Miracle-dz/UniFAR-FTUs huggingface dataset:
A Spectral Algorithm for Seriation and the Consecutive Ones Problem

In applications ranging from DNA sequencing through archeological dating to sparse matrix reordering, a recurrent problem is the sequencing of elements in such a way that highly correlated pairs of elements are near each other. That is, given a correlation function f reflecting the desire for each pair of elements to be near each other, find all permutations $\pi$ with the property that if $\pi(i)<\pi(j)<\pi(k)$ then $f(i,j) \ge f(i,k)$ and $f(j,k) \ge f(i,k)$. This seriation problem is a generalization of the well-studied consecutive ones problem. We present a spectral algorithm for this problem that has a number of interesting features. Whereas most previous applications of spectral techniques provide only bounds or heuristics, our result is an algorithm that correctly solves a nontrivial combinatorial problem. In addition, spectral methods are being successfully applied as heuristics to a variety of sequencing problems, and our result helps explain and justify these applications.
Isotopic Studies of Ore-Leads in the Hanson Lake-Flin Flon-Snow Lake Mineral Belt Saskatchewan and Manitoba

Lead isotope abundances in 4 stratabound sulfide ores are presented and show characteristics of being single-stage lead deposits. Model ages based on these data range from 1780 ± 44 to 1900 ± 44 m.y. and are considered to be close approximations of the time of ore formation. Geological evidence in the massive sulfide deposits suggests they are coeval with their host rocks, which are predominantly volcanics of the Amisk Group. If this assumption is correct the average model lead age of the ores is essentially the age of the enclosing rocks. Within error limits the results are in good agreement with published Rb-Sr ages for Amisk rocks of the Flin Flon area, and with U-Pb ages in zircons of rhyolites, which also contain similar, massive sulfide ores in the Churchill Province of Arizona. This is considered to be good evidence that the Hanson Lake-Flin Flon-Snow Lake volcanic mineral belt, previously regarded as Archean, is Aphebian in part.A previously published Archean, Rb-Sr isochron for volcanic rocks in .
Analysis of the Dynamic Sagittal Balance of the Lumbo-Pelvi-Femoral Complex

The acquisition of bipedalism has enabled the human species an intellectual, technological and social development. However, the transition to the standing position was possible only through morphological adaptations, particularly in the lower limbs, the pelvis and the spine. The pelvis has changed from an elongated shape (called “in tension”, typical of quadrupeds), to a more squat morphology (called “in pressure”, characteristic of bipedalism). The pelvis was indeed a key holder of these transformations as a pivot basis submitted to the loads of gravity from the trunk and to the reaction forces from the ground, transmitted by the femoral heads. Parallel to the adaptation of the pelvis, the appearance of the spinal curvatures has allowed establishing a balance defined as stable and economic in terms of stress on the musculo-ligamentous structures and of muscle contractions necessary for its maintenance. However, maintaining this balance when standing was precarious: all the stresses of gravity were to be maintained within this entire vertical body and inside a narrow sustentation polygon. (Figure 1).
Early Proterozoic structure and kinematic evolution of the southern mainland Lewisian

Summary The southern mainland region of the Lewisian is a belt of intense Early Proterozoic deformation with a minimum width of 55 km, in which all the main structures trend NW-SE. Archaean structures are dominant in the central block to the northeast, and in a small enclave (the Ruadh Mheallan block) between Gairloch and Loch Torridon. Major structures within the belt include upright NW-SE folds (the Carnmore antiform, the Letterewe synform, and the Tollie and Torridon antiforms) and the Gairloch and Diabaig shear zones. The structural history is divided into six phases: (1) Inverian (2600–2400 Ma)—the whole belt represents a major steep Inverian shear zone. Structures in areas little affected by subsequent deformation indicate a N-up overthrust movement with a small dextral component (dextral transpressional), (2) Emplacement of dykes and Loch Maree Group (2400–1900 Ma)—evidence of dextral shear during dyke emplacement indicates a change to a dextral transtensional regime, (3) Laxfordian D1 and, (4) D2 deformation (1900–1800 Ma)—oblique dip-slip shears and asymmetric shear folds suggest a continuation of the previous dextral transtensional movements on inclined lateral ramps, connected with major gently-inclined shear zone ‘flats’, (5) Laxfordian D3 deformation (c. 1600 Ma)—upright folding of previously sub-horizontal fabrics and a reversal of movement to N-up on the Gairloch shear zone indicate a change to a dextral transpressional regime, which is accompanied by retrogressive metamorphism, (6) Laxfordian D4 deformation (c. 1400 or c. 1000 Ma)—steeply plunging large and small-scale asymmetric folds and crush belts indicate a change to a sinistral strike-slip regime. We suggest that these phases of movement represent major changes in relative plate movement direction probably separated by relatively long periods of comparative stability.
Ecological processes: A key element in strategies for nature conservation

A common approach to nature conservation is to identify and protect natural ‘assets’ such as ecosystems and threatened species. While such actions are essential, protection of assets will not be effective unless the ecological processes that sustain them are maintained. Here, we consider the role of ecological processes and the complementary perspective for conservation arising from an emphasis on process. Many kinds of ecological processes sustain biodiversity: including climatic processes, primary productivity, hydrological processes, formation of biophysical habitats, interactions between species, movements of organisms and natural disturbance regimes. Anthropogenic threats to conservation exert their influence by modifying or disrupting these processes. Such threats extend across tenures, they frequently occur offsite, they commonly induce non-linear responses, changes may be irreversible and the full consequences may not be experienced for lengthy periods. While many managers acknowledge these considerations in principle, there is much scope for greater recognition of ecological processes in nature conservation and greater emphasis on long time-frames and large spatial scales in conservation planning. Practical measures that promote ecological processes include: monitoring to determine the trajectory and rate of processes; incorporating surrogates for processes in conservation and restoration projects; specific interventions to manipulate and restore processes; and planning for the ecological future before options are foreclosed. The long-term conservation of biodiversity and the well-being of human society depend upon both the protection of natural assets and maintaining the integrity of the ecological processes that sustain them.
Hypoxia Induces Late Preconditioning in the Rat Heart In Vivo

Background:Although hypoxic late preconditioning (LPC) limits ischemia-reperfusion injury in vitro, its cardioprotective effect is not established in vivo. Methods:In part 1, rats were exposed to 4 h of hypoxia (16%, 12%, 8% oxygen) before 24 h of reoxygenation. In part 2, normoxic rats received early preconditioning with sevoflurane (1 minimum alveolar concentration [MAC] for 3 × 5 min), continuous administration of 1 MAC sevoflurane, or 11 mg · kg · h propofol. Thereafter, all rats underwent 25 min of regional myocardial ischemia and 120 min of reperfusion. After reperfusion, hearts were excised for infarct staining. The expression of protein kinase C (PKC)&agr; and PKC&egr; was assessed by Western blot analysis and the expression of heme oxygenase-1 and vascular endothelial growth factor by reverse transcriptase polymerase chain reaction. Results:In normoxic control rats, infarct size was 62 ± 6% of the area at risk. Hypoxic LPC reduced infarct size (LPC16: 36 ± 11%, LPC12: 38 ± 10%, LPC8: 39 ± 11%; each P < 0.001) to approximately the same magnitude as sevoflurane-preconditioning (40 ± 8%; P < 0.001). Combined LPC16 and sevoflurane preconditioning was not superior to either substance alone. Continuous sevoflurane or propofol was not protective. The PKC inhibitor calphostin C abolished the cardioprotective effects of LPC16. PKC&egr;, but not PKC&agr;, expression was increased 6 and 28 h after hypoxic LPC. Heme oxygenase-1 and vascular endothelial growth factor were transiently up-regulated after 6 h. Conclusion:Hypoxic LPC at 8%, 12%, and 16% oxygen reduces infarct size in the rat heart in vivo. This effect is as powerful as sevoflurane-preconditioning. PKC&egr; is a key player in mediating hypoxic LPC.
Physically-based distributed soil erosion and sediment yield model (DREAM) for simulating individual storm events

Abstract A relatively simple process-oriented, physically-based distributed (PBD) hydrological model, the distributed runoff and erosion assessment model (DREAM), is described, and a validation study conducted in the semi-forested watershed of Pathri Rao, in the Garhwal Himalayas, India, is reported. DREAM takes account of watershed heterogeneity as reflected by land use, soil type, topography and rainfall, measured in the field or estimated through remote sensing, and generates estimates of runoff and sediment yield in spatial and temporal domains. The model is based on simultaneous solution of flow dynamics, based on kinematic wave theory, followed by solution of soil erosion dynamics. As the storm rainfall proceeds, the process of overland flow generation is dependent on the interception storage and infiltration rates. The components of the soil erosion model have been modified to provide better prediction of sediment flow rates and sediment yields. The validation study conducted to test the performance of the model in simulating soil erosion and sediment yield during different storm events monitored in the study watershed showed that the model outputs are satisfactory. Details of a sensitivity analysis, model calibration and the statistical evaluation of the results obtained are also presented and discussed. It is noteworthy that the distributed nature of the model combined with the use of geographical information system (GIS) techniques permits the computation and representation of the spatial distribution of sediment yield for simulated storm events, and a map of the spatial distribution of sediment yield for a simulated storm event is presented to highlight this capability. Citation Ramsankaran, R. , Kothyari, U.C. , Ghosh, S.K. , Malcherek, A. , and Murugesan, K. , 2013. Physically-based distributed soil erosion and sediment yield model (DREAM) for simulating individual storm events. Hydrological Sciences Journal, 58 (4), 872–891.
Diastolic filling in human severe sepsis: an echocardiographic study.

OBJECTIVE To determine if nonsurvivors have a more abnormal pattern of left ventricular relaxation than survivors with severe sepsis. DESIGN Prospective, observational, cohort study. SETTING Intensive care unit in a university-affiliated tertiary care hospital. PATIENTS Twenty-four adults with severe sepsis. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Baseline clinical and hemodynamic variables, Acute Physiology and Chronic Health Evaluation (APACHE) II scores and Doppler echocardiographic mitral inflow pattern (analyzed for normalized peak early filling rate [E/VTI, systolic volumes/sec], deceleration time [msec], and early to atrial filling velocity ratio [E/A]). There were seven deaths. The patients did not differ in baseline demographics, inotropic infusions, hemodynamic measurements or ventilatory settings or variables. Nonsurvivors had a more abnormal pattern of left ventricular relaxation (E/VTI, 4.7 [range 3.8 to 5.8] vs. 5.8 [range 3.8 to 8.9], p= .04; deceleration time, 235 [range 209 to 367] vs. 182 [range 155 to 255], p = .002). E/A showed a nonsignificant trend in the same direction (0.9 [range 0.8 to 1.6] vs. 1.2 [range 0.7 to 1.9], p = .12). In a multivariate analysis, deceleration time (p< .004) and APACHE II score (p < .02) were the only independent predictors of mortality. CONCLUSION Severe sepsis nonsurvivors have a more abnormal echocardiographic pattern of left ventricular relaxation than survivors.
Grain size of fluvial deposits and late Quaternary climate: A case study in the Po River valley (Italy)

By stacking the grain-size data interpreted from many logs of borings (down to 200 m deep) in a sector of the Po River valley, we have obtained a curve of the clay + silt fraction vs. depth that matches the oxygen isotope curve of paleotemperatures for the late Quaternary. Contour maps and plots for selected subzones show that the northern half of the study area is characterized by this correlation, whereas the southern part adds only a random low-amplitude noise to the curve. The suggested dependence of grain size of fluvial deposits on climate in a part of the study area would provide an indirect way to date these not otherwise datable sediments, allowing an evaluation of the sedimentation rates and of the total subsidence since the last interglacial.
A PILOT STUDY TO ASSESS DESIGNER'S MENTAL STRESS USING EYE GAZE SYSTEM AND ELECTROENCEPHALOGRAM

The study of mental stress is of great importance to design in that it enhances our understanding of designer’s cognitive model during the creative design process, among others. As the first step of this effort, this paper focuses on the assessment of mental stress based on the analysis of electroencephalogram (EEG) signals and the eye related data. The stress stimuli used is the computer based Stroop test with six difficulty levels. By using different parameters such as EEG power bands, and other eye behavior data, human mental stresses were assessed. Results indicate a strong correlation between the recorded physiological signals and the emotional state of the designers. This study provides a baseline for the further analysis of designer’s and users mental stresses during design-related tasks. 1 BACKGROUND
Pharmacokinetic models in clinical practice: What model to use for DCE-MRI of the breast?

Pharmacokinetic modeling is increasingly used in DCE-MRI high risk breast cancer screening. Several models are available. The most common models are the standard and extended Tofts, the shutter-speed, and the Brix model. Each model and the meaning of its parameters is explained. It was investigated which models can be used in a clinical setting by simulating a range of sampling rates and noise levels representing different MRI acquisition schemes. In addition, an investigation was performed on the errors introduced in the estimates of the pharmacokinetic parameters when using a physiologically less complex model, i.e. the standard Tofts model, to fit curves generated with more complex models. It was found that the standard Tofts model is the only model that performs within an error margin of 20% on parameter estimates over a range of sampling rates and noise levels. This still holds when small complex physiological effects are present.
PTB Domain-Directed Substrate Targeting in a Tyrosine Kinase from the Unicellular Choanoflagellate Monosiga brevicollis

Choanoflagellates are considered to be the closest living unicellular relatives of metazoans. The genome of the choanoflagellate Monosiga brevicollis contains a surprisingly high number and diversity of tyrosine kinases, tyrosine phosphatases, and phosphotyrosine-binding domains. Many of the tyrosine kinases possess combinations of domains that have not been observed in any multicellular organism. The role of these protein interaction domains in M. brevicollis kinase signaling is not clear. Here, we have carried out a biochemical characterization of Monosiga HMTK1, a protein containing a putative PTB domain linked to a tyrosine kinase catalytic domain. We cloned, expressed, and purified HMTK1, and we demonstrated that it possesses tyrosine kinase activity. We used immobilized peptide arrays to define a preferred ligand for the third PTB domain of HMTK1. Peptide sequences containing this ligand sequence are phosphorylated efficiently by recombinant HMTK1, suggesting that the PTB domain of HMTK1 has a role in substrate recognition analogous to the SH2 and SH3 domains of mammalian Src family kinases. We suggest that the substrate recruitment function of the noncatalytic domains of tyrosine kinases arose before their roles in autoinhibition.
The Luminosity Function of Field Galaxies in the CNOC1 Redshift Survey

We have computed the luminosity function for a sample of 389 field galaxies from the Canadian Network for Observational Cosmology cluster redshift survey (CNOC1) over the redshift range z = 0.2-0.6. We find Schechter parameters M*r-5 log h = -20.8 ± 0.4 and α = -1.3 ± 0.2 in rest-frame Gunn r, and M*BAB- 5 log h = -19.6 ± 0.3 and α = -0.9 ± 0.2 in rest-frame BAB. We have also split our sample at the color of a redshifted but nonevolving Sbc galaxy and find distinctly different luminosity functions for red and blue galaxies. Red galaxies have a shallow slope α ≈ -0.4 and dominate the bright end of the luminosity function, while blue galaxies have a steep α ≈ -1.4 and prevail at the faint end. Comparisons of the CNOC1 results to analogous intermediate-redshift luminosity functions from the Canada-France (CFRS) and Autofib redshift surveys show broad agreement among these independent samples, but there are also significant differences which will require larger samples to resolve. Also, in CNOC1 the red galaxy luminosity density stays about the same over the range z = 0.2-0.6, while the blue galaxy luminosity density increases steadily with redshift. These results are consistent with the trend of the luminosity density versus redshift relations seen in the CFRS, although the normalizations of the luminosity densities appear to differ for blue galaxies. Comparison to the local luminosity function from the Las Campanas redshift survey (LCRS) shows that the luminosity density at z ≈ 0.1 is only about half that seen at z ≈ 0.4. A change in the luminosity function shape, particularly at the faint end, appears to be required to match the CNOC1 and LCRS luminosity functions, if galaxy evolution is the sole cause of the differences seen. However, it should be noted that the specific details of the construction of different surveys may complicate the comparison of results and so may need to be considered carefully.
High accuracy event detection for Non-Intrusive Load Monitoring

This paper proposes a new event detection algorithm for the use in Non-Intrusive Load Monitoring (NILM). This latter is a field where the main concern is to break down, in a non-intrusive manner, the global electrical energy consumption into individual appliances consumption. Detecting events is thus of importance for appliance clustering in event-based NILM systems. A simple and fast algorithm that detects the variations of the signal's envelope is proposed in this paper. Its main advantage is the high localization accuracy of the start times of events. Its performance is evaluated using simulated and real data and is compared to one of the recently proposed algorithms in the field. Simulations show that the proposed detection algorithm gives 100 % precision and 97.13 % recall at a Signal-to-Noise Ratio (SNR) of 50 dB.
Differential expression of aquaporins in the kidneys of streptozotocin‐induced diabetic mice

Background and Aim Aquaporins (AQPs) are members of the water channel family and are important in renal physiology as it affects urinary concentration. The downregulation of aquaporins is often observed in polyuria associated with acquired nephrogenic diabetes insipidus. In this study, we examined the expression of AQP1, AQP2, AQP3 and AQP4 in streptozotocin (STZ)‐induced diabetic mice.
Coordinated localisation of mucins and trefoil peptides in the ulcer associated cell lineage and the gastrointestinal mucosa

BACKGROUND AND AIMS Trefoil factor family (TFF) peptides and the chromosome 11p15.5 mucin glycoproteins are expressed and secreted in a site specific fashion along the length of the gastrointestinal tract. Evidence for coexpression of mucins and trefoil peptides has been suggested in numerous gastrointestinal mucosal pathologies. The ulcer associated cell lineage (UACL) occurs at sites of chronic ulceration in Crohn's disease, expresses all three trefoil peptides, and is implicated in mucosal restitution. We tested the hypothesis that individual trefoil peptides are uniquely localised with specific mucins in the UACL and normal gastrointestinal epithelia. METHODS Expression of mucin genes in the UACL from small bowel tissue of patients with Crohn's disease was detected by in situ hybridisation, and localisation of the products by immunohistochemistry. Colocalisation of mucins and trefoil peptides was demonstrated by immunofluorescent colabelling in UACL and normal gastrointestinal epithelia. RESULTS MUC5AC and TFF1 were colocalised in distal ductular and surface elements of the UACL and in foveolar cells of the stomach, whereas MUC6 and TFF2 were colocalised to acinar and proximal ductular structures in the UACL, in the fundus and deep antral glands of the stomach, and in Brunner's glands of the duodenum. MUC5B was found sporadically throughout the UACL and gastric body. MUC2 was absent from the UACL, Brunner's glands, and stomach. MUC2 and TFF3 were colocalised throughout the large and small bowel mucosa. CONCLUSIONS The UACL has a unique profile of mucin gene expression. Coordinated localisation of trefoil peptides and mucins in UACL and normal gastrointestinal epithelia suggests they may assist each others' functions in protection and repair of gastrointestinal mucosa.
Backwater effects of Jambor weir sill

Compared with traditional weirs, Jambor weirs have the advantage that they reduce afflux due to their hydraulically-optimized shape. Hence, for identical discharge capacity, the height of the gate and thus the cost are reduced significantly. Although Jambor weir sills have been used in a combination with movable weirs for decades, the relationship between sill height, headwater and tailwater conditions and the resulting discharge has so far not been investigated systematically. Based on extensive tests in a hydraulic flume, an empirical equation and a dimensionless design chart were developed to estimate the backwater effect in the design phase to achieve the highest possible weir sill with an optimum hydraulic performance.
The hydraulic structure of a raised bog and its implications for ecohydrological modelling of bog development

Raised bogs are important ecohydrological systems in which there are strong two‐way links between plant succession, litter and peat decay, and hydrological functioning. Using recently established protocols, we measured the hydraulic structure of a raised bog in West Wales. We tested two hypotheses: (i) that the hydraulic conductivity (K) of the peat shows depth dependency such that lower layers of peat are effectively impermeable, and (ii) that the K of the marginal peat of the bog dome is lower than that in central areas. From 107 piezometer measurements we found there was depth dependency of K but that lower peat layers were not poorly permeable or impermeable. We also found that the K of the peat on the margin of the bog dome was generally significantly lower than that in central areas. Our results suggest that, for some bogs at least, it is important to simulate water flow through deeper peats when simulating peatland development or growth. They also raise the intriguing possibility that the low K of marginal peat is important in maintaining wet conditions in central bog areas, allowing bogs to reach greater thicknesses than they would do in the absence of the low‐K margin; an idea first proposed for blanket bogs by Lapen et al. (2005). Copyright © 2008 John Wiley & Sons, Ltd.