, but also on the diagonal part of the true Hessian matrix (which can often be obtained with reasonable complexity). The new algorithm is based on the well known Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm and has similar complexity. The proposed Diagonal-Augmented BFGS (DA-BFGS) method is shown to be stable and achieves a super-linear convergence rate in a local neighborhood of the optimal argument. Numerical experiments on logistic regression and factorization machines problems showcase that DA-BFGS consistently outperforms the baseline BFGS and Newton algorithms.