Miracle-dz/UniFAR-FTUs huggingface dataset:
Soil thermal conductivity parameterization establishment and application in numerical model of central Tibetan Plateau

Based on soil thermal conductivity parameterization of Farouki, Johansen and Cote, a new soil thermal conductivity parameterization scheme of central Tibetan Plateau has been established. The new soil thermal conductivity parameterization has been verified by the observed data of Bujiao (BJ) site in the Coordinated Enhanced Observing Period Asia Australia Monsoon Project on the Tibetan Plateau (CAMP/Tibet). And an off-line numerical simulation experiment by Common Land Model (CoLM) with new soil thermal conductivity parameterization scheme on the Tibetan Plateau is presented. The results show that in both unfrozen and frozen soil, the calculated soil thermal conductivity by the new scheme is better than Farouki scheme. The soil temperature simulation of CoLM with new soil thermal conductivity is better than that of original CoLM.
Character displacement and the evolution of mate choice: an artificial neural network approach

Interactions with heterospecifics can promote the evolution of divergent mating behaviours between populations that do and do not occur with heterospecifics. This process—reproductive character displacement—potentially results from selection to minimize the risk of mating with heterospecifics. We sought to determine whether heterospecific interactions lead to divergence of female preferences for aspects of conspecific male signals. We used artificial neural network models to simulate a mate recognition system in which females co-occur with different heterospecifics in different populations. Populations that evolved conspecific recognition in the presence of different heterospecifics varied in their preferences for aspects of conspecific male signals. When we tested networks for their preferences of conspecific versus heterospecific signals, however, we found that networks from allopatric populations were usually able to select against heterospecifics. We suggest that female preferences for aspects of conspecific male signals can result in a concomitant reduction in the likelihood that females will mate with heterospecifics. Consequently, even females in allopatry may discriminate against heterospecific mates depending on the nature of their preferences for conspecifics. Such a pattern could potentially explain cases where reproductive character displacement is expected, but not observed.
Detecting the Dusty Debris of Terrestrial Planet Formation

We use a multiannulus accretion code to investigate debris disks in the terrestrial zone at 0.7-1.3 AU around a 1 M☉ star. Terrestrial planet formation produces a bright dusty ring of debris with a lifetime of ≳106 yr. The early phases of terrestrial planet formation are observable with current facilities; the late stages require more advanced instruments with adaptive optics.
Construction of short block length irregular low-density parity-check codes

We present a construction algorithm for short block length irregular low-density parity-check (LDPC) codes. Based on a novel interpretation of stopping sets in terms of the parity-check matrix, we present an approximate trellis-based search algorithm that detects many stopping sets. Growing the parity check matrix by a combination of random generation and the trellis-based search, we obtain codes that possess error floors orders of magnitude below randomly constructed codes and significantly better than other comparable constructions.
Mammalian end binding proteins control persistent microtubule growth

End binding proteins (EBs) are highly conserved core components of microtubule plus-end tracking protein networks. Here we investigated the roles of the three mammalian EBs in controlling microtubule dynamics and analyzed the domains involved. Protein depletion and rescue experiments showed that EB1 and EB3, but not EB2, promote persistent microtubule growth by suppressing catastrophes. Furthermore, we demonstrated in vitro and in cells that the EB plus-end tracking behavior depends on the calponin homology domain but does not require dimer formation. In contrast, dimerization is necessary for the EB anti-catastrophe activity in cells; this explains why the EB1 dimerization domain, which disrupts native EB dimers, exhibits a dominant-negative effect. When microtubule dynamics is reconstituted with purified tubulin, EBs promote rather than inhibit catastrophes, suggesting that in cells EBs prevent catastrophes by counteracting other microtubule regulators. This probably occurs through their action on microtubule ends, because catastrophe suppression does not require the EB domains needed for binding to known EB partners.
Effects of vegetation and soil-surface cover treatments on the hydrologic behavior of low-level waste trench caps

Preliminary results are presented on a three-year field study at Los Alamos National Laboratory to evaluate the influence of different low-level radioactive waste trench cap designs on water balance under natural precipitation. Erosion plots having two different vegetative covers (shrubs and grasses) and with either gravel-mulched or unmulched soil surface treatments have been established on three different soil profiles on a decommissioned waste site. Total runoff and soil loss from each plot is measured after each precipitation event. Soil moisture is measured biweekly while plant canopy cover is measured seasonally. Preliminary results from the first year show that the application of a gravel mulch reduced runoff by 73 to 90%. Total soil loss was reduced by 83 to 93% by the mulch treatment. On unmulched plots, grass cover reduced both runoff and soil loss by about 50% compared to the shrub plots. Continued monitoring of the study site will provide data that will be used to analyze complex interactions between independent variables such rainfall amount and intensity, antecedent soil moisture, and soil and vegetation factors, as they influence water balance, and soil erosion. 18 refs., 2 figs., 3 tabs.
The development of data standards and a database to aid proteomic research.

The thesis reports new developments in the area of database support for proteomics experiments. We have developed a proposal for a data standard that will facilitate sharing and archival of data. We have also developed a database implementing the standard, which is a prototype of a public repository capable of storing large volumes of data. Our technology allows for the integration of results from both microarrays and proteomics. The database has been evaluated in the context of two investigations performed by collaborating biologists. We have demonstrated that our technology enables the discovery of new results by facilitating complex queries and providing novel visualisations of experimental data.
Comparison of Pole Placement and LQR Applied to Single Link Flexible Manipulator

This work presents a comparative study of two different control strategies for a flexible single-link manipulator. The dynamic model of the flexible manipulator involves modeling the rotational base and the flexible link as rigid bodies using the Euler Lagrange's method. The resulting system has one Degree-Of-Freedom (one DOF) and it provide freedom to increase the degree as well. Two types of regulators are studied, the State-Regulator using Pole Placement, and the Linear-Quadratic regulator (LQR). The LQR is obtained by resolving the Ricatti equation, in this work, we apply and compare two strategies to control the tip of the flexible link: state-feedback and linear quadratic regulator. These regulators are designed to reduce tip vibrations and increase system stability due to the flexibility of the arm.
Heteroduplex DNA in Meiotic Recombination in Drosophila mei-9 Mutants

Meiotic recombination gives rise to crossovers, which are required in most organisms for the faithful segregation of homologous chromosomes during meiotic cell division. Characterization of crossover-defective mutants has contributed much to our understanding of the molecular mechanism of crossover formation. We report here a molecular analysis of recombination in a Drosophila melanogaster crossover-defective mutant, mei-9. In the absence of mei-9 activity, postmeiotic segregation associated with noncrossovers occurs at the expense of crossover products, suggesting that the underlying meiotic function for MEI-9 is in crossover formation rather than mismatch repair. In support of this, analysis of the arrangement of heteroduplex DNA in the postmeiotic segregation products reveals different patterns from those observed in Drosophila Msh6 mutants, which are mismatch-repair defective. This analysis also provides evidence that the double-strand break repair model applies to meiotic recombination in Drosophila. Our results support a model in which MEI-9 nicks Holliday junctions to generate crossovers during meiotic recombination, and, in the absence of MEI-9 activity, the double Holliday junction intermediate instead undergoes dissolution to generate noncrossover products in which heteroduplex is unrepaired.
Measurement of human lower limb orientations and ground reaction forces using wearable sensor systems

This paper presents a study on quantitative dynamics analysis of human lower limb using developed wearable sensor systems that can measure reaction force and detect the following gait phases: initial contact, loading response, mid stance, terminal stance, pre-swing, initial swing, mid swing and terminal swing. Since conventional camera-based motion analysis system and reaction force plate system require costly devices, vast space as well as time-consuming calibration experiments, the wearable sensor-based system is much cheaper. Gyroscopes and two-axis accelerometers are incorporated in this wearable sensor system. The former are attached on the surface of the foot, shank and thigh to measure the angular velocity of each segment, and the latter are used to measure inclination of the attached leg segment (shank) in every single human motion cycle for recalibration. Ground reaction forces during human walking are synchronously measured using a wearable force sensor integrated in a shoes mechanism. Finally, experiment has been performed to compare the measurement results from the wearable sensor system with the data obtained from an optical motion analysis system and a force plate. The results showed that the measurement of human lower limb orientations and reaction forces for human dynamics analysis could be reliably implemented using the wearable sensor systems.
Progress in haematopoietic stem cell transplantation for multiple myeloma

Abstract. Gahrton G. & Björkstrand B. (Departments of Medicine and Hematology, Karolinska Institutet and Huddinge University Hospital, Huddinge, Sweden). Progress in haematopoietic stem cell transplantation for multiple myeloma (Review). J Intern Med 2000; 248: 185–201.
Growth of current shoot populations on white pine branches: test of a model.

WILSON, B. F. (Dept. Forestry and Wildlife Management, Univ. Massachusetts, Amherst, MA 01003). Growth of current shoot populations on White Pine branches: Test of a model. Bull. Torrey Bot. Club 117: 215-220. 1990. -Data from 49 8-year-old eastern white pine (Pinus strobus L.) branches were used to test a model which generates current shoot-length frequency distributions. The numbers and lengths of current shoots from parent shoots of all 1 cm length classes were determined. In the first simulation of each individual branch growth the annual elongation of the main axis for each year was specified for each branch; other population growth variables did not change from year to year. In simulated, compared to real, populations: total shoot numbers and lengths were similar (R2 of 0.60 and 0.66 respectively), but were overestimated in small branches and underestimated in large branches; shoot-length frequencies were similar except in the short length classes where the 1 and 2 cm classes were underestimated and the 3 cm class overestimated; and the number of long shoots was overestimated when annual elongation of the main axis decreased rapidly. A second simulation of each branch accounted for annual differences in terminal shoot elongation related to changes in elongation of the main axis. This simulation reduced, but did not eliminate, the systematic errors.
Data Integration through Proximity-Based Networks Provides Biological Principles of Organization across Scales[W]

Plant behaviors across levels of cellular organization, from biochemical components to tissues and organs, relate and reflect growth habitats. Quantification of the relationship between behaviors captured in various phenotypic characteristics and growth habitats can help reveal molecular mechanisms of plant adaptation. The aim of this article is to introduce the power of using statistics originally developed in the field of geographic variability analysis together with prominent network models in elucidating principles of biological organization. We provide a critical systematic review of the existing statistical and network-based approaches that can be employed to determine patterns of covariation from both uni- and multivariate phenotypic characteristics in plants. We demonstrate that parameter-independent network-based approaches result in robust insights about phenotypic covariation. These insights can be quantified and tested by applying well-established statistics combining the network structure with the phenotypic characteristics. We show that the reviewed network-based approaches are applicable from the level of genes to the study of individuals in a population of Arabidopsis thaliana. Finally, we demonstrate that the patterns of covariation can be generalized to quantifiable biological principles of organization. Therefore, these network-based approaches facilitate not only interpretation of large-scale data sets, but also prediction of biochemical and biological behaviors based on measurable characteristics.
Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells

Embryonic stem cells (ESC) have the potential to self-renew indefinitely and to differentiate into any of the three germ layers. The molecular mechanisms for self-renewal, maintenance of pluripotency and lineage specification are poorly understood, but recent results point to a key role for epigenetic mechanisms. In this study, we focus on quantifying the impact of histone 3 acetylation (H3K9,14ac) on gene expression in murine embryonic stem cells. We analyze genome-wide histone acetylation patterns and gene expression profiles measured over the first five days of cell differentiation triggered by silencing Nanog, a key transcription factor in ESC regulation. We explore the temporal and spatial dynamics of histone acetylation data and its correlation with gene expression using supervised and unsupervised statistical models. On a genome-wide scale, changes in acetylation are significantly correlated to changes in mRNA expression and, surprisingly, this coherence increases over time. We quantify the predictive power of histone acetylation for gene expression changes in a balanced cross-validation procedure. In an in-depth study we focus on genes central to the regulatory network of Mouse ESC, including those identified in a recent genome-wide RNAi screen and in the PluriNet, a computationally derived stem cell signature. We find that compared to the rest of the genome, ESC-specific genes show significantly more acetylation signal and a much stronger decrease in acetylation over time, which is often not reflected in a concordant expression change. These results shed light on the complexity of the relationship between histone acetylation and gene expression and are a step forward to dissect the multilayer regulatory mechanisms that determine stem cell fate.
Repair of tobacco carcinogen-induced DNA adducts and lung cancer risk: a molecular epidemiologic study.

BACKGROUND Only a fraction of cigarette smokers develop lung cancer, suggesting that people differ in their susceptibility to this disease. We investigated whether differences in DNA repair capacity (DRC) for repairing tobacco carcinogen-induced DNA damage are associated with differential susceptibility to lung cancer. METHODS From August 1, 1995, through April 30, 1999, we conducted a hospital-based, case-control study of 316 newly diagnosed lung cancer patients and 316 cancer-free control subjects matched on age, sex, and smoking status. DRC was measured in cultured lymphocytes with the use of the host-cell reactivation assay with a reporter gene damaged by a known activated tobacco carcinogen, benzo[a]pyrene diol epoxide. Statistical tests were two-sided. RESULTS Overall, lower DRC was observed in case patients than in control subjects (P:<.001) and was associated with a greater than twofold increased risk of lung cancer. Compared with the highest DRC quartile in the control subjects and after adjustment for age, sex, pack-years of smoking, family history of cancer, and other covariates, reduced DRC was associated with increased risk of lung cancer in a dose-dependent fashion (odds ratio [OR] = 1.8 with 95% confidence interval [CI] = 1.1-3.1, OR = 2.0 with 95% CI = 1.2-3.4, and OR = 4. 3 with 95% CI = 2.6-7.2 for the second, third, and fourth quartiles, respectively; P:(trend)<. 001). Case patients who were younger at diagnosis (<60 years old), female, or lighter smokers or who reported a family history of cancer exhibited the lowest DRC and the highest lung cancer risk among their subgroups, suggesting that these subgroups may be especially susceptible to lung cancer. CONCLUSION The results provide evidence that low DRC is associated with increased risk of lung cancer. The findings from this hospital-based, case-control study should be validated in prospective studies.
Antibody responses to influenza viruses in paediatric patients and their contacts at the onset of the 2009 pandemic in Mexico.

INTRODUCTION On April 2009, the Mexican Ministry of Health received notification of cases of severe pneumonia mostly affecting young healthy people; this was the beginning of the first influenza pandemic of the 21st century. The nature of the immune response to the influenza A(H1N1)2009 pandemic strain in Mexico at the beginning of the pandemic outbreak has not been completely defined. We describe the serological response to the 2009 pandemic influenza virus in paediatric patients with influenza-like illness, their household contacts (HHCs), and exposed health-care workers (HCWs) at the beginning of the pandemic outbreak in Mexico City. METHODOLOGY thirty pre-epidemic and 129 epidemic samples were collected and serum antibodies were measured against A(H1N1)2009 pandemic virus and two non-pandemic swine influenza viruses by an haemagglutination inhibition assay . RESULTS 91% (29/32) of the convalescence samples from confirmed patients had an antibody titre ≥ 10 (GMT 25), 63% (41/65) of the HHCs (GMT 12), 41% of HCWs (GMT 6) and 13% (4/30) of pre-epidemic samples (GMT 6) for the pandemic influenza virus. Of the 32 confirmed cases, 60% had an antibody titre ≥ 40 for the pandemic strain, 53% for the A/swine/Iowa(H1N1) virus (GMT 62) and 43% for the A/swine/Texas(H3N2) virus (GMT 66). CONCLUSION The antibody response to 2009 pandemic influenza virus was widespread in convalescence samples from patients with confirmed pandemic influenza infection but the GMT was below the protective titre. There was no evidence that antibodies to the swine influenza viruses had cross-protective effect against the 2009 pandemic influenza virus.
A prospective analysis of extended endoscopic mucosal resection for large rectal villous adenomas: an alternative technique to transanal endoscopic microsurgery

Introduction Endoscopic mucosal resection is a safe resection tool for selected flat, sessile and lateral spreading tumours of the colon. Transanal microsurgical resection of select rectal neoplastic lesions is another accepted modality. Recent data suggests transanal microsurgery may have high complication rates. We conducted a prospective clinicopathological evaluation of an extended endoscopic mucosal resection technique for highly selected lesions of the rectum and assessed outcome data over a maximal 24‐month period.
An improvement for accessing patterns through clustering in interactive VRML environments

Since the walkthrough system may contain large-scale VRML models, the massive objects are always stored and scattered in the storage units of the walkthrough system. But this situation will increase the search time and reduce the system performance. However, this problem is never considered in the traditional walkthrough system. In this paper, we present an efficient clustering method to improve the efficiency of accessing objects. Meanwhile, the clustering methodology is particularly appropriate for the exploration of interrelationships among objects to reduce the access time. In other words, we introduce the relationships among transactions, views and objects. Based on these relationships, the clustering algorithm will determine how to cluster these objects efficiently. Besides, we suggest two clustering criteria ntra-pattern similarity table and inter-pattern frequency table. Our experimental evaluation on the walkthrough data set shows that our algorithm doesn't only significantly cut down the access time, but also enhance the performance of our system.
A New Approach to Classification with the Least Number of Features

Recently, the so-called Support Feature Machine (SFM) was proposed as a novel approach to feature selection for classification, based on minimisation of the zero norm of a separating hyper plane. We propose an extension for linearly non-separable datasets that allows a direct trade-off between the number of misclassified data points and the number of dimensions. Results on toy examples as well as real-world datasets demonstrate that this method is able to identify relevant features very effectively.
Can Gait Signatures Provide Quantitative Measures for Aiding Clinical Decision-Making? A Systematic Meta-Analysis of Gait Variability Behavior in Patients with Parkinson's Disease

A disturbed, inconsistent walking pattern is a common feature of patients with Parkinson's disease (PwPD). Such extreme variability in both temporal and spatial parameters of gait has been associated with unstable walking and an elevated prevalence of falls. However, despite their ability to discretise healthy from pathological function, normative variability values for key gait parameters are still missing. Furthermore, an understanding of each parameter's response to pathology, as well as the inter-parameter relationships, has received little attention. The aim of this systematic literature review and meta-analysis was therefore to define threshold levels for pathological gait variability as well as to investigate whether all gait parameters are equally perturbed in PwPD. Based on a broader systematic literature search that included 13′195 titles, 34 studies addressed Parkinson's disease, presenting 800 PwPD and 854 healthy subjects. Eight gait parameters were compared, of which six showed increased levels of variability during walking in PwPD. The most commonly reported parameter, coefficient of variation of stride time, revealed an upper threshold of 2.4% to discriminate the two groups. Variability of step width, however, was consistently lower in PwPD compared to healthy subjects, and therefore suggests an explicit sensory motor system control mechanism to prioritize balance during walking. The results provide a clear functional threshold for monitoring treatment efficacy in patients with Parkinson's disease. More importantly, however, quantification of specific functional deficits could well provide a basis for locating the source and extent of the neurological damage, and therefore aid clinical decision-making for individualizing therapies.