Miracle-dz/UniFAR-FTUs huggingface dataset:
The APM Galaxy Survey — V. Catalogues of galaxy clusters

We describe the construction of catalogues of galaxy clusters from the APM Galaxy survey using an automated algorithm based on Abell-like selection criteria. We investigate the effects of varying several parameters in our selection algorithm, including the magnitude range and radius from the cluster centre used to estimate the cluster richnesses. We quantify the accuracy of the photometric distance estimates by comparing them with measured redshifts, and we investigate the stability and completeness of the resulting catalogues. We find that the angular correlation functions for different cluster catalogues are in good agreement with one another, and are also consistent with the observed amplitude of the spatial correlation function of rich clusters.
Linear diffusion with stationary switching regime

Let Y be a Ornstein–Uhlenbeck diffusion governed by a stationary and ergodic process X : dYt = a(Xt )Yt dt + σ(Xt ) dWt ,Y0 = y0 . We establish that under the condition α = Eµ (a(X0 )) with μ the stationary distribution of the regime process X , the diffusion Y is ergodic. We also consider conditions for the existence of moments for the invariant law of Y when X is a Markov jump process having a finite number of states. Using results on random difference equations on one hand and the fact that conditionally to X , Y is Gaussian on the other hand, we give such a condition for the existence of the moment of order s ≥ 0. Actually we recover in this case a result that Basak et al. [J. Math. Anal. Appl. 202 (1996) 604–622] have established using the theory of stochastic control of linear systems.
Uplink Performance Analysis of Dense Cellular Networks With LoS and NLoS Transmissions

In this paper, we analyze the coverage probability and the area spectral efficiency (ASE) for the uplink (UL) of dense small cell networks (SCNs) considering a practical path loss model incorporating both line-of-sight (LoS) and non-line-of-sight (NLoS) transmissions. Compared with the existing work, we adopt the following novel approaches in this paper: 1) we assume a practical user association strategy (UAS) based on the smallest path loss, or equivalently the strongest received signal strength; 2) we model the positions of both base stations (BSs) and the user equipments (UEs) as two independent homogeneous Poisson point processes; and 3) the correlation of BSs’ and UEs’ positions is considered, thus making our analytical results more accurate. The performance impact of LoS and NLoS transmissions on the ASE for the UL of dense SCNs is shown to be significant, both quantitatively and qualitatively, compared with existing work that does not differentiate LoS and NLoS transmissions. In particular, existing work predicted that a larger UL power compensation factor would always result in a better ASE in the practical range of BS density, i.e., <inline-formula> <tex-math notation="LaTeX">$10^{1}\sim 10^{3}\,\textrm {BSs/km}^{2}$ </tex-math></inline-formula>. However, our results show that a smaller UL power compensation factor can greatly boost the ASE in the UL of dense SCNs, i.e., <inline-formula> <tex-math notation="LaTeX">$10^{2}\sim 10^{3}\,\textrm {BSs/km}^{2}$ </tex-math></inline-formula>, while a larger UL power compensation factor is more suitable for sparse SCNs, i.e., <inline-formula> <tex-math notation="LaTeX">$10^{1}\sim 10^{2}\,\textrm {BSs/km}^{2}$ </tex-math></inline-formula>.
Conformational changes at benzodiazepine binding sites of GABAA receptors detected with a novel technique

Benzodiazepines are widely used for their anxiolytic, sedative, myorelaxant and anticonvulsant properties. They allosterically modulate GABAA receptor function by increasing the apparent affinity of the agonist GABA. We studied conformational changes induced by channel agonists at the benzodiazepine binding site. We used the rate of covalent reaction between a benzodiazepine carrying a cysteine reactive moiety with mutated receptor having a cysteine residue in the benzodiazepine binding pocket, α1H101Cβ2γ2, as a sensor of its conformation. This reaction rate is sensitive to local conformational changes. Covalent reaction locks the receptor in the conformation stabilized by positive allosteric modulators. By using concatenated subunits we demonstrated that the covalent reaction occurs either exclusively at the α/γ subunit interface, or if it occurs in both α1 subunits, exclusively reaction at the α/γ subunit interface can modulate the receptor. We found evidence for an increased rate of reaction of activated receptors, whereas reaction rate with the desensitized state is slowed down. The benzodiazepine antagonist Ro15–1788 efficiently inhibited the covalent reaction in the presence of 100 µm GABA but only partially in its absence or in the presence of 10 µm GABA. It is concluded that Ro15–1788 efficiently protects activated and desensitized states, but not the resting state.
Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding

A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because there is natural variation among sequences within a species, and because reference databases are incomplete and can have false annotations. However, most existing bioinformatics methods for taxonomic placement either exclude uncertainty, or quantify it using metrics other than probability. In this paper we evaluate the performance of a recently proposed probabilistic taxonomic placement method PROTAX by applying it to both annotated reference sequence data as well as unknown environmental data. Our four case studies include contrasting taxonomic groups (fungi, bacteria, mammals, and insects), variation in the length and quality of the barcoding sequences (from individually Sanger-sequenced sequences to short Illumina reads), variation in the structures and sizes of the taxonomies (from 800 to 130 000 species), and variation in the completeness of the reference databases (representing 15% to 100% of the species). Our results demonstrate that PROTAX yields essentially unbiased assessment of probabilities of taxonomic placement, and thus that its quantification of species identification uncertainty is reliable. As expected, the accuracy of taxonomic placement increases with increasing coverage of taxonomic and reference sequence databases, and with increasing ratio of genetic variation among taxonomic levels over within taxonomic levels. Our results show that reliable species-level identification from environmental samples is still challenging, and thus neglecting identification uncertainty can lead to spurious inference. A key aim for future research is the completion and pruning of taxonomic and reference sequence databases, and making these two types of data compatible.
Variable ovarian response to gonadotropin-releasing hormone antagonist-induced gonadotropin deprivation during different phases of the menstrual cycle.

The gonadotropin dependence of ovarian follicular maturation and corpus luteum function can now be examined in women using antagonistic analogs of GnRH. We studied the responses of three groups of women throughout a control cycle and during the administration of a potent GnRH antagonist, detirelix ([N-Ac-D-Nal(2)1,D-pCl-Phe2,D-Trp3,D-hArg(Et2)6,D-Ala10++ +] GnRH, Syntex Research). Detirelix (10 mg, sc) was administered for 3 consecutive days during the midfollicular phase (n = 4), preovulatory phase (n = 4), and early luteal phase (n = 4). The pituitary response to detirelix was similar throughout the three phases of the menstrual cycle. Immunoreactive LH concentrations decreased to 35% (mean +/- SEM) of pretreatment values within 8 h after the initial injection and remained suppressed for 72 h after discontinuance of treatment. Immunoreactive FSH concentrations decreased to 73 +/- 3% of pretreatment levels within 8 h and returned to baseline within 24 h after the third injection. In contrast, the ovarian response to detirelix varied markedly during different phases of the cycle. Midfollicular phase treatment was associated with a decline in estradiol (E2) levels from pretreatment values of 246 +/- 48 to 81 +/- 15 pmol/L within 24 h of the last injection. Vaginal bleeding ensued in three of four women. Follicular recruitment was then reinitiated, and an ovulatory LH surge occurred 18.2 +/- 2.9 days after the last injection. Similarly, treatment during the early luteal phase produced a decline in E2 concentrations from 286 +/- 29 to 70 +/- 7 pmol/L and a decline in progesterone concentrations from 20 +/- 1.6 to 1.9 +/- 0.3 nmol/L within 24 h after the last injection. Luteolysis was associated with menstrual bleeding in all four women. The subsequent ovulatory LH surge occurred 16.5 +/- 1.0 days after discontinuance of treatment. In contrast, treatment during the preovulatory phase resulted in a decline in E2 concentrations from 844 +/- 66 to 429 +/- 132 pmol/L during the first 48 h of treatment. Gonadotropin and E2 concentrations subsequently recovered from suppression, growth of the dominant follicle resumed, and a LH surge occurred 5.8 +/- 1.4 days after the last injection. These data indicate that the GnRH antagonist detirelix produces rapid and consistent suppression of pituitary gonadotropin secretion. The magnitude of suppression and preferential suppression of LH vs. FSH are similar throughout the cycle. In contrast, the ovarian response to gonadotropin deprivation varies during the menstrual cycle. (ABSTRACT TRUNCATED AT 400 WORDS)
Patterns of Medical Diagnosis and Treatment of Migraine and Probable Migraine in a Health Plan

The objectives of this study were to assess the proportion of subjects with strict migraine (SM, migraine with and without aura), probable migraine (PM), and all migraine (AM, SM and PM pooled together), who receive a medical diagnosis or a specific treatment within a health plan. Eligible participants were 18-55-year participants of a non-profit health maintenance organization (HMO) who had received out-patient, emergency department, or in-patient care from a physician within the past year. We used a validated computer-assisted telephone interview (CATI) survey to identify SM, PM and controls (received out-patient, emergency department, or in-patient care from a physician for any reason within the past year, but did not have SM or PM). Medical and prescription drug claims for the 24-month period were linked to participant files. Among 8579 respondents, we identified 1265 SM sufferers and 1252 PM sufferers, which were compared with 960 randomly selected controls. Just 194 (15.3%) SM, 21 (1.7%) PM, and 215 (8.5%) AM sufferers received an in-patient or out-patient primary migraine claim in the previous 24 months, compared with six (0.5%) controls; 240 (18.9%) SM, 39 (3.1%) PM, 279 (11.1%) AM sufferers, and eight controls (0.6%) received any migraine claim. There were claims for migraine drugs (ICD-9 code for triptans or ergot compounds) for just 140 (11.1%) SM and 34 (2.7%) PM sufferers, and migraine analgesics (butalbital and isomethepthene compounds), for 6.3% SM and 2.2% PM sufferers (0.7% of the controls). Migraine preventives were used for a larger number of SM and PM sufferers (19.6% and 13.1%), but also for controls (10.5%), indicating that they were probably used for other medical reasons. Both SM and PM are underdiagnosed and undertreated within a health plan. Educational strategies should focus on physician education addressing diagnosing the full spectrum of migraine and physician management of migraine with specific migraine therapy in appropriate patients.
Hydroxyurea is associated with lower prevalence of albuminuria in adults with sickle cell disease.

BACKGROUND Albuminuria is an early manifestation of sickle cell nephropathy. Prior small case series suggests benefit of hydroxyurea in reducing albuminuria, with a similar trend noted in pediatric studies. We aimed to comprehensively evaluate hydroxyurea use and prevalence of albuminuria in adult sickle cell patients. METHODS We performed a cross-sectional study of 149 adult patients followed between 2000 and 2011 in a comprehensive sickle cell clinic. All patients were assessed for albuminuria either by direct measurement or by urinary chemical strip (dipstick) testing. Urinary albumin-to-creatinine ratios (UACRs) were available for 112 patients. Hydroxyurea exposure was defined as ≥3 months of therapy before the assessment of albuminuria. Albuminuria was defined as either UACR ≥30 mg/g or ≥1+ proteinuria on two separate dipsticks. We constructed a multivariate logistic regression model to assess the association between hydroxyurea and albuminuria. RESULTS The prevalence of albuminuria was lower among patients on hydroxyurea (34.7 versus 55.4%; P = 0.01) as was median albumin excretion (17.9 versus 40.5 mg/g; P = 0.04). In multivariate analysis, hydroxyurea was associated with a lower likelihood of albuminuria (odds ratio 0.28, 95% CI: 0.11-0.75, P = 0.01), adjusting for age, angiotensin-converting enzyme inhibitor/angiotensin receptor blocker use, tricuspid regurgitant jet velocity, hypertension and acute chest syndrome. CONCLUSIONS In our population of sickle cell patients, those using hydroxyurea were less than one-third as likely to exhibit albuminuria. Hydroxyurea use may prevent development of overt nephropathy or the progression of sickle cell disease nephropathy to end-stage renal disease, and its use for this indication merits further investigation.
Proper Cyclin B3 Dosage Is Important for Precision of Metaphase-to-Anaphase Onset Timing in Caenorhabditis elegans

Cyclin-dependent kinases (CDK) and their compulsory cofactors, the cyclins, are the two key classes of regulatory molecules that determine the eukaryotic cell's progress through the cell cycle by substrate phosphorylation. Cdk1 forms complexes with B-type cyclins and phosphorylates a number of substrates as cells prepare to enter mitosis. CYB-3 (Cyclin B3) is a B-type cyclin that has been recently shown to be required for the timely metaphase-to-anaphase transition, presumably by alleviating a spindle assembly checkpoint (SAC) block. Previously, we have shown that doubling the CYB-3 dosage suppresses sterility in the absence of the essential SAC component MDF-1/Mad1. Here we demonstrate the importance of the Mos1-mediated single-copy insertion method for understanding the effects of gene dosage by generating strains that have more (two or three) copies of the cyb-3 in wild-type and mdf-1(gk2) backgrounds to investigate dosage effect of CYB-3 on mitotic progression as well as development and fertility in the absence and the presence of the MDF-1 checkpoint component. We show that tripling the dosage of CYB-3 results in a significantly variable metaphase-to-anaphase transition, both in wild-type and mdf-1(gk2) mutant backgrounds. Although a majority of embryos initiate anaphase onset normally, a significant number of embryos initiate anaphase with a delay. We also show that tripling the dosage of CYB-3 has no effect on viability in the wild-type background; however, it does reduce the sterility caused by the absence of MDF-1. Together, these data reveal that proper dosage of CYB-3 is important for precision of timely execution of anaphase onset regardless of the presence of the MDF-1 checkpoint component.
HIV/AIDS, health and wellbeing study among International Transport Workers' Federation (ITF) seafarer affiliates.

BACKGROUND Transport workers generally face a higher-than-average risk of HIV as well as other health challenges. In order to improve understanding of health issues in the maritime sector, including but not limited to HIV/AIDS, and to prepare appropriate responses the International Transport Workers' Federation (ITF) conducted a study of the views and needs of those affiliates. MATERIALS AND METHODS The ITF carried out two surveys. The first consisted of a questionnaire sent to all ITF seafarer affiliates to establish their concerns about health issues, including the impact of HIV/AIDS, and to assess the extent and nature of existing trade union programmes. The second consisted of a knowledge, attitude and behaviour survey on health, wellbeing and AIDS among a cross-section of individual members administered through anonymous and confidential questionnaires by maritime affiliates in four countries in different regions and an identical online questionnaire through Survey Monkey. RESULTS For the first survey, replies were received from 35 unions in 30 countries, including major seafarer supplying countries - India, Indonesia, Myanmar, Philippines, Turkey, Ukraine - and major beneficial ownership countries such as Germany, Italy, Norway, and South Korea. Health issues of concern included HIV and other sexually transmitted infections for over three-quarters of them, and then alcohol use, weight control, and mental health. All said they would welcome ITF support in starting or strengthening a programme on general health and/or HIV. Replies were received to the second survey from 615 individual seafarers. Half to three-quarters said they worried about their weight, lack of exercise and drinking; over half felt depressed sometimes or often. There were serious knowledge gaps in a number of areas, especially HIV transmission and prevention, as well as high levels of stigma towards workmates with HIV. CONCLUSIONS A number of health issues and information gaps remain unaddressed on board and pre-departure. Mental health is especially neglected but the needs emerge clearly. Seafarers believe that companies should provide programmes but also look to their unions for health information and services. The ITF has an important role to play in supporting affiliated unions in developing activities and in providing technical and strategic guidance.
The Geometry of First-Returning Photons for Non-Line-of-Sight Imaging

Non-line-of-sight (NLOS) imaging utilizes the full 5D light transient measurements to reconstruct scenes beyond the cameras field of view. Mathematically, this requires solving an elliptical tomography problem that unmixes the shape and albedo from spatially-multiplexed measurements of the NLOS scene. In this paper, we propose a new approach for NLOS imaging by studying the properties of first-returning photons from three-bounce light paths. We show that the times of flight of first-returning photons are dependent only on the geometry of the NLOS scene and each observation is almost always generated from a single NLOS scene point. Exploiting these properties, we derive a space carving algorithm for NLOS scenes. In addition, by assuming local planarity, we derive an algorithm to localize NLOS scene points in 3D and estimate their surface normals. Our methods do not require either the full transient measurements or solving the hard elliptical tomography problem. We demonstrate the effectiveness of our methods through simulations as well as real data captured from a SPAD sensor.
Assessment of design patterns during software reengineering: lessons learned from a large commercial project

Design patterns have been eagerly adopted by software developers in recent years. There is ample evidence that patterns can have a beneficial impact on software quality, but in some cases patterns have been inappropriately applied due to a lack of experience. The paper reports on a large commercial project where the uncontrolled use of patterns has contributed to severe maintenance problems. As a result, a substantial reengineering effort was undertaken, that led to the identification of a number of inappropriately applied patterns. At first glance the elimination of these patterns appears to be desirable, but often they are tightly coupled to other software artefacts, so that their removal is economically not viable.
Melatonin treatment increases the transcription of cell proliferation-related genes prior to inducing cell death in C6 glioma cells in vitro

A number of studies have suggested that melatonin possesses anticancer properties. However, conflicting data exists with regard to the role of melatonin in the treatment of cancer. In the present study, the effects of melatonin on the transcriptional regulation of three genes associated with cell proliferation (Nestin, Bmi-1 and Sox2), and on C6 glioma cell survival and viability, were investigated in vitro to evaluate the use of melatonin in cancer therapy. Melatonin was shown to increase the mRNA levels of Nestin, Bmi-1 and Sox2 in a similar pattern, with the highest mRNA levels noted at a concentration of 3 mM. At higher concentrations of melatonin (5 mM), the mRNA levels of Nestin, Bmi-1 and Sox2 were reduced from their peak levels, and were correlated with changes observed in immunofluorescence morphology studies, cell viability and survival assays. Immunofluorescence studies of Nestin-stained cells demonstrated that treatment with a higher concentration of melatonin (3 and 5 mM) led to the Nestin filaments condensing and rearranging around the cell nuclei, and an alteration in the cell morphology. C6 cell viability was also significantly decreased at 3 mM melatonin, and cell death was observed at 5 and 10 mM melatonin. These results suggested that Nestin, Bmi-1 and Sox2 were strongly correlated with the survival of C6 cells following treatment with melatonin, and that high therapeutic concentrations of melatonin (>5 mM) were required to induce cell death. These findings suggested that the implementation of melatonin in the treatment of glioma and other types of cancer may be inhibited by conflicting cell growth signals in cells. Therefore, adjunct therapy is required to improve the efficacy of melatonin in the treatment of cancer.
Surface Expression of the AMPA Receptor Subunits GluR1, GluR2, and GluR4 in Stably Transfected Baby Hamster Kidney Cells

Abstract: The surface expression of the α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionic acid (AMPA)‐type glutamate receptor (GluR) subunits GluR1, GluR2, and GluR4 was studied in cultures of stably transfected baby hamster kidney (BHK)‐570 cells. Two methods were used to quantify surface expression: cross‐linking with the membrane‐impermeant reagent bis(sulfosuccinimidyl)suberate (BS3) and labeling of surface receptors with the membrane‐impermeant biotinylating reagent sulfosuccinimidyl 2‐(biotinamido)ethyl‐1,3‐dithiopropionate (NHS‐ss‐biotin) followed by precipitation with neutravidin beads. Western blot analyses of control versus treated cultures revealed that, for all three GluR subunits examined, 25–40% of the total GluR population is located in the plasma membrane of the BHK‐570 cells. This finding was corroborated by analyses of the surface expression of [3H]AMPA binding sites in the GluR‐expressing BHK‐570 cells performed via the biotinylation/precipitation method; these studies revealed that 30–40% of the total binding site population is found in the plasma membrane. Analyses of combinations of the subunits, both GluR1 + GluR2 and GluR2 + GluR4, revealed that heteromeric combinations of the subunits are not trafficked to the surface more efficiently than homomeric receptors. For each of the three subunits, western blots revealed two distinct bands; removal of surface receptors reduced immunoreactivity for the upper band of each subunit by >90%, whereas immunoreactivity for the lower band was reduced by only 10–20%. Treatment of extracts from the various cell lines with glycopeptidase F resulted in the collapse of the two bands into a single band of lower molecular weight, suggesting that the two original bands represent differentially glycosylated forms of the same polypeptides. These data indicate that the majority of the stably expressed GluR subunits in these cell lines are incompletely glycosylated and that complete glycosylation is associated with trafficking of the GluR subunits to the cell surface.