Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Real-Time and Conventional PCR Targeting Complex 85 Genes for Detection of Mycobacterium leprae DNA in Skin Biopsy Samples from Patients Diagnosed with Leprosy

ABSTRACT In spite of the decrease in the number of registered leprosy patients, the number of new cases diagnosed each year (400,000) has remained essentially unchanged. Leprosy diagnosis is difficult due to the low sensitivity of current methodologies to identify new cases. In this study, conventional and TaqMan real-time PCR assays for detection of Mycobacterium leprae DNA were compared to current classification based on clinical, bacteriological, and histological evaluation. M. leprae DNA was extracted from frozen skin biopsy specimens from 69 leprosy patients enrolled in the study and was amplified using specific primers for either the antigen 85B-coding gene or the 85A-C intergenic region by using conventional and real-time PCR. The detection rate was 100% among multibacillary (MB) patients and ranged from 62.5% to 79.2% among paucibacillary (PB) patients according to the assay used. The TaqMan system for 85B gene amplification showed the highest sensitivity, although conventional PCR using the 85A-C gene as a target was also efficient. The cycle threshold (CT) values obtained using the TaqMan system were able to statistically (P < 0.0001) differentiate MB (mean CT, 28.06; standard deviation [SD], 4.51) from PB (mean CT, 33.06; SD, 2.24) patients. Also, there was a correlation between CT values and the bacteriological index for MB patients (Pearson's r, −0.444; P = 0.008). Within the PB patients' group, we tested normal skin from six patients exhibiting the pure neuritic form of leprosy (PNL). Five out of six PNL patients were positive for the presence of M. leprae DNA, even in the absence of skin lesions. In conclusion, the TaqMan real-time PCR developed here seems to be a useful tool for rapidly detecting and quantifying M. leprae DNA in clinical specimens in which bacilli were undetectable by conventional histological staining.
Inflammatory breast cancer of triple-negative subtype during lactation : a case report and review of the literature

Here we describe a breast cancer case from a 36-year-old female 4 months after delivery. During lactation, she had a painful large lump in the left breast, accompanied by erythema and edema of the 1/3 skin of the breast. Surgical biopsy confirmed that it was a case of invasive breast cancer without special type, grade 3, triple-negative/ basal-like subtype (ER-, PR-, HER2-, CK5&6+, EGFR+) and no dermal lymphatic involvement was observed. Although inflammatory breast cancer was diagnosed, the clinical evidence of metastasis was not found. After neoadjuvant chemotherapy, the patient underwent mastectomy with dissection of the axillary lymph nodes. The tumor did not invade her chest wall and skin. The tumor showed mild response to chemotherapy. No metastasis was identified in the axillary lymph nodes. The patient developed lung metastasis 8 months after mastectomy.
Serum leptin levels and body composition in postmenopausal women treated with tibolone and raloxifene

Objective: To compare body composition and serum leptin levels in untreated postmenopausal women and postmenopausal women treated with tibolone or raloxifene. Design: This was a prospective, randomized, controlled study. Sixty-eight postmenopausal women were randomized to receive either no treatment (group A, n = 21) or tibolone 2.5 mg/day (group B; n = 23) or raloxifene 60 mg/day (group C; n = 24). All women underwent height, weight, body mass index evaluation and dual energy x-ray absorptiometry determination of body composition at the beginning of the study and after 12 months. Serum leptin levels were determined at the beginning of the study and after 1, 3, 6, and 12 months in all groups. Results: Women in group A showed no significant changes in both fat and lean mass of arms and legs, whereas a significant increase in trunk fat mass, total fat mass, total percentage of body fat, and trunk percentage of fat was detected 1 year after the beginning of the study. After 12 months, the total percentage of fat mass was significantly higher in group A compared with group B, and the trunk percentage of fat mass was significantly higher in group A compared with groups. In subjects in groups B and C, after 1 year, fat mass, both total and at all areas evaluated, did not show any significant change compared with baseline values. In subjects in group B, total lean and lean mass of the trunk and legs increased significantly at the end of the study, whereas no significant changes were observed in lean mass, total and at all areas evaluated in subjects in group C. After 12 months, total lean mass and lean mass of the legs were significantly higher in group B compared with the other groups. In group A, serum leptin levels were significantly increased at the end of the study compared with baseline values. Leptin concentrations were significantly higher in group A compared with groups B and C after 6 and 12 months. No significant change in serum leptin levels in subjects in groups B and C was detected throughout the study. Serum leptin levels showed a positive, significant correlation with all body composition parameters and body mass index in all groups at the beginning and at the end of the study. Conclusions: The present study confirms that postmenopausal hypoestrogenism leads to increased fat content and serum leptin levels. Raloxifene and tibolone seem to prevent postmenopausal body composition changes without significant modifications of serum leptin levels.
Fast mixing for independent sets, colorings, and other models on trees

We study the mixing time of the Glauber dynamics for general spin systems on the regular tree, including the Ising model, the hard‐core model (independent sets), and the antiferromagnetic Potts model at zero temperature (colorings). We generalize a framework, developed in our recent paper (Martinelli, Sinclair, and Weitz, Tech. Report UCB//CSD‐03‐1256, Dept. of EECS, UC Berkeley, July 2003) in the context of the Ising model, for establishing mixing time O(nlog n), which ties this property closely to phase transitions in the underlying model. We use this framework to obtain rapid mixing results for several models over a significantly wider range of parameter values than previously known, including situations in which the mixing time is strongly dependent on the boundary condition. We also discuss applications of our framework to reconstruction problems on trees. © 2006 Wiley Periodicals, Inc. Random Struct. Alg. , 2007
Emotional maltreatment and depression: prospective prediction of depressive episodes

Background: Most research to date on the role of maltreatment experiences in depression has focused on physical and sexual maltreatment. However, several researchers have theorized that emotional maltreatment may be more strongly linked to depression. Furthermore, prospective studies in this area are lacking. This study addressed these issues by examining whether experiences of current emotional maltreatment predicted the development of new prospective episodes of major (MD) or minor depression (MiD), and the subtype of hopelessness depression (HD) in young adults. It also assessed whether current emotional maltreatment from peers and from authority figures separately predicted the occurrence of depressive episodes. Method: One hundred and sixty‐five participants from the Cognitive Vulnerability to Depression Project were followed prospectively for 2.5 years. Current emotional maltreatment and new depressive episodes were assessed with life event and diagnostic interviews administered every 6 weeks. Results: Greater overall emotional maltreatment predicted shorter time to onset of new MD, MiD, and HD episodes. Peer‐ and authority‐perpetrated emotional maltreatment separately predicted shorter time to development of new HD episodes. Conclusions: Greater emotional maltreatment in young adults prospectively predicts onset of depression, particularly HD. These findings highlight the importance of adult emotional maltreatment experiences in determining targets for prevention and treatment. Depression and Anxiety, 2009. © 2009 Wiley‐Liss, Inc.
Hard Equality Constrained Integer Knapsacks

We consider the following integer feasibility problem: Given positive integer numbersa0,a1, . , a n , with gcd( a1,., a n ) = 1 anda = ( a1,., a n ), does there exist a vectorx? Z n =0satisfyinga x= a0? We prove that if the coefficientsa1,. , a nhave a certain decomposable structure, then the Frobenius number associated witha1,. , a n , i.e., the largest value ofa0 for whicha x= a0 does not have a nonnegative integer solution, is close to a known upper bound. In the instances we consider, we takea0 to be the Frobenius number. Furthermore, we show that the decomposable structure ofa1,. , a nmakes the solution of a lattice reformulation of our problem almost trivial, since the number of lattice hyperplanes that intersect the polytope resulting from the reformulation in the direction of the last coordinate is going to be very small. For branch-and-bound such instances are difficult to solve, since they are infeasible and have large values ofa0/ a i , 1= i= n. We illustrate our results by some computational examples.
Qualitative and Quantitative Comparison of the Proteome of Erythroid Cells Differentiated from Human iPSCs and Adult Erythroid Cells by Multiplex TMT Labelling and NanoLC-MS/MS

Induced pluripotent stem cells (iPSC) are an attractive progenitor source for the generation of in vitro blood products. However, before iPSC-derived erythroid cells can be considered for therapeutic use their similarity to adult erythroid cells must be confirmed. We have analysed the proteome of erythroid cells differentiated from the iPSC fibroblast derived line (C19) and showed they express hallmark RBC proteins, including all those of the ankyrin and 4.1R complex. We next compared the proteome of erythroid cells differentiated from three iPSC lines (C19, OCE1, OPM2) with that of adult and cord blood progenitors. Of the 1989 proteins quantified <3% differed in level by 2-fold or more between the different iPSC-derived erythroid cells. When compared to adult cells, 11% of proteins differed in level by 2-fold or more, falling to 1.9% if a 5-fold threshold was imposed to accommodate slight inter-cell line erythropoietic developmental variation. Notably, the level of >30 hallmark erythroid proteins was consistent between the iPSC lines and adult cells. In addition, a sub-population (10–15%) of iPSC erythroid cells in each of the iPSC lines completed enucleation. Aberrant expression of some cytoskeleton proteins may contribute to the failure of the majority of the cells to enucleate since we detected some alterations in cytoskeletal protein abundance. In conclusion, the proteome of erythroid cells differentiated from iPSC lines is very similar to that of normal adult erythroid cells, but further work to improve the induction of erythroid cells in existing iPSC lines or to generate novel erythroid cell lines is required before iPSC-derived red cells can be considered suitable for transfusion therapy.
The new gatekeepers: The occupational ideology of game journalism

This paper will contextualize the occupational ideology of game journalism by providing a brief introduction to the political economy of game publications. The role of various industry actors (e.g. game publishers, PR agents and brand managers) will be positioned against those of the peripheral industry (e.g. critics, journalists, and editors). Because the game industry is the principal advertiser for many game publications, and because of its tight grip on the most valuable source material, i.e. (early) access to games and restricted insider information, the job of a game journalist consists in many ways of balancing acts between a perceived loyalty to the reading public and a dependency on industry material. Author Keywords Game journalism, game capital, political economy, game industry
Integration of high-resolution spatial and spectral data acquisition systems to provide complementary datasets for cultural heritage applications

Modern optical measuring systems are able to record objects with high spatial and spectral precision. The acquisition of spatial data is possible with resolutions of a few hundredths of a millimeter using active projection-based camera systems, while spectral data can be obtained using filter-based multispectral camera systems that can capture surface spectral reflectance with high spatial resolution. We present a methodology for combining data from these two discrete optical measuring systems by registering their individual measurements into a common geometrical frame. Furthermore, the potential for its application as a tool for the non-invasive monitoring of paintings and polychromy is evaluated. The integration of time-referenced spatial and spectral datasets is beneficial to record and monitor cultural heritage. This enables the type and extent of surface and colorimetric change to be precisely characterized and quantified over time. Together, these could facilitate the study of deterioration mechanisms or the efficacy of conservation treatments by measuring the rate, type, and amount of change over time. An interdisciplinary team of imaging scientists and art scholars was assembled to undertake a trial program of repeated data acquisitions of several valuable historic surfaces of cultural heritage objects. The preliminary results are presented and discussed.
Multiplayer Reach-Avoid Games via Pairwise Outcomes

A multiplayer reach-avoid game is a differential game between an attacking team with <inline-formula> <tex-math notation="LaTeX">$N_{A}$</tex-math></inline-formula> attackers and a defending team with <inline-formula> <tex-math notation="LaTeX">$N_{D}$</tex-math></inline-formula> defenders playing on a compact domain with obstacles. The attacking team aims to send <inline-formula> <tex-math notation="LaTeX">$M$</tex-math></inline-formula> of the <inline-formula> <tex-math notation="LaTeX">$N_{A}$</tex-math></inline-formula> attackers to some target location, while the defending team aims to prevent that by capturing attackers or indefinitely delaying attackers from reaching the target. Although the analysis of this game plays an important role in many applications, the optimal solution to this game is computationally intractable when <inline-formula> <tex-math notation="LaTeX">$N_{A} > 1$</tex-math></inline-formula> or <inline-formula> <tex-math notation="LaTeX">$N_{D} > 1$</tex-math></inline-formula>. In this technical note, we present two approaches for the <inline-formula> <tex-math notation="LaTeX">$N_{A}=N_{D}=1$</tex-math></inline-formula> case to determine pairwise outcomes, and a graph theoretic maximum matching approach to merge these pairwise outcomes for an <inline-formula> <tex-math notation="LaTeX">$N_{A},N_{D} > 1$</tex-math></inline-formula> solution that provides guarantees on the performance of the defending team. We will show that the four-dimensional Hamilton–Jacobi–Isaacs approach allows for real-time updates to the maximum matching, and that the two-dimensional “path defense” approach is considerably more scalable with the number of players while maintaining defender performance guarantees.
Kaposi's Sarcoma-Associated Herpesvirus K7 Induces Viral G Protein-Coupled Receptor Degradation and Reduces Its Tumorigenicity

The Kaposi's sarcoma-associated herpesvirus (KSHV) genome encodes a G protein-coupled receptor (vGPCR). vGPCR is a ligand-independent, constitutively active signaling molecule that promotes cell growth and proliferation; however, it is not clear how vGPCR is negatively regulated. We report here that the KSHV K7 small membrane protein interacts with vGPCR and induces its degradation, thereby dampening vGPCR signaling. K7 interaction with vGPCR is readily detected in transiently transfected human cells. Mutational analyses reveal that the K7 transmembrane domain is necessary and sufficient for this interaction. Biochemical and confocal microscopy studies indicate that K7 retains vGPCR in the endoplasmic reticulum (ER) and induces vGPCR proteasomeal degradation. Indeed, the knockdown of K7 by shRNA-mediated silencing increases vGPCR protein expression in BCBL-1 cells that are induced for KSHV lytic replication. Interestingly, K7 expression significantly reduces vGPCR tumorigenicity in nude mice. These findings define a viral factor that negatively regulates vGPCR protein expression and reveal a post-translational event that modulates GPCR-dependent transformation and tumorigenicity.
Temporal variations in the Earth's gravity field with emphasis on atmospheric effects

The determination of the Earth’s gravity eld is the main goal of the dedicated gravity eld missions CHAMP, GRACE and GOCE. The gravity eld comprises always a static part and a much smaller timevariable one in the order of millimeters to centimeters, if expressed in geoid heights. As the measurements always consist of both parts, one has to separate them to get a highly accurate static eld with high resolution. In this paper, we give a short description of the mathematical model of the time variations in the Earth’s gravity eld. We briey discuss the spatial and spectral behaviour of the main processes causing the variations. In detail, the atmospheric impact on the gravity eld variations is investigated, and its effect on the satellite missions resp. their measurements is shown. Finally the basic relationship between gravity eld coecien ts and Earth rotation parameters is given.
Strategic Cognitive Sequencing: A Computational Cognitive Neuroscience Approach

We address strategic cognitive sequencing, the “outer loop” of human cognition: how the brain decides what cognitive process to apply at a given moment to solve complex, multistep cognitive tasks. We argue that this topic has been neglected relative to its importance for systematic reasons but that recent work on how individual brain systems accomplish their computations has set the stage for productively addressing how brain regions coordinate over time to accomplish our most impressive thinking. We present four preliminary neural network models. The first addresses how the prefrontal cortex (PFC) and basal ganglia (BG) cooperate to perform trial-and-error learning of short sequences; the next, how several areas of PFC learn to make predictions of likely reward, and how this contributes to the BG making decisions at the level of strategies. The third models address how PFC, BG, parietal cortex, and hippocampus can work together to memorize sequences of cognitive actions from instruction (or “self-instruction”). The last shows how a constraint satisfaction process can find useful plans. The PFC maintains current and goal states and associates from both of these to find a “bridging” state, an abstract plan. We discuss how these processes could work together to produce strategic cognitive sequencing and discuss future directions in this area.
Effect of Different Luting Cements on Fracture Resistance in Endodontically Treated Teeth

INTRODUCTION: The aim of the present study was to evaluate the effect of three types of luting cements used for post cementation on the fracture resistance of endodontically treated maxillary premolars, restored with resin composite. MATERIALS AND METHODS: One hundred intact single-rooted human maxillary premolars were randomly divided into 5 groups of 20 each. In groups 2-5, post spaces were prepared after root canal treatment and clinical crown reduction up to 1.5 mm above the CEJ. Teeth were divided in groups as follows: Group 1: intact teeth, Group 2: active prefabricated metallic posts (PMP), Group 3: PMP cemented with zinc phosphate luting cement, Group 4: PMP cemented with glass ionomer luting cement and Group 5: PMP cemented with resin luting cement. In groups 2-5 the teeth were restored with resin composite. Following thermocycling, the palatal cusp of each specimen was loaded to compression at an angle of 150˚ to its longitudinal axis at a strain rate of 2 mm/min until fracture occurred. Data were analyzed using one-way ANOVA and a post hoc Tukey test. Chi-square test was used for comparison of failure mode. RESULTS: There were significant differences in fracture resistance between the test groups (P<0.001). The differences between group 2 with groups 1, 4 and 5 were statistically significant (P<0.05); whereas there were no significant differences in fracture resistance between the two other groups (P>0.05). Furthermore, there were no significant differences in the mode of failure between the 5 groups (P>0.05). CONCLUSION: Zinc phosphate, glass ionomer and resin luting cements showed similar behaviors and achieved fracture resistance comparable to intact teeth. However, the use of active post (without cement) adversely affected the fracture resistance of root canal treated teeth.
Hierarchical Translation Equivalence over Word Alignments

We present a theory of word alignments in machine translation (MT) that equips every word alignment with a hierarchical representation with exact semantics defined over the translation equivalence relations known as hierarchical phrase pairs. The hierarchical representation consists of a set of synchronous trees (called Hierarchical Alignment Trees – HATs), each specifying a bilingual compositional build up for a given word aligned, translation equivalent sentence pair. Every HAT consists of a single tree with nodes decorated with local transducers that conservatively generalize the asymmetric bilingual trees of Inversion Transduction Grammar (ITG). The HAT representation is proven semantically equivalent to the word alignment it represents, and minimal (among the semantically equivalent alternatives) because it densely represents the subsumption order between pairs of (hierarchical) phrase pairs. We present an algorithm that interprets every word alignment as a semantically equivalent set of HATs, and contribute an empirical study concerning the exact coverage of subclasses of HATs that are semantically equivalent to subclasses of manual and automatic word alignments.
Single-cell Characterization of Autotransporter-mediated Escherichia coli Surface Display of Disulfide Bond-containing Proteins*

Background: The ability of autotransporter (AT) to translocate polypeptides with multiple disulfide bonds is controversial. Results: Surface display of functional chymotrypsin (4 S-S) and M18 scFv (2 S-S) was quantitatively characterized. Conclusion: Surface display of functional recombinant protein with multiple disulfide bonds can be achieved using AT system. Significance: Displaying recombinant proteins with disulfide bonds enhances utility of ATs. Autotransporters (ATs) are a family of bacterial proteins containing a C-terminal β-barrel-forming domain that facilitates the translocation of N-terminal passenger domain whose functions range from adhesion to proteolysis. Genetic replacement of the native passenger domain with heterologous proteins is an attractive strategy not only for applications such as biocatalysis, live-cell vaccines, and protein engineering but also for gaining mechanistic insights toward understanding AT translocation. The ability of ATs to efficiently display functional recombinant proteins containing multiple disulfides has remained largely controversial. By employing high-throughput single-cell flow cytometry, we have systematically investigated the ability of the Escherichia coli AT Antigen 43 (Ag43) to display two different recombinant reporter proteins, a single-chain antibody (M18 scFv) that contains two disulfides and chymotrypsin that contains four disulfides, by varying the signal peptide and deleting the different domains of the native protein. Our results indicate that only the C-terminal β-barrel and the threaded α-helix are essential for efficient surface display of functional recombinant proteins containing multiple disulfides. These results imply that there are no inherent constraints for functional translocation and display of disulfide bond-containing proteins mediated by the AT system and should open new avenues for protein display and engineering.