Miracle-dz/UniFAR-FTUs huggingface dataset:
A Late Occurring “Hipparion” from the middle Villafranchian of Monopoly, Italy (early Pleistocene; MN16b; ca. 2.5 Ma)

We report here for the first time the occurrence in the Montopoli large mammal fossil assemblage of a small equid taxon identified as “Hipparion” sp. , associated to the monodactyl large horse Equus cf. livenzovensis. This occurrence has been recognised on a specimen that the late De Giuli (1938-1988) identified as Hipparion sp. in unpublished notes available in the archives of the Vertebrate Palaeontology Laboratory of the Dipartimento di Scienze della Terra at the Università degli Studi di Firenze. Although fragmentary, the specimen documents the occurrence of “Hipparion” at the middle Villafranchian (early Pleistocene, ca. 2.5 Ma) site of Montopoli, one of the latest occurrences of an hipparionine horse in western Europe. The western Eurasian “Hipparion” evolutionary history is summarised herein. RIASSUNTO [Una forma tardiva di “Hipparion” nell’associazione faunistica del Villafranchiano medio di Montopoli, Italia (Pleistocene inferiore; MN16b; ca. 2.5 Ma)] Si segnala per la prima volta la presenza nell’associazione faunistica a vertebrati di Montopoli Val d’Arno di un equide di piccolo taglia identificato come “Hipparion” sp. , associato all’equide monodattilo di grande taglia Equus cf. livenzovensis. La segnalazione si basa sullo studio di un reperto che lo scomparso Claudio De Giuli (1938-1988) aveva identificato come Hipparion sp. in un manoscritto inedito conservato negli archivi del Laboratorio di Paleontologia dei Vertebrati del Dipartimento di Scienze della Terra dell’Università degli Studi di Firenze. Sebbene frammentario, il campione documenta chiaramente la presenza di “Hipparion” all’inizio del Villafranchiano medio (Pleistocene inferiore, ca. 2.5 Ma) a Montopoli, e rappresenta una delle ultime presenze di un equide ipparionino in Europa. Viene infine presentata una sintesi della storia evolutiva di “Hipparion” nel record fossile dell’Europa occidentale.
Predictive Factors Associated with Left Ventricular Hypertrophy at Baseline and in the Follow‐Up Period in Non‐Diabetic Hemodialysis Patients

Hemodialysis (HD) patients frequently have an elevated left ventricular mass index (LVMI). Currently, left ventricular (LV) hypertrophy and dysfunction are considered to be the strongest predictors of cardiovascular mortality in dialysis patients. The objectives of the present study are to investigate the factors associated with elevated LVMI and to discuss therapeutic implications for the treatment strategy for pre‐dialysis and HD patients. The correlation among biochemical values, physical specimens, and LVMI using echocardiography was prospectively analyzed in 30 non‐diabetic HD patients in the Juntendo University Hospital. Measurement of these parameters was performed at 0, 12, and 24 months after initiation of HD. Systolic blood pressure (SP), human atrial natriuretic peptide (hANP), and hemoglobin (Hb) levels were significantly correlated with LVMI. SBP, residual glomerular filtration rate (rGFR), and serum albumin levels were identified as independent risk factors for LVMI in multivariate regression analysis at initiation of HD. SBP, hANP, and Hb levels were identified as independent risk factors for LVMI in multivariate regression analysis after 24 months. SBP, rGFR, and serum albumin levels were predictive factors for LVMI at initiation of HD. SBP, hANP, and Hb levels were also predictive factors for LVMI after initiation of HD.
Stylizing 2.5-D video

In recent years considerable interest has been given to nonphotorealistic rendering of photographs, video, and 3D models for illustrative or artistic purposes. Conventional 2D inputs such as photographs and video are easy to create and capture, while 3D models allow for a wider variety of stylization techniques, such as cross-hatching. In this paper, we propose using video with depth information (2.5-D video) to combine the advantages of 2D and 3D input. 2.5-D video is becoming increasingly easy to capture, and with the additional depth information, stylization techniques that require shape information can be applied. However, because 2.5-D video contains only limited shape information and 3D correspondence over time is unknown, it is difficult to create temporally coherent stylized animations directly from raw 2.5-D video. In this paper, we present techniques for processing 2.5-D video to overcome these drawbacks, and demonstrate several styles that can be created using these techniques.
Improved cyclopropanation activity of histidine-ligated cytochrome P450 enables the enantioselective formal synthesis of levomilnacipran.

Engineering enzymes capable of modes of activation unprecedented in nature will increase the range of industrially important molecules that can be synthesized through biocatalysis. However, low activity for a new function is often a limitation in adopting enzymes for preparative-scale synthesis, reaction with demanding substrates, or when a natural substrate is also present. By mutating the proximal ligand and other key active-site residues of the cytochrome P450 enzyme from Bacillus megaterium (P450-BM3), a highly active His-ligated variant of P450-BM3 that can be employed for the enantioselective synthesis of the levomilnacipran core was engineered. This enzyme, BM3-Hstar, catalyzes the cyclopropanation of N,N-diethyl-2-phenylacrylamide with an estimated initial rate of over 1000 turnovers per minute and can be used under aerobic conditions. Cyclopropanation activity is highly dependent on the electronic properties of the P450 proximal ligand, which can be used to tune this non-natural enzyme activity.
Inflation Band Targeting and Optimal Inflation Contracts

In this paper we examine how target ranges work in the context of a Barro-Gordon (1983) type model, in which the time-inconsistency problem stems from political pressures from the government. We show that target ranges turn out to be an excellent way to cope with the time-inconsistency problem, and achieve many of the benefits that arise under practically less attractive solutions such as the conservative central banker and optimal inflation contracts. Our theoretical model also shows how an inflation targeting range should be set and how it should respond to changes in the nature of shocks to the economy
Revisiting rainfall to explore exam questions and performance on CS1

The Rainfall problem comprises small tasks that have been used to investigate student performance in introductory programming. We conducted several kinds of analyses to inform our understandings of student performance in CS1 relating to this problem. We analyzed implementation approaches and program errors, as in related studies, and also explored the role of test writing vis-à-vis the most common student error. Finally, using correlation analyses and manual inspection of the exam answers, we studied how well the Rainfall problem served as an exam question. The students' implementation choices reflected their familiarity with particular loop constructs, while the single most common error concerned division by zero (DivZ), as in many previous studies. Although many students wrote unit tests to guard against DivZ, they often failed to implement according to the tests, which could be partly attributed to the pen-and-paper exam format. From the correlation analyses, we concluded that some students had difficulties with knowledge transfer and that their conceptual understandings of program constructs were insufficient, regardless of them being able to produce working code. The results inform CS1 teachers in preparing materials and exams.
Organotypic Culture of Physiologically Functional Adult Mammalian Retinas

Background The adult mammalian retina is an important model in research on the central nervous system. Many experiments require the combined use of genetic manipulation, imaging, and electrophysiological recording, which make it desirable to use an in vitro preparation. Unfortunately, the tissue culture of the adult mammalian retina is difficult, mainly because of the high energy consumption of photoreceptors. Methods and Findings We describe an interphase culture system for adult mammalian retina that allows for the expression of genes delivered to retinal neurons by particle-mediated transfer. The retinas retain their morphology and function for up to six days— long enough for the expression of many genes of interest—so that effects upon responses to light and receptive fields could be measured by patch recording or multielectrode array recording. We show that a variety of genes encoding pre- and post-synaptic marker proteins are localized correctly in ganglion and amacrine cells. Conclusions In this system the effects on neuronal function of one or several introduced exogenous genes can be studied within intact neural circuitry of adult mammalian retina. This system is flexible enough to be compatible with genetic manipulation, imaging, cell transfection, pharmacological assay, and electrophysiological recordings.
Herpesvirus Entry Mediator HVEM Mediates Cell-Cell Spread in BHK(TK−) Cell Clones

ABSTRACT 95-19 and US11cl19.3 are BHK(TK−)-derived cell lines that are highly resistant to postattachment entry of herpes simplex virus type 1 (HSV-1) and HSV-2 but not to later steps in single-step replication. The resistance properties of these two cell types are not identical. US11cl19.3 cells are fully susceptible to pseudorabies virus (PRV), as shown by single-step growth experiments, whereas 95-19 cells are resistant to entry of free PRV but not to entry by cell-cell spread. We have tested the ability of HVEM to overcome the block to infection in both cell lines following transient and stable transfection. HVEM was able to mediate entry of free HSV-1 into both cell lines, as shown by an increase in the number of β-galactosidase-expressing cells in cultures transiently transfected with an HVEM expression plasmid and infected withlacZ-expressing HSV-1. In stably transfected 95-19 cells, HVEM enhanced infection by free HSV-1, as shown by an increase in the number of infectious centers obtained following infection. In both cell types, HVEM strongly enhanced entry of HSV-1 and HSV-2 by cell-cell spread, suggesting that HVEM can function as an entry mediator both in entry of free virus and in entry by cell-cell spread.
A Combined MAP + MLLR Approach for Speaker Adaptation

A new approach for speaker adaptation consisting of MLLR adaptation enriched by a special weighting scheme followed by MAP adaptation is presented. While the standard MLLR approach increases the error rate for the considered small amounts of adaptation data in on-line, unsupervised adaptation, our approach can reduce the error by up to 30%. This result can further be improved by switching to MAP adaptation, yielding a final reduction in error rate of 38.6% compared to the speaker independent (SI) system.
Ecohydrological dynamics in the Alps: Insights from a modelling analysis of the spatial variability

Mountain ecosystems are experiencing rapid warming resulting in ecological changes worldwide. Projecting the response of these ecosystems to climate change is thus crucial, but also uncertain due to complex interactions between topography, climate, and vegetation. Here, we performed numerical simulations in a real and a synthetic spatial domain covering a range of contrasting climatic conditions and vegetation characteristics representative of the European Alps. Simulations were run with the mechanistic ecohydrological model Tethys–Chloris to quantify the drivers of ecosystem functioning and to explore the vulnerability of Alpine ecosystems to climate change. We correlated the spatial distribution of ecohydrological responses with that of meteorological and topographic attributes and computed spatially explicit sensitivities of net primary productivity, transpiration, and snow cover to air temperature, radiation, and water availability. We also quantified how the variance in several ecohydrological processes, such as transpiration, quickly diminishes with increasing spatial aggregation, which highlights the importance of fine spatial resolution for resolving patterns in complex topographies. We conducted controlled numerical experiments in the synthetic domain to disentangle the effect of catchment orientation on ecohydrological variables, such as streamflow. Our results support previous studies reporting an altitude threshold below which Alpine ecosystems are water‐limited in the drier inner‐Alpine valleys and confirm that the wetter areas are temperature‐limited. High‐resolution simulations of mountainous areas can improve our understanding of ecosystem functioning across spatial scales. They can also locate the areas that are the most vulnerable to climate change and guide future measurement campaigns.
Rendering diffuse objects using particle systems inside voxelized surface geometry

This paper presents an unique method for rendering complex shapes as fuzzy or diffuse objects inside virtual environments. It uses surface geometry that is converted into a voxel-like grid to specify the appearance of the shape. A particle system displays the outline of the object at runtime. Particles are allowed to move freely inside the voxel-grid but obtain certain attributes from the voxels they currently reside in. Those attributes assign color, size, textures, transparency to the particles, as well as forces that influence the movement of the particles. Force effects include linear and spiral movements, gravitational points, and helix-shaped motion of particles. Through this, complex movement of the particles inside the voxel-space can be created at interactive rates, while still maintaining the approximate form of the original surface geometry.
Green chemistry approach for the synthesis of biocompatible graphene

Background Graphene is a single-atom thick, two-dimensional sheet of hexagonally arranged carbon atoms isolated from its three-dimensional parent material, graphite. One of the most common methods for preparation of graphene is chemical exfoliation of graphite using powerful oxidizing agents. Generally, graphene is synthesized through deoxygenation of graphene oxide (GO) by using hydrazine, which is one of the most widespread and strongest reducing agents. Due to the high toxicity of hydrazine, it is not a promising reducing agent in large-scale production of graphene; therefore, this study focused on a green or sustainable synthesis of graphene and the biocompatibility of graphene in primary mouse embryonic fibroblast cells (PMEFs). Methods Here, we demonstrated a simple, rapid, and green chemistry approach for the synthesis of reduced GO (rGO) from GO using triethylamine (TEA) as a reducing agent and stabilizing agent. The obtained TEA reduced GO (TEA-rGO) was characterized by ultraviolet (UV)–visible absorption spectroscopy, X-ray diffraction (XRD), particle size dynamic light scattering (DLS), scanning electron microscopy (SEM), Raman spectroscopy, and atomic force microscopy (AFM). Results The transition of graphene oxide to graphene was confirmed by UV–visible spectroscopy. XRD and SEM were used to investigate the crystallinity of graphene and the surface morphologies of prepared graphene respectively. The formation of defects further supports the functionalization of graphene as indicated in the Raman spectrum of TEA-rGO. Surface morphology and the thickness of the GO and TEA-rGO were analyzed using AFM. The presented results suggest that TEA-rGO shows significantly more biocompatibility with PMEFs cells than GO. Conclusion This is the first report about using TEA as a reducing as well as a stabilizing agent for the preparation of biocompatible graphene. The proposed safe and green method offers substitute routes for large-scale production of graphene for several biomedical applications.
Inference of population structure using multilocus genotype data: dominant markers and null alleles

Dominant markers such as amplified fragment length polymorphisms (AFLPs) provide an economical way of surveying variation at many loci. However, the uncertainty about the underlying genotypes presents a problem for statistical analysis. Similarly, the presence of null alleles and the limitations of genotype calling in polyploids mean that many conventional analysis methods are invalid for many organisms. Here we present a simple approach for accounting for genotypic ambiguity in studies of population structure and apply it to AFLP data from whitefish. The approach is implemented in the program structure version 2.2, which is available from http://pritch.bsd. uchicago.edu/structure.html.
CRISPR interference and priming varies with individual spacer sequences

CRISPR–Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring ‘spacer’ sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid ‘primed’ adaptation. Here, we use multiple spacer sequences to reexamine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR–Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed and the PAM than previously reported, and this mutational tolerance, as well as priming activity, is highly dependent on spacer sequence. We identify a large number of functional PAMs that can promote interference, priming or both activities, depending on the associated spacer sequence. Functional PAMs are preferentially acquired during unprimed ‘naïve’ adaptation, leading to a rapid priming response following infection. Our results provide numerous insights into the importance of both spacer and target sequences for interference and priming, and reveal that priming is a major pathway for adaptation during initial infection.
Identification of OmpR-Family Response Regulators Interacting with Thioredoxin in the Cyanobacterium Synechocystis sp. PCC 6803

The redox state of the photosynthetic electron transport chain is known to act as a signal to regulate the transcription of key genes involved in the acclimation responses to environmental changes. We hypothesized that the protein thioredoxin (Trx) acts as a mediator connecting the redox state of the photosynthetic electron transport chain and transcriptional regulation, and established a screening system to identify transcription factors (TFs) that interact with Trx. His-tagged TFs and S-tagged mutated form of Trx, TrxMC35S, whose active site cysteine 35 was substituted with serine to trap the target interacting protein, were co-expressed in E. coli cells and Trx-TF complexes were detected by immuno-blotting analysis. We examined the interaction between Trx and ten OmpR family TFs encoded in the chromosome of the cyanobacterium Synechocystis sp. PCC 6803 (S.6803). Although there is a highly conserved cysteine residue in the receiver domain of all OmpR family TFs, only three, RpaA (Slr0115), RpaB (Slr0946) and ManR (Slr1837), were identified as putative Trx targets. The recombinant forms of wild-type TrxM, RpaA, RpaB and ManR proteins from S.6803 were purified following over-expression in E. coli and their interaction was further assessed by monitoring changes in the number of cysteine residues with free thiol groups. An increase in the number of free thiols was observed after incubation of the oxidized TFs with Trx, indicating the reduction of cysteine residues as a consequence of interaction with Trx. Our results suggest, for the first time, the possible regulation of OmpR family TFs through the supply of reducing equivalents from Trx, as well as through the phospho-transfer from its cognate sensor histidine kinase.
Adaptive transmission power control and rate selection scheme for maximizing energy efficiency of IEEE 802.11 stations

Energy efficiency in wireless communications is one of important research issues. Previous studies on reducing the energy consumption of IEEE 802.11 WLAN systems mainly focused on the energy consumption of a single-link transmission only. However, due to its carrier sensing property, all the WLAN stations in the network receive the transmitted frames. Hence, this single-link transmission not only consumes the energy of the transmitter and receiver of the link, but also consumes the energy of the other stations. Moreover, most of the previous work on energy efficiency optimization problems were considered in MAC perspectives. In this paper, we show that the energy efficiency of all the stations in WLAN network can be optimized by our proposed adaptive transmission power control and rate selection scheme, with more accurate analysis of the energy consumption in IEEE 802.11 MAC and IEEE 802.11n PHY. The proposed adaptive transmission power control and rate selection scheme achieves an increase in an average energy efficiency of 34% at the cost of 5% throughput degradation for 800bits payload size and 20 users, for varying the distance from 0m to 90m.
Regularized channel inversion with quantized feedback in down-link multiuser channels

We consider regularized channel inversion (RI) precoding in the multiuser multiple input multiple output (Mu-MIMO) broadcast channels. To make the RI operate in quantized channel feedback condition, we analyze the quantization error variance and its effect on the signal to interference plus noise power ratio (SINR) of the user signals. The regularization parameter ¿ is optimized to balance the additive noise, the multiuser interference and the interference due to the quantization error and to maximize SINR. Analysis and simulations show that regularization enhances the performance of zero forcing beam forming (ZFBF) over the whole signal to noise power ratio (SNR) range. This is contrasting to the perfect channel status information (CSI) case, where the enhancement is observed in the low SNR region.
Data-driven methodology to extending workflows to e-services over the Internet

E-services refer to the services offered over the Internet. The globalization of economy accelerates the provision of e-services across organizations. Instead of being built from scratch, e-services are mostly extended from existing internal workflows or information systems. In this paper, we examine the requirements of extending a workflow to the provision of e-services, in order to fulfill predefined business processes and data requirements. We also discuss the support of exception handling and asynchronous events across organizational boundaries, through an event publish-and-subscribe mechanism. We demonstrate the feasibility of this approach with the E-ADOME extension layer of our ADOME-WFMS, further illustrated with a system integration example. Our event-driven execution model provides a unified framework for both synchronous execution of workflow and asynchronous handling of events and exceptions. Illustrations are also given on the provision of such e-services over the infrastructure of Web services and Enterprise JavaBeans.