Miracle-dz/UniFAR-FTUs huggingface dataset:
Studies on Human Antibodies

The 1-(m-nitrophenyl) flavazoles (NPF1) of the isomaltose oligosaccharides obtained by condensation of o-phenylenediamine, m-nitrophenyl hydrazine sulfate with the isomaltose oligosaccharides were used to study their interaction with human antidextran by the quantitative hapten inhibition and fluorescence-quenching techniques. The NPF1 haptens inhibited in the dextran-antidextran system in whole serum in the same order as did the isomaltose oligosaccharides; that is, NPF1 of isomaltoheptaose (NPF1IM7) was the best inhibitor, inhibitory potency decreased progressively to the NPF1 of isomaltotetraose (NPF1IM4). Studies with antidextrans purified on a specific immunoadsorbent and eluted sequentially by isomaltotriose (IM3) and isomaltohexaose (IM6) showed that NPF1IM4 and NPF1IM5 inhibited the IM3 antidextran eluate better than the IM6 eluate, confirming the previous finding that antidextrans consist of subpopulations with different size combining sites. All NPF1 of isomaltose oligosaccharides caused specific fluorescence quenching of the purified antidextrans which could be reversed specifically by addition of unlabeled IM6. Since relatively large amounts of nonspecific attenuation also occurred with γ globulin devoid of antidextran activity or with L-tryptophan solution, absolute values of maximum quenching (Qmax) could not be obtained, but the relative value of Qmax for each NPF1 was estimated from Scatchard plots by using various values of Qmax and taking the one which gave an extrapolated value of two combining sites since purified antidextrans are IgG and have two combining sites/molecule. NPF1IM3 with the NPF1 group closest to the immunodominant non-reducing end of IM3, which would be closest to the antibody-combining site, gave the largest Qmax and NPF1IM7 with the NPF1 group farthest from the immunodominant end gave the smallest Qmax. Differences in Qmax values were seen for the various antidextran fractions eluted by methyl α-D-glucoside, IM3 and IM6. Average intrinsic association constants, K0, of the purified antidextrans obtained from the Scatchard plots ranged from 5 to 8 × 104 for NPF1IM7 and from 1 to 1.3 × 104 for NPF1IM3. NPF1IM3 and NPF1IM4 gave smaller K0 values with the IM6 antidextran eluate than with the IM3 and methyl α-D-glucoside eluates, providing further evidence that small haptens are bound less effectively in combining sites of larger size.
Syn‐rift sequence development in a fault‐controlled embayment (Early Permian Irwin River Coal Measures, Northern Perth Basin, Western Australia)

Stratigraphic patterns and sequence development in tectonically active extensional basins remain poorly documented in comparison with passive‐margin settings. Rift basin fills are generally characterized by coarsening‐upward trends in response to the rapid creation of accommodation by extensional faulting, and the progressive filling of graben during more quiescent periods. The Early Permian Irwin River Coal Measures in the Northern Perth Basin (Western Australia) record a complex stratigraphic arrangement of conglomerate, sandstone, mudstone and coal, and have been attributed to delta plain depositional environments that developed in a cool–temperate climatic setting during syn‐rift activity. Sedimentary analysis of outcrop and core data from the fault‐bounded Irwin Terrace is used to distinguish nine facies associations reflecting deposition in braided rivers, fixed‐anastomosed channel belts, tide‐influenced coastal environments and storm‐affected distal bays. The broader depositional system is interpreted as a morphologically asymmetrical tide‐dominated embayment with a fluvial and wave influence. The stratigraphic architecture of the Irwin River Coal Measures was strongly influenced by the evolving rift basin margin. Fault reactivation of the major basin‐bounding Darling Fault in the early syn‐rift phase caused footwall uplift and the inception of transverse palaeo‐valleys occupied by braided fluvial systems. Fault block subsidence during the subsequent balanced, backstepping and drowning phases resulted in a dominantly retrogradational stacking pattern indicating progressive flooding of marginal‐marine areas and culminating in deposition of distal marine elements. In the active rift basin, it is proposed that preservation of a shallow‐marine syn‐rift sequence was promoted by the geomorphological confinement of the embayed system increasing tidal current acceleration and hampering transgressive ravinement. The proposed sequence model demonstrates that transgressive successions can develop in the early syn‐rift phase in response to footwall uplift and tectonic subsidence. The syn‐rift sequence recording the filling of an embayment on a rift basin margin may be applied in similar tectonic and/or depositional contexts worldwide.
A 2.5-Gb/s On-Chip Interconnect Transceiver With Crosstalk and ISI Equalizer in 130 nm CMOS

In this paper, a crosstalk compensation scheme for high speed single-ended on-chip signaling is presented. To reduce the effect of crosstalk in bandwidth enhanced channel employing capacitively driven interconnect, a crosstalk feed-forward equalizer is proposed, which compensates for the low-pass nature of the crosstalk. The proposed scheme is verified using a three-channel 10 mm on-chip interconnect implemented in 130 nm CMOS process. Measurement results show that the proposed transceiver effectively removes the crosstalk for data rates of up to 2.5-Gb/s while consuming 0.96 mW, which corresponds to energy efficiency of 0.41 pJ/bit.
Customer Acquisition via Display Advertising Using Multi-Armed Bandit Experiments

Firms using online advertising regularly run experiments with multiple versions of their ads since they are uncertain about which ones are most effective. Within a campaign, firms try to adapt to intermediate results of their tests, optimizing what they earn while learning about their ads. But how should they decide what percentage of impressions to allocate to each ad? This paper answers that question, resolving the well-known "learn-and-earn'' trade-off using multi-armed bandit (MAB) methods. The online advertiser's MAB problem, however, contains particular challenges, such as a hierarchical structure (ads within a website), attributes of actions (creative elements of an ad), and batched decisions (millions of impressions at a time), that are not fully accommodated by existing MAB methods. Our approach captures how the impact of observable ad attributes on ad effectiveness differs by website in unobserved ways, and our policy generates allocations of impressions that can be used in practice. We implemented this policy in a live field experiment delivering over 700 million ad impressions in an online display campaign with a large retail bank. Over the course of two months, our policy achieved an 8% improvement in the customer acquisition rate, relative to a control policy, without any additional costs to the bank. Beyond the actual experiment, we performed counterfactual simulations to evaluate a range of alternative model specifications and allocation rules in MAB policies. Finally, we show that customer acquisition would decrease about 10% if the firm were to optimize click through rates instead of conversion directly, a finding that has implications for understanding the marketing funnel.
Robust receiver design for MIMO single-carrier block transmission over time-varying dispersive channels against imperfect channel knowledge

We consider MIMO single-carrier block transmission over time-varying multipath channels, under the assumption that the channel parameters are not exactly known but are estimated via the least-squares training technique. While the channel temporal variation is known to negate the tone-by-tone frequency-domain equalization facility, it is otherwise shown that in the time domain the signal signatures can be arranged into groups of orthogonal components, leading to a very natural yet efficient group-by-group symbol recovery scheme. To realize this figure of merit we propose a constrained-optimization based receiver which also takes into account the mitigation of channel mismatch effects caused by time variation and imperfect estimation. The optimization problem is formulated in an equivalent unconstrained generalized-sidelobe-canceller setup. This enables us to directly model the channel mismatch effect into the system equations through the perturbation technique and, in turn, to further exploit the statistical assumptions on channel temporal variation and estimation errors for deriving a closedform solution. Within the considered framework the proposed robust equalizer can be combined with the successive interference cancellation mechanism for further performance enhancement. Flop count evaluation and numerical simulation are used to evidence the advantages of the proposed scheme.
Méthodes proximales pour la résolution de problèmes inverses : application à la tomographie par émission de positrons. (Proximal methods for the resolution of inverse problems : application to positron emission tomography)

L'objectif de cette these est de proposer des methodes fiables, efficaces et rapides pour minimiser des criteres convexes apparaissant dans la resolution de problemes inverses en imagerie. Ainsi, nous nous interesserons a des problemes de restauration/reconstruction lorsque les donnees sont degradees par un operateur lineaire et un bruit qui peut etre non additif. La fiabilite de la methode sera assuree par l'utilisation d'algorithmes proximaux dont la convergence est garantie lorsqu'il s'agit de minimiser des criteres convexes. La quete d'efficacite impliquera le choix d'un critere adapte aux caracteristiques du bruit, a l'operateur lineaire et au type d'image a reconstruire. En particulier, nous utiliserons des termes de regularisation bases sur la variation totale et/ou favorisant la parcimonie des coefficients du signal recherche dans une trame. L'utilisation de trames nous amenera a considerer deux approches : une formulation du critere a l'analyse et une formulation du critere a la synthese. De plus, nous etendrons les algorithmes proximaux et leurs preuves de convergence aux cas de problemes inverses multicomposantes. La recherche de la rapidite de traitement se traduira par l'utilisation d'algorithmes proximaux parallelisables. Les resultats theoriques obtenus seront illustres sur differents types de problemes inverses de grandes tailles comme la restauration d'images mais aussi la stereoscopie, l'imagerie multispectrale, la decomposition en composantes de texture et de geometrie. Une application attirera plus particulierement notre attention ; il s'agit de la reconstruction de l'activite dynamique en Tomographie par Emission de Positrons (TEP) qui constitue un probleme inverse difficile mettant en jeu un operateur de projection et un bruit de Poisson degradant fortement les donnees observees. Pour optimiser la qualite de reconstruction, nous exploiterons les caracteristiques spatio-temporelles de l'activite dans les tissus
Interpretable human action recognition in compressed domain

Compressed domain human action recognition algorithms are extremely efficient, because they only require a partial decoding of the video bit stream. However, the question what exactly makes these algorithms decide for a particular action is still a mystery. In this paper, we present a general method, Layer-wise Relevance Propagation (LRP), to understand and interpret action recognition algorithms and apply it to a state-of-the-art compressed domain method based on Fisher vector encoding and SVM classification. By using LRP, the classifiers decisions are propagated back every step in the action recognition pipeline until the input is reached. This methodology allows to identify where and when the important (from the classifier's perspective) action happens in the video. To our knowledge, this is the first work to interpret a compressed domain action recognition algorithm. We evaluate our method on the HMDB51 dataset and show that in many cases a few significant frames contribute most towards the prediction of the video to a particular class.
Self-Help: Towards the Next Generation

In the UK, recent guidelines on the treatment of depression and anxiety recommend CBT-based self-help materials as one important component of services. However, despite being based on specific CBT techniques or “empirically grounded interventions”, early optimism has been dented by data from recent studies that have cast doubt on the effectiveness of the current generation of these materials. As a consequence, it may be necessary to consider that other factors may contribute to the overall magnitude of CBT effects. Indeed, it is logically inconsistent to argue that specific factors are pre-eminent in CBT whilst maintaining that delivery via therapists is more likely to be effective than self-help. The contribution of “common factors” that operate in personal therapeutic encounters, for example, therapist responsiveness and the patient-therapist alliance, may be one possible overlooked reason for the reduced ef-fectiveness of self-help materials. The development of the next generation of self-help materials, therefore, may benefit from the testing of materials that combine common and specific factors, including specific measurement of the strength of common factors and their relationship to clinical outcomes. We discuss a model of such common factors and suggest how they could be incorporated into the next generation of CBT based self-help materials.
Beyond Mental Illness

The association between violence and serious mental illness (SMI)—schizophrenia, other psychotic disorder, bipolar disorder, or major depressive disorder—was examined and guided by the I3 model to frame analysis of the National Epidemiologic Survey on Alcohol and Related Conditions Waves 1 and 2, enrolling N = 34,653 participants representative of the U.S. population. SMI was related to subsequent violent behavior but in multivariable analysis had the weakest link to severe violence. Risk factors postulated to increase dispositional impellance (anger, perceived threats), situational impellance (recent divorce/separation, financial crisis, victimization), and disinhibition (alcohol/drug abuse) fully mediated the relationship between SMI and violence. Clinical research, interventions, and policies on violence should use conceptual models and consider SMI not in isolation but relative to other risk factors. Violence prevention targeting only psychiatric diagnosis is likely to have limited impact given lack of a strong or direct connection found between SMI and violent behavior.
Appropriate target interactions prevent abnormal cytoskeletal changes in neurons: a study with intra-sciatic grafts of the septum and the hippocampus

Transplantation of embryonic CNS regions into the PNS provides an opportunity to study temporal and spatial changes in the cytoskeleton that are associated with aging and neurodegenerative diseases. In this study, the fetal septum was transplanted alone or with the hippocampus into the sciatic nerves of young adult rats to determine whether the proper central neural target could prevent the expression of abnormal cytoskeletal changes. The substantia nigra, a non-target area of the septum, served as control co-grafts. After 1, 3, 6, 12, and 18 months of survival, the grafts were examined by immunocytochemistry with antibodies to phosphorylated and nonphosphorylated neurofilaments, microtubule-associated proteins (MAPs), and glial fibrillary acidic protein (GFAP). Subpopulations of neurons in the septal transplants expressed CAT and the NGF receptor (192-IgG). Long-term (12–18 months) expression of these two markers was only observed when the septum was combined with the hippocampus. Although isolated single grafts of septum survived within the PNS substratum, significant neuronal loss, extensive graft shrinkage, and aberrant cytoskeletal immunoreactivity were prominent in the long-term group. Changes that reflected an aging process included the ectopic expression of phosphorylated neurofilaments in neuronal perikarya, swollen axons, and a loss of MAP2 immunoreactivity that paralleled dendrite regression. In addition, abnormal “curly” fibers in the neuropil were also immunolabeled with an antibody directed against tau (5E2). Introduction of hippocampal co- grafts increased the final size of the septal transplants and prevented the cytoskeletal changes that accompanied the degeneration in the single septal grafts. The degree of GFAP immunostaining in the septum corresponded with advancing graft age and was minimized when grafted with the hippocampal formation. When the septum was combined with the substantia nigra, the grafts also underwent shrinkage and no protective influence from aberrant cytoskeletal staining was observed. These experiments exemplify the importance of an appropriate CNS neural target on the maintenance of long-term cholinergic neuron survival and normal morphology at the cytoskeletal level and illustrate the usefulness of these CNS-PNS constructs to examine conditions that influence the cytoskeleton.
Mycoplasma agalactiae MAG_5040 is a Mg2+-Dependent, Sugar-Nonspecific SNase Recognised by the Host Humoral Response during Natural Infection

In this study the enzymatic activity of Mycoplasma agalactiae MAG_5040, a magnesium-dependent nuclease homologue to the staphylococcal SNase was characterized and its antigenicity during natural infections was established. A UGA corrected version of MAG_5040, lacking the region encoding the signal peptide, was expressed in Escherichia coli as a GST fusion protein. Recombinant GST-MAG_5040 exhibits nuclease activity similar to typical sugar-nonspecific endo- and exonucleases, with DNA as the preferred substrate and optimal activity in the presence of 20 mM MgCl2 at temperatures ranging from 37 to 45°C. According to in silico analyses, the position of the gene encoding MAG_5040 is consistently located upstream an ABC transporter, in most sequenced mycoplasmas belonging to the Mycoplasma hominis group. In M. agalactiae, MAG_5040 is transcribed in a polycistronic RNA together with the ABC transporter components and with MAG_5030, which is predicted to be a sugar solute binding protein by 3D modeling and homology search. In a natural model of sheep and goats infection, anti-MAG_5040 antibodies were detected up to 9 months post infection. Taking into account its enzymatic activity, MAG_5040 could play a key role in Mycoplasma agalactiae survival into the host, contributing to host pathogenicity. The identification of MAG_5040 opens new perspectives for the development of suitable tools for the control of contagious agalactia in small ruminants.
The origin and identity of embryonic stem cells

Embryonic stem (ES) cells are used extensively in biomedical research and as a model with which to study early mammalian development, but their exact origin has been subject to much debate. They are routinely derived from pre-implantation embryos, but it has been suggested that the cells that give rise to ES cells might arise from epiblast cells that are already predisposed to a primordial germ cell (PGC) fate, which then progress to ES cell status via the PGC lineage. Based on recent findings, we propose here that ES cells can be derived directly from early epiblast cells and that ES cells might arise via two different routes that are dictated by their culture conditions.
One-Hour Postload Plasma Glucose Levels and Left Ventricular Mass in Hypertensive Patients

OBJECTIVE Left ventricular hypertrophy (LVH), an independent risk factor for cardiovascular (CV) morbidity and mortality, recognizes a multifactorial pathogenesis. A plasma glucose value ≥155 mg/dL for the 1-h postload plasma glucose during an oral glucose tolerance test (OGTT) identifies subjects with normal glucose tolerance (NGT) at high risk for type 2 diabetes. We addressed the question if glucose tolerance status, particularly 1-h postload plasma glucose levels, affects left ventricular mass (LVM) and cardiac geometry in essential hypertension. RESEARCH DESIGN AND METHODS We enrolled 767 never-treated hypertensive subjects, 393 women and 374 men (mean age 49.6 ± 8.5 years). All patients underwent an OGTT for the evaluation of glucose tolerance and standard echocardiography. LVM was calculated using the Devereux formula and normalized by body surface area (LVM index [LVMI]). Insulin sensitivity was assessed by the Matsuda index. Among all participants, 514 had NGT, 168 had impaired glucose tolerance (IGT), and 85 had type 2 diabetes. According to the 1-h postload plasma glucose cutoff point of 155 mg/dL, we divided normotolerant subjects into two groups: NGT <155 mg/dL (n = 356) and NGT ≥155 mg/dL (n = 158). RESULTS Subjects in the NGT ≥155 mg/dL group had worse insulin sensitivity than subjects in the NGT <155 mg/dL group (Matsuda index 63.9 vs. 88.8; P < 0.0001). Men with NGT ≥155 mg/dL had a higher LVMI than men with NGT <155 mg/dL (126.6 vs. 114.3 g/m2; P = 0.002) and a different LVH prevalence (41.1 vs. 25.8%; P < 0.0001). At multiple regression analysis, 1-h glucose resulted in the major determinant of LVMI in normotolerant, IGT, and diabetic groups. CONCLUSIONS These data show that NGT ≥155 mg/dL subjects, compared with NGT <155 mg/dL subjects, have a higher LVMI and a greater prevalence of LVH similar to that of IGT and diabetic patients.
Meningococcal pilin: a glycoprotein substituted with digalactosyl 2,4‐diacetamido‐2,4,6‐trideoxyhexose

Neisseria meningitidis pili are filamentous protein structures that are essential adhesins in capsulate bacteria. Pili of adhesion variants of meningococcal strain C311 contain glycosyl residues on pilin (PilE), their major structural subunit. Despite the presence of three potential N‐linked glycosylation sites, none appears to be occupied in these pilins. Instead, a novel O‐linked trisaccharide substituent, not previously found as a constituent of glycoproteins, is present within a peptide spanning amino acid residues 45 to 73 of the PilE molecule. This structure contains a terminal 1‐4‐linked digalactose moiety covalently linked to a 2,4‐diacetamido‐2,4,6‐trideoxyhexose sugar which is directly attached to pilin. Pilins derived from galactose epimerase (galE) mutants lack the digalactosyl moiety, but retain the diacetamidotrideoxyhexose substitution. Both parental (#3) pilins and those derived from a hyper‐adherent variant (#16) contained identical sugar substitutions in this region of pilin, and galE mutants of #3 were similar to the parental phenotype in their adherence to host cells. These studies have confirmed our previous observations that meningococcal pili are glycosylated and provided the first structural evidence for the presence of covalently linked carbohydrate on pili. In addition, they have revealed a completely novel protein/saccharide linkage.