Miracle-dz/UniFAR-FTUs huggingface dataset:
Reaction Trajectory Revealed by a Joint Analysis of Protein Data Bank

Structural motions along a reaction pathway hold the secret about how a biological macromolecule functions. If each static structure were considered as a snapshot of the protein molecule in action, a large collection of structures would constitute a multidimensional conformational space of an enormous size. Here I present a joint analysis of hundreds of known structures of human hemoglobin in the Protein Data Bank. By applying singular value decomposition to distance matrices of these structures, I demonstrate that this large collection of structural snapshots, derived under a wide range of experimental conditions, arrange orderly along a reaction pathway. The structural motions along this extensive trajectory, including several helical transformations, arrive at a reverse engineered mechanism of the cooperative machinery (Ren, companion article), and shed light on pathological properties of the abnormal homotetrameric hemoglobins from α-thalassemia. This method of meta-analysis provides a general approach to structural dynamics based on static protein structures in this post genomics era.
The Accounting Based Valuation of Corporate R&D

The issue is how to extract realized R&D benefits from income statement numbers and is important given the current accounting policy of expensing R&D as incurred. To the extent that market participants can determine realized benefits and expect these benefits to persist in the future, they will use accounting earnings numbers to value current R&D. This study uses cross-sectional data to estimate a recursive system of two equations: one for earnings and one for valuation. The earnings equation associates earnings with recorded assets, advertising, and R&D expenditures. It extracts realized R&D benefits from reported earnings numbers. The valuation equation relates market values of equity to book values, earnings, and R&D expenditures. It determines how the accounting and R&D numbers are valued in the market. The coefficients derived from these two equations are then used to estimate the investment value of R&D. This system of equations assumes that past R&D generates earnings that create market value. The results from the earnings model indicate that reported earnings, adjusted for the expensing of R&D, do reflect realized benefits from R&D. On average, a one-dollar increase in R&D expenditures leads to a two-dollar increase in profit over a seven-year period. The results from the valuation model indicate that investors place a high value on R&D investments. On average, a one-dollar increase in R&D expenditure produces a five-dollar increase in market value. This effect of R&D on market values can be separated into an indirect and a direct component. The indirect effect, when R&D outlays affect market values through
On the number of eigenvalues of a rational eigenproblem

where A,B,Cj are linear, continuous and symmetric operators on a real Hilbert space H. A and B are positive definite, B is completely continuous and the operators Cj are positive semidefinite and have finite dimensional range. The poles σj of problem (1.1) are assumed to be positive and ordered by magnitude: 0 < σ1 < σ2 < · · · < σp. Problems of this type govern eigenvibrations of plates with elastically attached loads, and mechanical vibrations of fluid-solid structures, e.g. In [1], [6], [7] the second author studied iterative projection methods of JacobiDavidson and of Arnoldi type for the rational sparse matrix eigenproblem (1.1). These methods determine eigenvalues quite efficiently, however, it was an open question whether all eigenvalues in a given interval (in particular between consecutive poles) had been found or not. The question can be easily answered for intervals (μ1, μ2] such that no pole σk is contained in [μ1, μ2] considering the parameter dependent linear eigenproblem
Asymmetric compute-and-forward

This paper generalizes the compute-and-forward framework to allow for unequal (or asymmetric) power allocation across transmitters. Each transmitter's codebook is formed using a fine lattice that is chosen to ensure decodability as well as a coarse lattice that is chosen to enforce the power constraint. The employed lattices are drawn from a nested lattice chain, which makes it possible for the receivers to decode integer-linear combinations of the transmitted codewords. Like the original compute-and-forward framework, this scheme has a natural interpretation in terms of sending linear combinations of messages that are vectors over a finite field. Interestingly, each transmitter's power constraint and noise tolerance can be viewed in terms of restrictions on the available “signal levels”. That is, transmitters with less power must send zeros along higher order levels and transmitters that need to tolerate more noise must send zeros along lower order levels.
(Semi)Classical Limit of the Hartree Equation with Harmonic Potential

Nonlinear Schrodinger equations (NLS) of the Hartree type occur in the modeling of quantum semiconductor devices. Their "semiclassical" limit of vanishing (scaled) Planck constant is both a mathematical challenge and practically relevant when coupling quantum models to classical models. With the aim of describing the semiclassical limit of the three-dimensional (3D) Schrodinger--Poisson system with an additional harmonic potential, we study some semiclassical limits of the Hartree equation with harmonic potential in space dimension $n \geq 2$. The harmonic potential is confining and causes focusing periodically in time. We prove asymptotics in several cases, showing different possible nonlinear phenomena according to the interplay of the size of the initial data and the power of the Hartree potential. In the case of the 3D Schrodinger--Poisson system with harmonic potential, we can give only a formal computation since the need for modified scattering operators for this long-range scattering case goes beyo.
Molecular Pathogenesis of Genetic and Inherited Diseases Aging Analysis Reveals Slowed Tau Turnover and Enhanced Stress Response in a Mouse Model of Tauopathy

We have extensively analyzed the biochemical and histochemical profiles of the tau protein from the rTg4510 transgenic mouse model in which the animals uniquely develop forebrain tau pathologies similar to those found in human tauopathies. Levels of several soluble phosphorylated tau species were highest at 1 month relative to later time points, suggesting that certain tau hyperphosphorylation events were insufficient to drive tangle formation in young mice. Despite a robust, pre-tangle-like accumulation of phospho-tau in 1-month-old mice, this material was cleared by 3 months, indicating that the young mouse brain either fails to facilitate tau insolubility or possesses an enhanced ability to clear tau relative to the adult. We also found that while heat shock protein expression increased with normal aging, this process was accelerated in rTg4510 mice. Moreover, by exploiting an exon 10 ( ) specific antibody, we demonstrated that endogenous mouse tau turnover was slowed in response to human tau over-expression, and that this endogenous tau adopted disease-related properties. These data suggest that a younger brain fails to develop lasting tau pathology despite elevated levels of phosphorylated tau, perhaps because of reduced expression of stress-related proteins. Moreover , we show that the active production of small amounts of abnormal tau protein facilitates dysfunction and accumulation of otherwise normal tau, a significant implication for the pathogenesis of patients with Alzheimer’s disease. (Am J Pathol 2009, 174:000–000; DOI: 10.2353/ajpath.2009.080764)
Radio Variability of Sagittarius A*—a 106 Day Cycle

We report the presence of a 106 day cycle in the radio variability of Sagittarius A* based on an analysis of data observed with the Very Large Array over the past 20 years. The pulsed signal is most clearly seen at 1.3 cm with a ratio of cycle frequency to frequency width f/Δf = 2.2 ± 0.3. The periodic signal is also clearly observed at 2 cm. At 3.6 cm the detection of a periodic signal is marginal. No significant periodicity is detected at both 6 and 20 cm. Since the sampling function is irregular, we performed a number of tests to ensure that the observed periodicity is not the result of noise. Similar results were found for a maximum entropy method and a periodogram with a CLEAN method. The probability of false detection for several different noise distributions is less than 5% based on Monte Carlo tests. The radio properties of the pulsed component at 1.3 cm are a spectral index α ~ 1.0 ± 0.1 (for S ∝ να), an amplitude ΔS = 0.42 ± 0.04 Jy, and a characteristic timescale ΔtFWHM ≈ 25 ± 5 days. The lack of a VLBI detection of a secondary component suggests that the variability occurs within Sgr A* on a scale of ~5 AU, suggesting an instability of the accretion disk.
THE NUMBER OF LINEARLY INDUCIBLE ORDERINGS OF POINTS IN d-SPACE*

where nSk iS the sum of the n-2Ck = (n 2) ! /(n 2 k)! k! possible products of numbers taken k at a time without repetition from the set {2, 3, *,n-1}. Thus we have found Q(n, d), the number of ways that an art judge can rank n paintings, each having d numerical attributes, by forming weighted averages of the attributes. Our interest in this problem stems from work [1], [2], [3] on classification of vector-valued patterns by means of linear discriminants. Notice that the number of linearly inducible orderings is independent of configuration (up to general position). Two examples, however, will show
Increased nanoparticle penetration in collagenase-treated multicellular spheroids

The extracellular matrix of solid tumors presents a transport barrier that restricts nanoparticle penetration, thereby limiting the efficacy of nanosized delivery vehicles for cancer imaging and therapy. In this study, the effect of nanoparticle size and collagenase treatment on penetration of carboxylated polystyrene nanoparticles was systematically assessed in a multicellular spheroid model. Penetration of the nanoparticles into the spheroid core was limited to particles smaller than 100 nm. Collagenase treatment of spheroids resulted in significantly increased penetration of nanoparticles up to 100 nm with only a minor increase in particle penetration observed for particles larger than 100 nm. Collagenase was immobilized onto the surface of nanoparticles for site-specific degradation of ECM proteins. Collagenase-coated, 100 nm nanoparticles demonstrated a 4-fold increase in the number of particles delivered to the spheroid core compared with control nanoparticles. Thus, nanoparticle delivery to solid tumors may be substantially improved by the incorporation of ECM-modulating enzymes in the delivery formulation.
Impact of the 13-Valent Pneumococcal Conjugate Vaccine on Pneumococcal Meningitis in US Children.

BACKGROUND The impact of 13-valent pneumococcal conjugate vaccine (PCV13) on pneumococcal meningitis (PM) in US children is unknown. We compared the serotype distribution, antibiotic susceptibility, hospital course, and outcomes of children with PM 3 years before and 3 years after the introduction of PCV13. METHODS We identified patients ≤ 18 years of age with PM at 8 children's hospitals in the United States. Pneumococcal isolates were collected prospectively. Serotyping and antibiotic susceptibility were performed in a central laboratory. Clinical data were abstracted from medical records. Patients were divided into 3 subgroups: pre-PCV13 (2007-2009), transitional year (2010), and post-PCV13 (2011-2013). Categorical variables were analyzed by the χ(2) test and continuous variables by the Mann--Whitney U test. RESULTS During the study period, 173 of 1207 episodes (14%) of invasive pneumococcal disease were identified as PM; 76 of 645 (12%) were during 2007-2009 and 69 of 394 (18%) during 2011-2013 (50% increase; P = .03). The proportion of PCV13 serotype cases decreased from 54% in 2007-2009 to 27% in 2011-2013 (P = .001). Non-PCV13 serotype cases represented 73% of the isolates in 2011-2013. Isolates with ceftriaxone minimum inhibitory concentration ≥ 1 µg/mL decreased (13% to 3%) from 2007-2009 to 2011-2013 (P = .03). No significant differences were identified for hospital course or outcome, with the exception that a greater proportion of patients had subdural empyema and hemiparesis in 2011-2013. CONCLUSIONS After the introduction of PCV13, the number of cases of PM in children remained unchanged compared with 2007-2009, although the proportion of PCV13 serotypes decreased significantly. Serotype 19A continued to be the most common serotype in 2011-2013. Antibiotic resistance decreased significantly. Morbidity and case-fatality rate due to PM remain substantial.
Placental Invasiveness Mediates the Evolution of Hybrid Inviability in Mammals

A central question in evolutionary biology is why animal lineages differ strikingly in rates and patterns of the evolution of reproductive isolation. Here, we show that the maximum genetic distance at which interspecific mammalian pregnancies yield viable neonates is significantly greater in clades with invasive (hemochorial) placentation than in clades with noninvasive (epitheliochorial or endotheliochorial) placentation. Moreover, sister species with invasive placentation exhibit higher allopatry in their geographic ranges, suggesting that formerly separated populations in mammals with this placental type fuse more readily on recontact. These differences are apparently driven by the stronger downregulation of maternal immune responses under invasive placentation, where fetal antigens directly contact the maternal bloodstream. Our results suggest that placental invasiveness mediates a major component of reproductive isolation in mammals.
Death, Dying and Bereavement in Norway and Sweden in Recent Times

One of my research projects examines pictorial symbols and epitaphs on gravestones in Norway and Sweden. The focus has been on the 1990s and the 2000s. The choice of this period is motivated by the fact that new national burial laws were adopted in both countries in the early 1990s. These laws provided the next of kin with the possibility of choosing memorial symbols and inscriptions more freely than had previously been the case. To judge from the data under study, individual symbols have gained popularity, especially in Sweden, while Norway has been more faithful to earlier traditions of a collective character; moreover, secular motifs are more manifest on the gravestones in Sweden than in Norway. Another research project analyses memorial websites on the Internet related to persons who have died in recent years. The all-inclusive issue in these studies concerns mourners’ expressions of their emotions and beliefs regarding the deceased person’s afterlife, that is, beliefs in after-death existence. Belief in the deceased being somewhere in heaven is common. Belief in angels is also a popular concept in memorial websites. Moreover, in Sweden, this includes deceased pets as well. The previously strictly observed distinction between humans and pets has become indiscernible in Sweden. Norwegian practice, however, remains critical towards this type of “humanlike characterization”. In Norway, memorial websites for the deceased are generally associated with more traditional Christian concepts than are similar sites in Sweden. By contrast, in Sweden, one observes a kind of diffuse religiosity reminiscent of New Age ways of thinking, according to which the individual plays the central role, and glorification of afterlife existence prevails. Secularization, that is, a decline in the influence of traditional forms of religious experience, is conspicuously more prominent in Sweden. Within the project on memorial websites, I have performed a special study of memorials of persons who have committed suicide. In Norway, differences between suicide and deaths by other causes are conceived in an entirely different manner than on memorial websites in Sweden. There, the contrast between suicide and other forms of death has been increasingly wiped out. Norway has preserved earlier mortuary traditions to a greater extent, and no notions of a bright afterlife, or of angels, are to be found in connection with suicides.
Does host ideology shape populist parties’ attitudes towards the EU? The links of populism and Euroscepticism in Southern Europe

espanol? Puede un estudio de partidos populistas en el sur de Europa arrojar luz sobre la relacion entre el populismo y el euroescepticismo? Este trabajo comparativo examina los diferentes grados y tipos de euroescepticismo de los partidos populistas en la region sur, ya que esperamos que la naturaleza mas variada de los partidos populistas en esta region amplie el conocimiento sobre las relaciones entre el populismo y el euroescepticismo. En general, nuestro articulo muestra que los partidos populistas de izquierda y derecha comparten lo que inicialmente puede parecer un perfil euroesceptico homogeneo. Sin embargo, un examen mas exhaustivo confirma que los partidos populistas de izquierda tienen opiniones mas positivas sobre el proceso de integracion en los indicadores relacionados con el lado politico de la UE (poderes del Parlamento Europeo y proceso de ampliacion). EnglishCan a study of populist parties in Southern Europe shed light on the relation between populism and Euroscepticism? The proposed comparative framework examines the different degrees and types of Euroscepticism of populist parties in the Southern region. We expect that the variety of populist parties in this region, more oriented to the left, will help to expand our knowledge of the links between populism and Euroscepticism. Overall, our article shows that left and right-wing populist parties share what may initially look as a homogeneous Eurosceptic profile. However, further examination supports that left-wing populist parties hold more positive views of the EU in indicators related to the political side of the EU (powers of the European Parliament and enlargement).
Photosynthetic thermotolerance of woody savanna species in China is correlated with leaf life span.

BACKGROUND AND AIMS Photosynthetic thermotolerance (PT) is important for plant survival in tropical and sub-tropical savannas. However, little is known about thermotolerance of tropical and sub-tropical wild plants and its association with leaf phenology and persistence. Longer-lived leaves of savanna plants may experience a higher risk of heat stress. Foliar Ca is related to cell integrity of leaves under stresses. In this study it is hypothesized that (1) species with leaf flushing in the hot-dry season have greater PT than those with leaf flushing in the rainy season; and (2) PT correlates positively with leaf life span, leaf mass per unit area (LMA) and foliar Ca concentration ([Ca]) across woody savanna species. METHODS The temperature-dependent increase in minimum fluorescence was measured to assess PT, together with leaf dynamics, LMA and [Ca] for a total of 24 woody species differing in leaf flushing time in a valley-type savanna in south-west China. KEY RESULTS The PT of the woody savanna species with leaf flushing in the hot-dry season was greater than that of those with leaf flushing in the rainy season. Thermotolerance was positively associated with leaf life span and [Ca] for all species irrespective of the time of flushing. The associations of PT with leaf life span and [Ca] were evolutionarily correlated. Thermotolerance was, however, independent of LMA. CONCLUSIONS Chinese savanna woody species are adapted to hot-dry habitats. However, the current maximum leaf temperature during extreme heat stress (44·3 °C) is close to the critical temperature of photosystem II (45·2 °C); future global warming may increase the risk of heat damage to the photosynthetic apparatus of Chinese savanna species.
Recursive reconstruction on periodic trees

A periodic tree Tn consists of full n-level copies of a finite tree T. The tree Tn is labeled by random bits. The root label is chosen randomly, and the probability of two adjacent vertices to have the same label is 1−ϵ. This model simulates noisy propagation of a bit from the root, and has significance both in communication theory and in biology. Our aim is to find an algorithm which decides for every set of values of the boundary bits of T, if the root is more probable to be 0 or 1. We want to use this algorithm recursively to reconstruct the value of the root of Tn with a probability bounded away from ½ for all n. In this paper we find for all T, the values of ϵ for which such a reconstruction is possible. We then compare the ϵ values for recursive and nonrecursive algorithms. Finally, we discuss some problems concerning generalizations of this model. © 1998 John Wiley & Sons, Inc. Random Struct. Alg. , 13, 81–97, 1998
Reversal of Early Diffusion-Weighted Magnetic Resonance Imaging Abnormalities Does Not Necessarily Reflect Tissue Salvage in Experimental Cerebral Ischemia

Background and Purpose— Diffusion-weighted MRI (DWI) can detect early ischemic changes and is sometimes used as a surrogate neurological end point in clinical trials. Recent experimental stroke studies have shown that with brief periods of ischemia, some DWI lesions transiently reverse, only to recur later. This study examined the histological condition of the tissue during the period of DWI reversal. Methods— Rats underwent 30 minutes of middle cerebral artery occlusion followed by reperfusion. DWI images were obtained during ischemia and 3 to 5 hours, 1 day, and 7 days later. MRI scans were compared with histology (5 hours, n=5; 7 days, n=5) with the use of neuronal (microtubule-associated protein 2 [MAP2]) and astrocytic (glial fibrillary acidic protein [GFAP]) markers and heat-shock protein 72 (HSP72). Results— DWI abnormalities reversed 3 to 5 hours after ischemia onset but recurred at 1 day. Four animals showed complete reversal of the initial DWI hyperintensity, and 6 showed partial reversal. When the 5-hour DWI was completely normal, there was significant loss of MAP2 immunoreactivity, comprising approximately 30% of the initial DWI lesion. However, GFAP staining revealed morphologically normal astrocytes. HSP72 immunoreactivity at 5 hours was extensive and corresponded to the initial DWI lesion. Conclusions— After brief ischemic periods, normalization of the DWI does not necessarily imply that the tissue is normal. Neurons already exhibit evidence of structural damage and stress. Normal GFAP staining suggests that other nonneuronal cell populations may partially compensate for altered fluid balances at the time of DWI reversal despite the presence of neuronal injury. These observations suggest that caution is warranted when relying solely on DWI for assessment of ischemic damage.
Automatic Egyptian hieroglyph recognition by retrieving images as texts

In this paper we propose an approach for automatically recognizing ancient Egyptian hieroglyph from photographs. To this end we first manually annotated and segmented a large collection of nearly 4,000 hieroglyphs. In our automatic approach we localize and segment each individual hieroglyph, determine the reading order and subsequently evaluate 5 visual descriptors in 3 different matching schemes to evaluate visual hieroglyph recognition. In addition to visual-only cues, we use a corpus of Egyptian texts to learn language models that help re-rank the visual output.