Miracle-dz/UniFAR-FTUs huggingface dataset:
Urban birds have broader environmental tolerance

Urbanization dramatically changes the composition and diversity of biotic communities. The characteristics distinguishing species that persist in urban environments, however, are poorly understood. Here we test the hypothesis that broadly adapted organisms are better able to tolerate urbanization, using a phylogenetically controlled, global comparison of birds. We compared elevational and latitudinal distributions of 217 urban birds found in 73 of the world's largest cities with distributions of 247 rural congeners to test the hypothesis that urban birds possess broader environmental tolerance. Urban birds had markedly broader environmental tolerance than rural congeners, as estimated by elevational and latitudinal distributions. Our results suggest that broad environmental tolerance may predispose some birds to thrive in urban habitats. The mechanisms mediating such environmental tolerance warrant further investigation, but probably include greater behavioural, physiological and ecological flexibility.
Response to sensory uncertainty in Parkinson’s disease: a marker of cerebellar dysfunction?

Motor performance is profoundly influenced by sensory information, yet sensory input can be noisy and uncertain. The basal ganglia and the cerebellum are important in processing sensory uncertainty, as the basal ganglia incorporate the uncertainty of predictive reward cues to reinforce motor programs, and the cerebellum and its connections mitigate the effect of ambiguous sensory input on motor performance through the use of forward models. Although Parkinson’s disease (PD) is classically considered a primary disease of the basal ganglia, alterations in cerebellar activation are also observed, which may have consequences for the processing of sensory uncertainty. The aim of this study was to investigate the effect of visual uncertainty on motor performance in 15 PD patients and ten age‐matched control subjects. Subjects performed a visually guided tracking task, requiring large‐amplitude arm movements, by tracking with their index finger a moving target along a smooth trajectory. To induce visual uncertainty, the target position randomly jittered about the desired trajectory with increasing amplitudes. Tracking error was related to target ambiguity to a significantly greater degree in PD subjects off medication compared with control subjects, indicative of susceptibility to visual uncertainty in PD. l‐Dopa partially ameliorated this deficit. We interpret our findings as suggesting an inability of PD subjects to create adequate forward models and/or de‐weight less informative visual input. As these computations are normally associated with the cerebellum and connections, we suggest that alterations in normal cerebellar functioning may be a significant contributor to altered motor performance in PD.
Unusual Polymorphisms in Human Immunodeficiency Virus Type 1 Associated with Nonprogressive Infection

ABSTRACT Factors accounting for long-term nonprogression may include infection with an attenuated strain of human immunodeficiency virus type 1 (HIV-1), genetic polymorphisms in the host, and virus-specific immune responses. In this study, we examined eight individuals with nonprogressing or slowly progressing HIV-1 infection, none of whom were homozygous for host-specific polymorphisms (CCR5-Δ32, CCR2-64I, andSDF-1-3′A) which have been associated with slower disease progression. HIV-1 was recovered from seven of the eight, and recovered virus was used for sequencing the full-length HIV-1 genome; full-length HIV-1 genome sequences from the eighth were determined following amplification of viral sequences directly from peripheral blood mononuclear cells (PBMC). Longitudinal studies of one individual with HIV-1 that consistently exhibited a slow/low growth phenotype revealed a single amino acid deletion in a conserved region of the gp41 transmembrane protein that was not seen in any of 131 envelope sequences in the Los Alamos HIV-1 sequence database. Genetic analysis also revealed that five of the eight individuals harbored HIV-1 with unusual 1- or 2-amino-acid deletions in the Gag sequence compared to subgroup B Gag consensus sequences. These deletions in Gag have either never been observed previously or are extremely rare in the database. Three individuals had deletions in Nef, and one had a 4-amino-acid insertion in Vpu. The unusual polymorphisms in Gag, Env, and Nef described here were also found in stored PBMC samples taken 3 to 11 years prior to, or in one case 4 years subsequent to, the time of sampling for the original sequencing. In all, seven of the eight individuals exhibited one or more unusual polymorphisms; a total of 13 unusual polymorphisms were documented in these seven individuals. These polymorphisms may have been present from the time of initial infection or may have appeared in response to immune surveillance or other selective pressures. Our results indicate that unusual, difficult-to-revert polymorphisms in HIV-1 can be found associated with slow progression or nonprogression in a majority of such cases.
Serotonin‐immunoreactive axon terminals innervate pyramidal cells and interneurons in the rat basolateral amygdala

The basolateral nuclear complex of the amygdala (BLC) receives a dense serotonergic innervation that appears to play a critical role in the regulation of mood and anxiety. However, little is known about how serotonergic inputs interface with different neuronal subpopulations in this region. To address this question, dual‐labeling immunohistochemical techniques were used at the light and electron microscopic levels to examine inputs from serotonin‐immunoreactive (5‐HT+) terminals to different neuronal subpopulations in the rat BLC. Pyramidal cells were labeled by using antibodies to calcium/calmodulin‐dependent protein kinase II, whereas different interneuronal subpopulations were labeled by using antibodies to a variety of interneuronal markers including parvalbumin (PV), vasoactive intestinal peptide (VIP), calretinin, calbindin, cholecystokinin, and somatostatin. The BLC exhibited a dense innervation by thin 5‐HT+ axons. Electron microscopic examination of the anterior basolateral nucleus (BLa) revealed that 5‐HT+ axon terminals contained clusters of small synaptic vesicles and a smaller number of larger dense‐core vesicles. Serial section reconstruction of 5‐HT+ terminals demonstrated that 76% of these terminals formed synaptic junctions. The great majority of these synapses were symmetrical. The main targets of 5‐HT+ terminals were spines and distal dendrites of pyramidal cells. However, in light microscopic preparations it was common to observe apparent contacts between 5‐HT+ terminals and all subpopulations of BLC interneurons. Electron microscopic analysis of the BLa in sections dual‐labeled for 5‐HT/PV and 5‐HT/VIP revealed that many of these contacts were synapses. These findings suggest that serotonergic axon terminals differentially innervate several neuronal subpopulations in the BLC. J. Comp. Neurol. 505:314–335, 2007. © 2007 Wiley‐Liss, Inc.
HSV-2 incidence by sex over four age periods to age 38 in a birth cohort

Objectives To examine herpes simplex virus type 2 (HSV-2) incidence over four periods to age 38 in a birth cohort, and to compare risks for men and women, taking into account sexual behaviour. Methods At ages 21, 26, 32 and 38, participants in the Dunedin Multidisciplinary Health and Development Study were invited to provide serum for HSV-2 serology, and information on sexual behaviour. HSV-2 incidence rates were calculated for four age periods, and comparisons made by sex and period, taking into account number of sexual partners. Results By age 38, 17.3% of men and 26.8% of women had ever been seropositive for HSV-2. Incidence peaked for women from age 21 to 26 (19.1 per 1000 person-years) and men from age 26 to 32 (14.1 per 1000 person-years); it fell markedly for both from age 32 to 38 (5.1 and 6.8 per 1000 person-years for men and women, respectively). Overall risk was significantly higher for women: adjusted incidence rate ratio 1.9 (95% CI 1.4 to 2.7); the sex difference was most marked from age 21 to 26 (3.4, 95% CI 1.9 to 6.3). Conclusions Our findings are consistent with a greater biological susceptibility to HSV-2 among women, and with the increasing risk to the early/mid-20s for women and late 20s/early 30s for men, being driven by an increasing pool of prevalent infection. The reduced risk in the mid-30s is consistent with declining infectivity of long-term prevalent infections.
Photodynamic therapy for cosmetic applications

ABSTRACT: With the advent of short contact and pulsed light techniques, topical 5‐aminolevulinic acid photodynamic therapy (5‐ALA PDT) has become a viable clinical modality. Intense pulsed light, the pulsed dye laser, and blue light‐emitting lamps have become the most commonly used devices in inducing a cosmetic PDT effect. More recently, by combining the photothermal effects of pulsed light with the photochemical effects of PDT, an enhanced cosmetic effect has been demonstrated in a variety of dermatologic conditions. In addition, the use of shorter 5‐ALA incubation times allows for improved patient tolerance during treatment and subsequently fewer adverse effects in the postoperative period. A review of the current literature on cosmetic uses of PDT as well as our personal techniques are discussed in detail.
Surprising but true: Half the decisions in organizations fail

Executive Overview Half the decisions in organizations fail. Studies of 358 decisions in medium to large organizations in the U.S. and Canada reveal that these failures can be traced to managers who impose solutions, limit the search for alternatives, and use power to implement their plans. Managers who make the need for action clear at the outset, set objectives, carry out an unrestricted search for solutions, and get key people to participate are more apt to be successful. Tactics prone to fail were used in two of every three decisions that were studied.
Dynamic General Equilibrium Analysis At the State Level: Assessing the Economic Implications of the Kyoto Protocol

This paper addresses a question central to the way climate change policy impacts are discussed in the United States: What are the economic costs for individual states of carbon abatement proposals? We present a dynamic computable general equilibrium model of a single U.S. state facing carbon limits. We consistently incorporate the competitive impacts resulting from carbon abatement in other states and regions. Specifically we assess the impacts on Colorado of the 1997 Kyoto agreement. Our analysis suggests that the competitive impacts which affect a state’s terms-of-trade are of crucial importance when assessing the economic cost impacts of the Kyoto agreement for a given state. Also, the overall economic impacts on Colorado are largely dependent on the extent of international trade in emissions permits.
Oral immunoadjuvant activity of Lactobacillus casei subsp. casei in dextran-fed layer chickens

We recently reported that synbiotic Lactobacillus casei subsp. casei together with specific substrate dextran elicited an enhancement in humoral immune response against bovine serum albumin (BSA) as a model antigen in BALB/c mice. The present study was designed to evaluate the oral immunoadjuvant effects of the synbiotic in layer chickens. Using a PCR assay, L. casei subsp. casei was detected specifically in the intestinal chyme of chickens (10d of age, Julia strain) fed ad libitum on a diet supplemented with 75mg dextran/kg (dextran-supplemented diet, DSD) and administered orally with 107 colony-forming units (CFU) L. casei subsp. casei in 0·1ml PBS with the aid of an intubation needle at 1, 2 and 3d of age. Furthermore, oral administration of 107 CFU L. casei subsp. casei at 1–3d of age significantly enhanced the production of anti-BSA antibody in DSD-fed chickens (60d of age) administered orally with 1mg BSA at 32 and 33d of age and subcutaneously with 5μg BSA at 33d of age. In addition, among bacterial numbers tested, 106 CFU L. casei subsp. casei together with dextran induced an effective increase in humoral immune response to mixed inactivated vaccines against Newcastle disease and avian infectious bronchitis, and the treatment may be advantageous in protecting against these infectious diseases in chickens in actual application. These results suggest that dietary supplementation of L. casei subsp. casei with dextran leads to immunomodulation of humoral immune responses.
On the Informational Content of Dividends

In his recent paper entitled "The Information Content of Dividends," Ross Watts set out to determine if "dividends convey information about future earnings-information that enables market participants to predict future earnings more accurately. "' Based on information presented in some of my work,2 his conclusion was that the dividend process should be specified on an annual basis and that, although there may be some informational content to dividends, the amount is trivial. The purpose of this paper is to express disagreement with both of these conclusions and to present evidence to support this contrary position.
PIER: Protein interface recognition for structural proteomics

Recent advances in structural proteomics call for development of fast and reliable automatic methods for prediction of functional surfaces of proteins with known three‐dimensional structure, including binding sites for known and unknown protein partners as well as oligomerization interfaces. Despite significant progress the problem is still far from being solved. Most existing methods rely, at least partially, on evolutionary information from multiple sequence alignments projected on protein surface. The common drawback of such methods is their limited applicability to the proteins with a sparse set of sequential homologs, as well as inability to detect interfaces in evolutionary variable regions. In this study, the authors developed an improved method for predicting interfaces from a single protein structure, which is based on local statistical properties of the protein surface derived at the level of atomic groups. The proposed Protein IntErface Recognition (PIER) method achieved the overall precision of 60% at the recall threshold of 50% at the residue level on a diverse benchmark of 490 homodimeric, 62 heterodimeric, and 196 transient interfaces (compared with 25% precision at 50% recall expected from random residue function assignment). For 70% of proteins in the benchmark, the binding patch residues were successfully detected with precision exceeding 50% at 50% recall. The calculation only took seconds for an average 300‐residue protein. The authors demonstrated that adding the evolutionary conservation signal only marginally influenced the overall prediction performance on the benchmark; moreover, for certain classes of proteins, using this signal actually resulted in a deteriorated prediction. Thorough benchmarking using other datasets from literature showed that PIER yielded improved performance as compared with several alignment‐free or alignment‐dependent predictions. The accuracy, efficiency, and dependence on structure alone make PIER a suitable tool for automated high‐throughput annotation of protein structures emerging from structural proteomics projects. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Progressive Obesity Alters Ovarian Folliculogenesis with Impacts on Pro-Inflammatory and Steroidogenic Signaling in Female Mice1

ABSTRACT Diet-induced obesity induces immune cell infiltration and inflammation in peri-ovarian adipose tissue and mRNA expression of inflammatory markers in ovarian tissue. Whether these changes are associated with obesity-related ovarian dysfunction remains unknown. In the present study, qRT-PCR and Western blotting techniques were used to compare mRNA and protein abundance of ovarian immune cell and inflammation markers, along with NF-kappaB and steroidogenic pathway members in normal wild-type non-agouti (a/a; lean) and lethal yellow mice (KK.CG-Ay/J; obese) at 6, 12, 18, or 24 wk of age. Our data revealed that, beginning at 12 wk of age, NF-kappaB inflammatory signaling members were elevated (P < 0.05) in obese females. Interestingly obesity had opposing and temporal effects on the steroidogenic enzyme pathway. Obesity decreased (P < 0.05) STAR protein at 12, 18, and 24 wk of age. CYP11A1 and CYP19A1 proteins were increased (P < 0.05) at 12 wk but were decreased (P < 0.05) at 18 and 24 wk. Interestingly, CYP19A1 was increased in lethal yellow mouse ovaries at 6 wk of age, potentially indicating early puberty onset. These data demonstrate that obesity alters expression of ovarian inflammatory and steroidogenic pathway genes in ways which could adversely affect ovarian function.
Peptidergic neurons of Aplysia lose their response to cyclic adenosine 3':5'-monophosphate during a prolonged refractory period

Although the peptidergic bag cell neurons of Aplysia are ordinarily silent, they respond to brief electrical stimulation by producing an afterdischarge of about 30 min duration. This afterdischarge is followed by a refractory period lasting many hours during which electrical stimulation either fails to initiate afterdischarges or produces discharges of much shorter duration. Previous work has demonstrated that cyclic AMP plays a role in the genesis of afterdischarge, both in intact bag cell clusters and in isolated cultured bag cells. We have now examined the hypothesis that in the refractory period either the synthesis of cyclic AMP or the response to cyclic AMP is attenuated. Direct measurements of cyclic AMP showed that cyclic AMP levels in the bag cell neurons are elevated to a similar extent after stimulation in refractory and nonrefractory clusters of neurons. We have found, however, that the response to cyclic AMP is altered during the refractory period. The electrophysiological responses of bag cell neurons were first examined in intact clusters of cells within the abdominal ganglion. Cyclic AMP levels were elevated using the adenylate cyclase activator, forskolin, in the presence of theophylline (FT). The duration of a first bag cell afterdischarge could be greatly increased if FT was added before stimulation. The duration of a stimulated second bag cell afterdischarge could also be significantly increased if FT was added within a brief period following the end of the first afterdischarge. Furthermore, at these times the addition of FT often resulted in the onset of spontaneous afterdischarges.
Analysis of a periodic review inventory control system with perishables having random lifetime

We consider an order up to level policy for perishable items with random lifetime. We investigate two cases: the first one is the case where excess demand is completely lost and the second one deals with full backorders. Demands arrive according to a Poisson process. The lifetime of each item is assumed to be exponentially distributed and the procurement lead time is constant. We also assume that there is at most one outstanding order at any time. We model this inventory system as a Markov process in which stationary regime can be characterised. This model allows us to get insights on the impact of the model parameters on the overall system performance in terms of costs.
Performance Evaluation of Line Symmetry-Based Validity Indices on Clustering Algorithms

Abstract Finding the optimal number of clusters and the appropriate partitioning of the given dataset are the two major challenges while dealing with clustering. For both of these, cluster validity indices are used. In this paper, seven widely used cluster validity indices, namely DB index, PS index, I index, XB index, FS index, K index, and SV index, have been developed based on line symmetry distance measures. These indices provide the measure of line symmetry present in the partitioning of the dataset. These are able to detect clusters of any shape or size in a given dataset, as long as they possess the property of line symmetry. The performance of these indices is evaluated on three clustering algorithms: K-means, fuzzy-C means, and modified harmony search-based clustering (MHSC). The efficacy of symmetry-based validity indices on clustering algorithms is demonstrated on artificial and real-life datasets, six each, with the number of clusters varying from 2 to n, $\sqrt n ,$ where n is the total number of data points existing in the dataset. The experimental results reveal that the incorporation of line symmetry-based distance improves the capabilities of these existing validity indices in finding the appropriate number of clusters. Comparisons of these indices are done with the point symmetric and original versions of these seven validity indices. The results also demonstrate that the MHSC technique performs better as compared to other well-known clustering techniques. For real-life datasets, analysis of variance statistical analysis is also performed.
Information fusion feature preprocessor based on FRFT for analog circuits fault diagnosis

This paper presents a new fault feature preprocessor method for analog circuit fault diagnosis. An information fusion method based on fractional Fourier transform (FRFT) is introduced to extract features from voltages of the circuit under test (CUT). Firstly, the voltage signals gathered from test nodes of the CUT are preprocessed by FRFT, the fractional order p of the FRFT changes from 0 to 1 with a given step. Then, we gain the amplitudes of the transformed signals in fractional space and extract the mutual information entropies as features by a defined division scale. After normalization, the extracted features are used to train a neural network to diagnose faulty components in the CUT. The proposed feature preprocessor method is applied to two CUTs and is compared with three ordinary preprocessing methods in analog circuit fault diagnosis. The experiment results reveal that the proposed method can simplify the structure of the network and improve the diagnosis performance.
The Disconnected Innovation of New Urbanity in Zuidas Amsterdam, Ørestad Copenhagen and Forum Barcelona

In the latest generation of large-scale European peripheral development projects, a growing ambition is visible to plan more urban environments. We refer to this intention as planning for “new urbanity” since the aim is to reintroduce into a new timeframe and location the traditional urban concepts of density and mixing uses. Empirical evidence shows, however, that the path to realize such ambitions has been very difficult. This article presents a study on governance factors influencing the trajectory from initial ambitions towards the first physical results in three cases. An analysis is made of the different dimensions of framing of these projects in their respective metropolitan action space and of the rules that structure their operational domains. This is the basis to question the extent to which the ambition for new urbanity has developed in a social norm influencing acceptable behaviour among actors. The conclusion is that the narrowly defined operation spheres of these projects are weakly connected to important societal domains that could have better supported these ambitions. New urbanity has, therefore, predominantly remained a disconnected, free-floating, “good idea” without strong material results. It is also in danger of becoming an extremely privatized planning concept, deviating from its original spatial and socially integrative nature.