Miracle-dz/UniFAR-FTUs huggingface dataset:
Determinants of the trans-Dominant Negative Effect of Truncated Forms of the CCR5 Chemokine Receptor*

The human immunodeficiency virus, type 1 (HIV-1) entry process is triggered by interaction between the viral envelope and a seven membrane-spanning domain receptor at the cell surface, usually the CCR5 chemokine receptor. Different naturally occurring mutations in the CCR5 gene abolish receptor function, the most frequent being a 32-nucleotide deletion resulting in a truncated protein (Δ32) lacking the last three transmembrane domains (TM5–7). This mutant is retained in the endoplasmic reticulum and exerts atrans-dominant negative (TDN) effect on the wild type, preventing its exit from this compartment. This TDN effect is often considered as evidence for the oligomerization of CCR5 during transport to the cell surface. Here we use a genetic approach to define the structural determinants of the TDN effect of the Δ32 mutant. It was abolished by certain deletions and by mutations of cysteine residues preventing formation of a disulfide link between the first and second extracellular loops, suggesting that conformation of Δ32 is important for its interaction with CCR5. To circumvent this problem, we used chimeric forms of the Δ32 and wild type CCR5, consisting in substitutions with homologous domains from the mouse CCR5. All chimeric full-length receptors were expressed at the cell surface and were functional for interaction with HIV-1 or with a chemokine ligand, when assayed. The TDN effect was only observed if both the TM3 domain in CCR5 and the TM4 domain in Δ32 were from human origin, whereas the rest of the proteins could be from either origin. This suggests that the TDN effect involves some form of interaction between these transmembrane domains. Alternatively, but less likely to us, substitutions in TM4 could affect the conformation of CCR5 in the endoplasmic reticulum but not at the cell surface. However that may be, it seems that the TDN effect of the Δ32 mutant has no bearing to the issue of CCR5 dimerization and to its possible role in the processing of the receptor to the cell surface.
HLA Monomers as a Tool to Monitor Indirect Allorecognition

Background Recognition of donor antigens can occur through two separate pathways: the direct pathway (non-self HLA on donor cells) and the indirect pathway (self-restricted presentation of donor derived peptides on recipient cells). Indirect allorecognition is important in the development of humoral rejection; therefore, there is an increasing interest in the monitoring of indirect alloreactive T-cells. We have used an in vitro model to determine the optimal requirements for indirect presentation and assessed the risk for semidirect presentation in this system. Methods HLA-typed monocyte-derived dendritic cells (moDCs) were incubated with cellular fragments or necrotic cells and incubated with either indirect or direct alloreactive T-cell clones. T-cell reactivity was measured through proliferation or cytokine secretion. HLA-typed moDC, monocytes, or PBMCs were incubated with HLA class I monomers, in combination with either direct/indirect T-cell clones. Results Although both were efficiently taken up, alloreactivity was limited to the semi-direct pathway, as measured by allospecific CD4 (indirect) and CD8 T-cell clones (direct) when cells were used. In contrast, HLA-A2 monomers were not only efficiently taken up but also processed and presented by HLA-typed moDC, monocytes, and PBMCs. Activation was shown by a dose-dependent induction of IFN-&ggr; production and proliferation by the CD4 T-cell clone. Antigen presentation was most efficient when the monomers were cultured for longer periods (24–48 hr) in the presence of the T-cells. Using this method, no reactivity was observed by the CD8 T-cell clone, confirming no semidirect alloreactivity. Conclusion We have developed a system that could be used to monitor indirect alloreactive T-cells.
An improved low-frequency transformer model for use in GIC studies

A hysteresis model based on the Jiles-Atherton theory is incorporated into a power transformer model in an electromagnetic transient program (EMTP)-type program. The eddy current effects are also included in the same model. Comparisons are made between recorded and simulated waveforms using a single-phase distribution transformer. A good agreement is achieved between recorded and simulated data.
Massive Perturber-driven Interactions between Stars and a Massive Black Hole

We study the role of massive perturbers (MPs) in deflecting stars and binaries to almost radial ("loss cone") orbits, where they pass near the central massive black hole (MBH), interact with it at periapse, and are ultimately destroyed. MPs dominate dynamical relaxation when the ratio of the second moments of the MP and star mass distributions, μ2 ≡ Np⟨M⟩/N⋆⟨M⟩, satisfies μ2 ≫ 1. We compile the MP mass function from published observations and show that MPs in the nucleus of the Galaxy (mainly giant molecular clouds), and plausibly in late-type galaxies generally, have 102 ≲ μ2 ≲ 108. MPs thus shorten the relaxation timescale by 101-107 relative to two-body relaxation by stars alone. We show that this increases by 101-103 the rate of large-periapse interactions with the MBH, where loss cone refilling by stellar two-body relaxation is inefficient. We extend the Fokker-Planck loss cone formalism to approximately account for relaxation by rare encounters with MPs. We show that binary star-MBH exchanges driven by MPs can explain the origin of the young main-sequence B stars that are observed very near the Galactic MBH and can increase by orders of magnitude the ejection rate of hypervelocity stars. In contrast, the rate of small-periapse interactions of single stars with the MBH, such as tidal disruption, is only increased by a factor of a few. We suggest that MP-driven relaxation plays an important role in the three-body exchange capture of stars on very tight orbits around the MBH. These captured stars may later be disrupted by the MBH via tidal orbital decay or direct scattering into the loss cone; captured compact objects may inspiral into the MBH by the emission of gravitational waves from zero-eccentricity orbits.
Composite Statistical Inference for Semantic Segmentation

In this paper we present an inference procedure for the semantic segmentation of images. Different from many CRF approaches that rely on dependencies modeled with unary and pairwise pixel or super pixel potentials, our method is entirely based on estimates of the overlap between each of a set of mid-level object segmentation proposals and the objects present in the image. We define continuous latent variables on super pixels obtained by multiple intersections of segments, then output the optimal segments from the inferred super pixel statistics. The algorithm is capable of recombine and refine initial mid-level proposals, as well as handle multiple interacting objects, even from the same class, all in a consistent joint inference framework by maximizing the composite likelihood of the underlying statistical model using an EM algorithm. In the PASCAL VOC segmentation challenge, the proposed approach obtains high accuracy and successfully handles images of complex object interactions.
Precise measurement of theW-boson mass with the Collider Detector at Fermilab

We present a measurement of the W -boson mass, M W , using data corresponding to 2.2 fb − 1 of integrated luminosity collected in p ¯ p collisions at √ s = 1.96 TeV with the CDF II detector at the Fermilab Tevatron. The selected sample of 470 126 W → e ν candidates and 624 708 W → μ ν candidates yields the measurement M W = 80 387 ± 12 ( stat ) ± 15 ( syst ) = 80 387 ± 19 MeV / c 2 . This is the most precise single measurement of the W -boson mass to date.
Not Without My Smartphone! Impacts of Smartphone Addiction on Smartphone Usage

The widespread diffusion of smartphones and their growing importance for private and business use have created new challenges for IS research. This study explores the potential negative effects of smartphone addiction on beliefs and implications for technology use. Using a quantitative survey linking smartphone addiction with technology acceptance, we investigate whether beliefs distorted by addiction, termed maladaptive cognitions, influence usage behavior and thereby potentially lead to smartphone over-use. We thereby assume that addicted users follow their own versions of rationality by acting on distorted beliefs. Based on our PLS-SEM results of 296 responses, we claim that beliefs are positively inflated by smartphone addiction in relation to perceived security, usefulness, and enjoyment, and that these beliefs ultimately bias a person’s smartphone usage behavior. Moreover, we discuss the relatively most important role of perceived enjoyment and conclude with implications.
A Hidden Markov Model of Customer Relationship Dynamics

This research models the dynamics of customer relationships using typical transaction data. Our proposed model permits not only capturing the dynamics of customer relationships, but also incorporating the effect of the sequence of customer-firm encounters on the dynamics of customer relationships and the subsequent buying behavior. Our approach to modeling relationship dynamics is structurally different from existing approaches. Specifically, we construct and estimate a nonhomogeneous hidden Markov model to model the transitions among latent relationship states and effects on buying behavior. In the proposed model, the transitions between the states are a function of time-varying covariates such as customer-firm encounters that could have an enduring impact by shifting the customer to a different (unobservable) relationship state. The proposed model enables marketers to dynamically segment their customer base and to examine methods by which the firm can alter long-term buying behavior. We use a hierarchical Bayes approach to capture the unobserved heterogeneity across customers. We calibrate the model in the context of alumni relations using a longitudinal gift-giving data set. Using the proposed model, we probabilistically classify the alumni base into three relationship states and estimate the effect of alumni-university interactions, such as reunions, on the movement of alumni between these states. Additionally, we demonstrate improved prediction ability on a hold-out sample.
[Expression of fatty acid synthase and its association with HER2 in invasive ductal carcinoma of breast].

OBJECTIVE To investigate the expression of fatty acid synthase (FAS) in adenosis, atypical ductal epithelial hyperplasia, ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) of breast, and the correlation of FAS expression with HER2 gene amplification in IDC. METHODS Immunohistochemical EnVision method staining for FAS was performed in 100 cases of breast lesions and 10 normal breast tissues. HER2 gene amplification was detected with FISH in 60 cases of IDC. RESULTS The cohort included 10 cases of adenosis, 10 atypical ductal epithelial hyperplasia, 20 DCIS (8 high-grade, 9 intermediated-grade and 3 low-grade), and 60 cases of IDC (5 grade 1, 40 grade 2 and 15 grade 3). FAS expression was negative in all 10 normal breast tissues; in the 10 cases of adenosis, strongly positive FAS expression was detected in one case, positive in 2, weakly positive in 4, and negative in 3; in the 10 cases of atypical ductal epithelial hyperplasia, FAS immunohistochemistry showed that 1 was strongly positive, 4 positive, 4 weakly positive, and 1 negative; in the 20 cases of DCIS, FAS immunostaining showed that 12 were strongly positive, 5 positive, 1 weakly positive, and 2 negative; FAS expression showed a clear increasing trend from normal breast tissue, atypical ductal epithelial hyperplasia to DCIS (χ(2) = 42.02, P < 0.01). Likewise, the increasing trend was also demonstrated from adenosis to DCIS (χ(2) = 34.69, P < 0.01). There was also a positive correlation between FAS expression and extent of lesion among normal breast tissue, adenosis, atypical ductal epithelial hyperplasia and DCIS (χ(2) = 86.02, P < 0.01; r = 0.568, P < 0.01). FAS expression was not correlated with the grade of DCIS (χ(2) = 9.12, P = 0.16). In the five cases of grade 1 IDC, FAS immunostaining showed that 4 cases were strongly positive and 1 positive; in the 40 cases of grade 2 IDC, FAS immunostaining showed that 27 strongly positive, 12 positive, and 1 negative; in the 15 cases of grade 3 IDC, FAS immunostaining showed that 6 were strongly positive, 5 positive, 3 weakly positive, and 1 negative; FAS expression was stronger and more extensive in DCIS, IDC grades 1 and 2 than that in other groups. However, FAS expression was weaker in the IDC grade 3 (χ(2) = 11.26, P = 0.01). The positive expression rate of FAS in IDC was generally higher than that in benign breast lesions (χ(2) = 47.19, P < 0.01). In the 60 cases of IDC, FISH showed HER2 gene amplification in 22 cases, but not in the remaining 38 cases. FAS expression in IDC was highly correlated with HER2 gene amplification (r = 0.44, P < 0.01). The expression of FAS had significant correlation with status of ER and PR and tumor size (P < 0.05). There was no significant correlation with age, immunohistochemical HER2 expression, lymph node metastasis and clinical stage (P > 0.05). CONCLUSIONS FAS may be closely related to the carcinogenesis of breast IDC. FAS expression is closely associated with HER2 gene amplification in IDC.
An Infinite Latent Attribute Model for Network Data

Latent variable models for network data extract a summary of the relational structure underlying an observed network. The simplest possible models subdivide nodes of the network into clusters; the probability of a link between any two nodes then depends only on their cluster assignment. Currently available models can be classified by whether clusters are disjoint or are allowed to overlap. These models can explain a "flat" clustering structure. Hierarchical Bayesian models provide a natural approach to capture more complex dependencies. We propose a model in which objects are characterised by a latent feature vector. Each feature is itself partitioned into disjoint groups (subclusters), corresponding to a second layer of hierarchy. In experimental comparisons, the model achieves significantly improved predictive performance on social and biological link prediction tasks. The results indicate that models with a single layer hierarchy over-simplify real networks.
Evaluation of a Recombinant Antigen-Based Enzyme Immunoassay for the Diagnosis of Noninvasive Aspergillosis

ABSTRACT Antibody detection is a key diagnostic tool for noninvasive aspergillosis (NIA) such as allergic bronchopulmonary aspergillosis and chronic pulmonary aspergillosis. Specific immunoprecipitin detection (IPD) is considered as the reference but lacks standardization and is time-consuming. To evaluate the performance of a new anti-Aspergillus fumigatus IgG enzyme immunoassay (EIA) kit using a recombinant A. fumigatus antigen (Bio-Rad), a retrospective study was performed on 551 sera collected from patients with a definite diagnosis of NIA (group 1; n = 64), bronchial Aspergillus colonization (group 2; n = 26), and probable aerial Aspergillus contamination (group 3; n = 44); from patients suspected of NIA with negative serological and mycological investigations (group 4; n = 49); and from a group of 222 patients not suspected of NIA (group 5). The EIA exhibited excellent reproducibility with coefficients of variation below 10%. Agreement with IPD was calculated between 62.5 and 84.4% according to the group of patients with Cohen's kappa coefficient at 0.6196 ± 0.077. Taking as reference a composite status including clinical, radiological, mycological, and serological data, sensitivity (group 1) and specificity (other groups) were calculated between 90.2 and 93.8% and 54.3 and 100%, respectively. Lower specificity was observed for patients with Aspergillus colonization. However, Yule Q coefficients estimating the correlation between EIA result and the definite diagnosis of NIA were calculated between 0.97 and 0.98. The method is a highly useful screening tool for the diagnosis of NIA, reducing the need for confirmatory IPD tests.
Perfusion Index Derived from a Pulse Oximeter Can Detect Changes in Peripheral Microcirculation during Uretero-Renal-Scopy Stone Manipulation (URS-SM)

Background The objective of this study was to test the effect of removal of a ureteral obstruction (renal calculus) from anesthetized patients on the perfusion index (PI), as measured by a pulse oximeter, and on the estimated glomerular filtration rate (eGFR). Patients and Methods This prospective study enrolled 113 patients with unilateral ureteral obstructions (kidney stones) who were scheduled for ureteroscopy (URS) laser lithotripsy. One urologist graded patient hydronephrosis before surgery. A pulse oximeter was affixed to each patient's index finger ipsilateral to the intravenous catheter, and a non-invasive blood pressure cuff was placed on the contralateral side. Ipsilateral double J stents and Foley catheters were inserted and left indwelling for 24 h. PI and mean arterial pressure (MAP) were determined at baseline, 5 min after anesthesia, and 10 min after surgery; eGFR was determined at admission, 1 day after surgery, and 14 days after surgery. Results Patients with different grades of hydronephrosis had similar age, eGFR, PI, mean arterial pressure (MAP), and heart rate (HR). PI increased significantly in each hydronephrosis group after ureteral stone disintegration. None of the groups had significant post-URS changes in eGFR, although eGFR increased in the grade I hydronephrosis group after 14 days. The percent change of PI correlates significantly with the percent change of MAP, but not with that of eGFR. Conclusion Our results demonstrate that release of a ureteral obstruction leads to a concurrent increase of PI during anesthesia. Measurement of PI may be a valuable tool to monitor the successful release of ureteral obstructions and changes of microcirculation during surgery. There were also increases in eGFR after 14 days, but not immediately after surgery.
Detecting Disjoint Inconsistent Subformulas for Computing Lower Bounds for Max-SAT

Many lower bound computation methods for branch and bound Max-SAT solvers can be explained as procedures that search for disjoint inconsistent subformulas in the Max-SAT instance under consideration. The difference among them is the technique used to detect inconsistencies. In this paper, we define five new lower bound computation methods: two of them are based on detecting inconsistencies via a unit propagation procedure that propagates unit clauses using an original ordering; the other three add an additional level of forward look-ahead based on detecting failed literals. Finally, we provide empirical evidence that the new lower bounds are of better quality than the existing lower bounds, as well as that a solver with our new lower bounds greatly outperforms some of the best performing state-of-the-art Max-SAT solvers on Max-2SAT, Max-3SAT, and Max-Cut instances.
Regulation of Connexin Hemichannels by Monovalent Cations

Opening of connexin hemichannels in the plasma membrane is highly regulated. Generally, depolarization and reduced extracellular Ca2+ promote hemichannel opening. Here we show that hemichannels formed of Cx50, a principal lens connexin, exhibit a novel form of regulation characterized by extraordinary sensitivity to extracellular monovalent cations. Replacement of extracellular Na+ with K+, while maintaining extracellular Ca2+ constant, resulted in >10-fold potentiation of Cx50 hemichannel currents, which reversed upon returning to Na+. External Cs+, Rb+, NH4 +, but not Li+, choline, or TEA, exhibited a similar effect. The magnitude of potentiation of Cx50 hemichannel currents depended on the concentration of extracellular Ca2+, progressively decreasing as external Ca2+ was reduced. The primary effect of K+ appears to be a reduction in the ability of Ca2+, as well as other divalent cations, to close Cx50 hemichannels. Cx46 hemichannels exhibited a modest increase upon substituting Na+ with K+. Analyses of reciprocal chimeric hemichannels that swap NH2- and COOH-terminal halves of Cx46 and Cx50 demonstrate that the difference in regulation by monovalent ions in these connexins resides in the NH2-terminal half. Connexin hemichannels have been implicated in physiological roles, e.g., release of ATP and NAD+ and in pathological roles, e.g., cell death through loss or entry of ions and signaling molecules. Our results demonstrate a new, robust means of regulating hemichannels through a combination of extracellular monovalent and divalent cations, principally Na+, K+, and Ca2+.
Sleep, recovery, and metaregulation: explaining the benefits of sleep

A commonly held view is that extended wakefulness is causal for a broad spectrum of deleterious effects at molecular, cellular, network, physiological, psychological, and behavioral levels. Consequently, it is often presumed that sleep plays an active role in providing renormalization of the changes incurred during preceding waking. Not surprisingly, unequivocal empirical evidence supporting such a simple bi-directional interaction between waking and sleep is often limited or controversial. One difficulty is that, invariably, a constellation of many intricately interrelated factors, including the time of day, specific activities or behaviors during preceding waking, metabolic status and stress are present at the time of measurement, shaping the overall effect observed. In addition to this, although insufficient or disrupted sleep is thought to prevent efficient recovery of specific physiological variables, it is also often difficult to attribute specific changes to the lack of sleep proper. Furthermore, sleep is a complex phenomenon characterized by a multitude of processes, whose unique and distinct contributions to the purported functions of sleep are difficult to determine, because they are interrelated. Intensive research effort over the last decades has greatly progressed current understanding of the cellular and physiological processes underlying the regulation of vigilance states. Notably, it also highlighted the infinite complexity within both waking and sleep, and revealed a number of fundamental conceptual and technical obstacles that need to be overcome in order to fully understand these processes. A promising approach could be to view sleep not as an entity, which has specific function(s) and is subject to direct regulation, but as a manifestation of the process of metaregulation, which enables efficient moment-to-moment integration between internal and external factors, preceding history and current homeostatic needs.