Miracle-dz/UniFAR-FTUs huggingface dataset:
On global self-organizing maps

Self-Organizing Feature-Mapping (SOFM) algorithm is frequently used for visualization of high-dimensional (input) data in a lower-dimensional (target) space. This algorithm is based on adaptation of parameters in local neighborhoods and therefore does not lead to the best global visualization of the input space data clusters. SOFM is compared here with alternative methods of global visualization of multidimensional data, such as the multidimensional scaling (MDS) and Sammon non-linear mapping, methods based on minimization of error function measuring topographical distortions. SOFM is inferior as a visualization method but facilitates faster classification. A combination of global methods with SOFM should be useful for visualization and classification.
Motor response to a dopamine D3 receptor preferring agonist compared to apomorphine in levodopa-primed 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine monkeys.

The profile of dopamine receptor subtype activation contributing to the therapeutic efficacy and motor response complications of levodopa (nonselective pro-agonist) in Parkinson's disease remains unclear. Potent, selective, short-acting dopamine D2 receptor subfamily agonists show good antiparkinsonian efficacy but produce dyskinesias comparable to levodopa. Nonetheless, agonists displaying higher affinity for dopamine receptors other than the D2 subtype may have a better therapeutic index. To clarify this issue, we compared the nonselective dopamine D1/D2 receptor subfamilies agonist apomorphine to the dopamine D3 receptor preferring agonist [R-(+)-trans-3,4,4a,10b-tetrahydro-4-propyl-2H,5H-[1]benzopyrano[4 , 3-b]-1,4-oxazin-9-ol] (PD 128,907) in 6 levodopa-primed , 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-lesioned parkinsonian monkeys with reproducible dyskinesias. Single s.c. dosing with the lowest fully effective dose of apomorphine (averaging 27.9 +/- 4.5 microg/kg) and PD 128,907 (averaging 41.7 +/- 4.4 microg/kg) yielded equivalent antiparkinsonian efficacy on the behavioral scale and portable activity monitoring used. A comparable significant dose-dependent increase in the response magnitude and duration was seen with two higher doses. The severity of dyskinesia was also similar between the two drugs. When the lower dose for each drug was administered six times at a fixed 90-min interval, both drugs remained efficacious with no significant tolerance observed. The D3 receptor preferring antagonist U-99194A significantly reduced the motor effects of both apomorphine and PD 128,907. Thus, increased D3 receptor tone does not acutely ameliorate dyskinesias in levodopa-primed parkinsonian monkeys. Given the reported lack of affinity of PD 128,907 for central D1 receptors, our data support the concept that the pharmacological activation of D1 receptors is not mandatory for relief of parkinsonism and production of dyskinesia.
Global analyses of gene expression in early experimental osteoarthritis.

OBJECTIVE To analyze genome-wide changes in chondrocyte gene expression in a surgically induced model of early osteoarthritis (OA) in rats, to assess the similarity of this model to human OA, and to identify genes and mechanisms leading to OA pathogenesis. METHODS OA was surgically induced in 5 rats by anterior cruciate ligament transection and partial medial meniscectomy. Sham surgery was performed in 5 additional animals, which were used as controls. Both groups underwent 4 weeks of forced mobilization, 3 times per week. RNA was extracted directly from articular chondrocytes in the OA (operated), contralateral, and sham-operated knees. Affymetrix GeneChip expression arrays were used to assess genome-wide changes in gene expression. Expression patterns of selected dysregulated genes, including Col2a1, Mmp13, Adamts5, Ctsc, Ptges, and Cxcr4, were validated by real-time polymerase chain reaction, immunofluorescence, or immunohistochemistry 2, 4, and 8 weeks after surgery. RESULTS After normalization, comparison of OA and sham-operated samples showed 1,619 differentially expressed probe sets with changes in their levels of expression > or = 1.5-fold, 722 with changes > or = 2-fold, 135 with changes > or = 4-fold, and 20 with changes of 8-fold. Dysregulated genes known to be involved in human OA included Mmp13, Adamts5, and Ptgs2, among others. Several dysregulated genes (e.g., Reln, Phex, and Ltbp2) had been identified in our earlier microarray study of hypertrophic chondrocyte differentiation. Other genes involved in cytokine and chemokine signaling, including Cxcr4 and Ccl2, were identified. Changes in gene expression were also observed in the contralateral knee, validating the sham operation as the appropriate control. CONCLUSION Our results demonstrate that the animal model mimics gene expression changes seen in human OA, supporting the relevance of newly identified genes and pathways to early human OA. We propose new avenues for OA pathogenesis research and potential targets for novel OA treatments, including cathepsins and cytokine, chemokine, and growth factor signaling pathways, in addition to factors controlling the progression of chondrocyte differentiation.
AmtB Is Necessary for NH4+-Induced Nitrogenase Switch-Off and ADP-Ribosylation in Rhodobacter capsulatus

ABSTRACT Rhodobacter capsulatus possesses two genes potentially coding for ammonia transporters, amtB and amtY. In order to better understand their role in the physiology of this bacterium and their possible significance in nitrogen fixation, we created single-knockout mutants. Strains mutated in either amtB or amtY did not show a growth defect under any condition tested and were still capable of taking up ammonia at nearly wild-type rates, but an amtB mutant was no longer capable of transporting methylamine. The amtB strain but not the amtY strain was also totally defective in carrying out ADP-ribosylation of Fe-protein or the switch-off of in vivo nitrogenase activity in response to NH4+ addition. ADP-ribosylation in response to darkness was unaffected in amtB and amtBY strains, and glutamine synthetase activity was normally regulated in these strains in response to ammonium addition, suggesting that one role of AmtB is to function as an ammonia sensor for the processes that regulate nitrogenase activity.
Neo-oogenesis in mammals

Summary Recently, the existence of a mechanism for neo-oogenesis in the ovaries of adult mammals has generated much controversy within reproductive biology. This mechanism, which proposes that the ovary has cells capable of renewing the follicular reserve, has been described for various species of mammals. The first evidence was found in prosimians and humans. However, these findings were not considered relevant because the predominant dogma for reproductive biology at the time was that of Zuckerman. This dogma states that female mammals are born with finite numbers of oocytes that decline throughout postnatal life. Currently, the concept of neo-oogenesis has gained momentum due to the discovery of cells with mitotic activity in adult ovaries of various mammalian species (mice, humans, rhesus monkeys, domestic animals such as pigs, and wild animals such as bats). Despite these reports, the concept of neo-oogenesis has not been widely accepted by the scientific community, generating much criticism and speculation about its accuracy because it has been impossible to reproduce some evidence. This controversy has led to the creation of two positions: one in favour of neo-oogenesis and the other against it. Various animal models have been used in support of both camps, including both classic laboratory animals and domestic and wild animals. The aim of this review is to critically present the current literature on the subject and to evaluate the arguments pro and contra neo-oogenesis in mammals.
Effect of Freeze-Drying on the Antioxidant Compounds and Antioxidant Activity of Selected Tropical Fruits

The effects of freeze-drying on antioxidant compounds and antioxidant activity of five tropical fruits, namely starfruit (Averrhoa carambola L.), mango (Mangifera indica L.), papaya (Carica papaya L.), muskmelon (Cucumis melo L.), and watermelon Citruluss lanatus (Thunb.) were investigated. Significant (p < 0.05) differences, for the amounts of total phenolic compounds (TPC), were found between the fresh and freeze-dried fruit samples, except muskmelon. There was no significant (p > 0.05) change, however, observed in the ascorbic acid content of the fresh and freeze-dried fruits. Similarly, freeze-drying did not exert any considerable effect on β-carotene concentration of fruits, except for mango and watermelon, where significantly (p < 0.05) higher levels were detected in the fresh samples. The results of DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging and reducing power assays revealed that fresh samples of starfruit and mango had relatively higher antioxidant activity. In case of linoleic acid peroxidation inhibition measurement, a significant (p < 0.05) but random variation was recorded between the fresh and freeze-dried fruits. Overall, in comparison to β-carotene and ascorbic acid, a good correlation was established between the result of TPC and antioxidant assays, indicating that phenolics might have been the dominant compounds contributing towards the antioxidant activity of the fruits tested.
The Mars Organic Molecule Analyzer (MOMA) Instrument: Characterization of Organic Material in Martian Sediments

Abstract The Mars Organic Molecule Analyzer (MOMA) instrument onboard the ESA/Roscosmos ExoMars rover (to launch in July, 2020) will analyze volatile and refractory organic compounds in martian surface and subsurface sediments. In this study, we describe the design, current status of development, and analytical capabilities of the instrument. Data acquired on preliminary MOMA flight-like hardware and experimental setups are also presented, illustrating their contribution to the overall science return of the mission. Key Words: Mars—Mass spectrometry—Life detection—Planetary instrumentation. Astrobiology 17, 655–685.
1-2002 Market-Driven Multi-Robot Exploration

For many real-world applications, autonomous robots must execute complex tasks in unknown or partially known unstructured environments. This work presents a novel approach to efficient multi-robot mapping and exploration which exploits a market architecture in order to maximize information gain while minimizing incurred costs. This system is reliable and robust in that it can accommodate dynamic introduction and loss of team members in addition to communication interruptions and failures. Results showing the capabilities of our system on a team of exploring autonomous robots are also given.
Streptococcus pseudopneumoniae: an emerging respiratory tract pathogen

Background & objectives: Streptococcus pseudopneumoniae a member of the Viridans Streptococci, is known to be associated with chronic obstructive pulmonary disease and respiratory tract infections (RTI). Very scanty information is available on the isolation of S. pseudopneumoniae from India. Hence, the present study was an attempt to isolate S. pseudopneumoniae from clinical samples and to study their drug resistance pattern. Methods: Sputum samples (n=150) submitted to the microbiology laboratory for routine culture from patients clinically suspected to have lower respiratory tract infection were inoculated onto sheep blood agar and chocolate agar plates. Alpha haemolytic colonies were identified as S. pseudopneumoniae based on absence of capsule, bile solubility and optochin susceptibility in 5 per cent CO2 and ambient air. Disk diffusion method was used for antibiotic susceptibilily testing. Results: Among the samples screened, 4 per cent showed the growth of only S. pseudopneumoniae. Other pathogens isolated were Streptococcus pneumoniae, Moraxella catarrhalis, Klebsiella spp. , Enterococcus spp. , Pseudomonas spp. , Haemophilus influenzae, Staphylococcus aureus, Candida albicans. All the S. pseudopneumoniae isolates were resistant to erythromycin. Interpretation & conclusions: Our preliminary results showed presence of S. pseudopneumoniae in this part of the country and these were associated with RTI. Currently, most clinical laboratories report optochin susceptible isolates in 5 per cent CO2 as S. pneumoniae and the resistant ones are not further tested for susceptibility in ambient air. As a result, S. pseudopneumoniae may be missed out. Hence, performance of at least two tests, viz. optochin susceptibility with incubation in 5 per cent CO2 and ambient air along with bile solubility is necessary to differentiate S. pneumoniae from S. pseudopneumoniae
Patients presenting with AIDS in the HAART era: a collaborative cohort analysis

Objective:Many patients infected with HIV still present with an AIDS diagnosis. The aim of this study was to evaluate the virological, immunological and clinical outcomes of HAART in these patients. Design:The present study was a multi-cohort study. All patients with an AIDS diagnosis between 30 days before and 14 days after HIV diagnosis, recruited between 1997 and 2004 from eight hospital cohorts, were evaluated. Results:A total of 760 patients were included [268 (35.3%) had pneumocystis and 168 (22.1%) tuberculosis]. Six hundred and twenty-four patients (82.1%) started HAART a median of 31 days after HIV diagnosis. One hundred and fifty-three patients started a nonnucleoside transcriptase inhibitor-based regimen (20.1%), 409 a protease inhibitor-based regimen (53.8%) and 62 other regimens (8.2%). In adjusted analyses, HAART was started sooner in more recent years, in patients with lower CD4 cell count and in those with Kaposi's sarcoma, whereas it was started later in those with tuberculosis. Five hundred and five patients (89%) attained a viral load of less than 500 copies/ml. The factors associated with a better virological response were later calendar year, lower initial viral load and cytomegalovirus disease. Virological rebound was more common in those receiving nucleoside reverse transcriptase inhibitor-based regimens, in those with tuberculosis and in earlier calendar years. One hundred and twenty-five (16%) patients died; 61 had received HAART (48.6%). Mortality was more likely in those who were older, those with a higher viral load at diagnosis, those with nonsexual HIV risks and those with lower CD4 cell count and haemoglobin levels over follow-up. Conclusion:Virological suppression was achieved in most AIDS patients, though mortality remains high in these individuals.
Multiple Molecular Pathways in Melanomagenesis: Characterization of Therapeutic Targets

Molecular mechanisms involved in pathogenesis of malignant melanoma have been widely studied and novel therapeutic treatments developed in recent past years. Molecular targets for therapy have mostly been recognized in the RAS–RAF–MEK–ERK and PI3K–AKT signaling pathways; small-molecule inhibitors were drawn to specifically target key kinases. Unfortunately, these targeted drugs may display intrinsic or acquired resistance and various evidences suggest that inhibition of a single effector of the signal transduction cascades involved in melanoma pathogenesis may be ineffective in blocking the tumor growth. In this sense, a wider comprehension of the multiple molecular alterations accounting for either response or resistance to treatments with targeted inhibitors may be helpful in assessing, which is the most effective combination of such therapies. In the present review, we summarize the known molecular mechanisms underlying either intrinsic and acquired drug resistance either alternative roads to melanoma pathogenesis, which may become targets for innovative anticancer approaches.
Apolipoprotein AI and High-Density Lipoprotein Have Anti-Inflammatory Effects on Adipocytes via Cholesterol Transporters: ATP-Binding Cassette A-1, ATP-Binding Cassette G-1, and Scavenger Receptor B-1

Rationale: Macrophage accumulation in adipose tissue associates with insulin resistance and increased cardiovascular disease risk. We previously have shown that generation of reactive oxygen species and monocyte chemotactic factors after exposure of adipocytes to saturated fatty acids, such as palmitate, occurs via translocation of NADPH oxidase 4 into lipid rafts (LRs). The anti-inflammatory effects of apolipoprotein AI (apoAI) and high-density lipoprotein (HDL) on macrophages and endothelial cells seem to occur via cholesterol depletion of LRs. However, little is known concerning anti-inflammatory effects of HDL and apoAI on adipocytes. Objective: To determine whether apoAI and HDL inhibit inflammation in adipocytes and adipose tissue, and whether this is dependent on LRs. Methods and Results: In 3T3L-1 adipocytes, apoAI, HDL, and methyl-&bgr;-cyclodextrin inhibited chemotactic factor expression. ApoAI and HDL also disrupted LRs, reduced plasma membrane cholesterol content, inhibited NADPH oxidase 4 translocation into LRs, and reduced palmitate-induced reactive oxygen species generation and monocyte chemotactic factor expression. Silencing ATP-binding cassette A-1 abrogated the effect of apoAI, but not HDL, whereas silencing ATP-binding cassette G-1 or scavenger receptor B-1 abrogated the effect of HDL but not apoAI. In vivo, apoAI transgenic mice fed a high-fat, high-sucrose, cholesterol-containing diet showed reduced chemotactic factor and proinflammatory cytokine expression and reduced macrophage accumulation in adipose tissue. Conclusions: ApoAI and HDL have anti-inflammatory effects in adipocytes and adipose tissue similar to their effects in other cell types. These effects are consistent with disruption and removal of cholesterol from LRs, which are regulated by cholesterol transporters, such as ATP-binding cassette A-1, ATP-binding cassette G-1, and scavenger receptor B-1.
Association between polymorphisms in serotonin transporter gene and attention deficit hyperactivity disorder in Chinese Han subjects

Prior work has shown reduced serotonin transmission to be associated with impulsivity and behavioral problems. The current study assessed the association between ADHD and two variants of the serotonin transporter gene: the 44‐bp deletion/insertion polymorphism (5‐HTTLPR) and the 17 bp‐repeat polymorphism in intron 2 (STin2.VNTR). We hypothesized that ADHD phenotypes associated with impulsivity would show an association with these variants. Two‐hundred and ninety‐three ADHD trios were genotyped and analyzed using transmission disequilibrium test (TDT) analysis and haplotype analysis. We found no association between the STin2.VNTR and ADHD, but did find preferential transmission of the S allele of the 5‐HTTLPR polymorphism (χ2 = 5.751, P = 0.016) to probands with ADHD. Haplotype analysis found the L/10 haplotype was over‐transmitted (χ2 = 6.172, P = 0.013), while L/12 was under‐transmitted to probands with ADHD (χ2 = 4.866, P = 0.027). © 2006 Wiley‐Liss, Inc.
Prognostic value of brain perfusion single-photon emission computed tomography (SPECT) for language recovery in patients with aphasia

AimTo determine the prognostic value of brain perfusion single-photon emission computed tomography (SPECT) in patients with aphasia after a stroke. MethodsBrain perfusion SPECT with 99mTc-ethyl cysteinate dimer (99mTc-ECD) was used in 16 right-handed patients with aphasia after a left-sided cerebrovascular accident (CVA) in the early chronic period after the onset of CVA. The region of interest (ROI) method was used to calculate the relative regional cerebral blood flow (rCBF) in each cerebral lobe, the thalamus, the putamen and the cerebellum as ratios to the count in the left cerebellar hemisphere. The Standard Language Test of Aphasia (SLTA) was performed twice, once at the same time as SPECT, a mean of 2.3 months after CVA onset (early SLTA), and again a mean of 17.0 months after CVA onset (late SLTA). In addition to the overall language function score, scores for taking dictation (Dictation), oral reading (Speaking) and comprehension (Comprehension) were calculated, and the correlations with each of the rCBF values were evaluated. ResultsLeft temporal CBF correlated with the late Dictation score; bilateral frontal, bilateral temporal and right parietal CBF correlated with the late Speaking score; and right frontal, left temporal and left occipital CBF correlated with the late Comprehension score. ConclusionBrain perfusion SPECT in the early chronic stage was shown to be useful for predicting recovery from aphasia, recovery of oral reading, ability to take dictation and comprehension.
A nation-wide retrospective epidemiological study of gastroenteropancreatic neuroendocrine neoplasms in china

Background Representative data on the gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) in Asian patients is rare, especially in China. This study aims to create a GEP-NENs profile of Chinese patients. Methods This was a hospital-based, nation-wide, and multi-center 10-year (2001-2010) retrospective study which collected GEP-NEN patients’ information in tertiary referral hospitals. All 2010 inpatient GEP-NEN cases with confirmed pathology in the selected hospitals were included. The primary GEP-NEN sites were measured and the epidemiological and clinical information of each tumor site were compared. Results The most common primary sites for GEP-NEN were the pancreas (31.5%) and rectum (29.6%), followed by the cardia (11.6%) and body (15.4%) of stomach. Small intestinal and colonic NENs took up a relatively small proportion of all patients. Pancreatic and rectal NENs, rather than cardiac and gastric body NENs, tended to be found in younger (P<0.001), female (P<0.001), urban (P<0.001) residents with a higher education level (P=0.032) and were also diagnosed at earlier stage (P<0.001) and lower grade (P<0.001). Surgery remained the primary treatment method in all groups. Conclusions More studies on the commonality and heterogeneity of GEP-NENs are warranted to improve diagnosis efficiencies and treatment outcomes.
Three in One—Multiple Faunal Elements within an Endangered European Butterfly Species

Ice ages within Europe forced many species to retreat to refugia, of which three major biogeographic basic types can be distinguished: "Mediterranean", "Continental" and "Alpine / Arctic" species. However, this classification often fails to explain the complex phylogeography of European species with a wide range of latitudinal and altitudinal distribution. Hence, we tested for the possibility that all three mentioned faunal elements are represented within one species. Our data was obtained by scoring 1,307 Euphydryas aurinia individuals (46 European locations) for 17 allozyme loci, and sequencing a subset of 492 individuals (21 sites) for a 626 base pairs COI fragment. Genetic diversity indices, F statistics, hierarchical analyses of molecular variance, individual-based clustering, and networks were used to explore the phylogeographic patterns. The COI fragment represented 18 haplotypes showing a strong geographic structure. All but one allozyme loci analysed were polymorphic with a mean F ST of 0.20, supporting a pronounced among population structure. Interpretation of both genetic marker systems, using several analytical tools, calls for the recognition of twelve genetic groups. These analyses consistently distinguished different groups in Iberia (2), Italy, Provence, Alps (3), Slovenia, Carpathian Basin, the lowlands of West and Central Europe as well as Estonia, often with considerable additional substructures. The genetic data strongly support the hypothesis that E. aurinia survived the last glaciation in Mediterranean, extra-Mediterranean and perialpine refugia. It is thus a rare example of a model organism that combines attributes of faunal elements from all three of these sources. The observed differences between allozymes and mtDNA most likely result from recent introgression of mtDNA into nuclear allozyme groups. Our results indicate discrepancies with the morphologically-based subspecies models, underlining the need to revise the current taxonomy.