Miracle-dz/UniFAR-FTUs huggingface dataset:
1 VARIABLE SELECTION AND ESTIMATION WITH THE SEAMLESS-L 0 PENALTY

Penalized least squares procedures that directly penalize the number of variables in a regression model (L0 penalized least squares procedures) enjoy nice theoretical properties and are intuitively appealing. On the other hand, L0 penalized least squares methods also have significant drawbacks in that implementation is NP-hard and computationally unfeasible when the number of variables is even moderately large. One of the challenges is the discontinuity of the L0 penalty. We propose the seamless-L0 (SELO) penalty, a smooth function on [0,∞) that very closely resembles the L0 penalty. The SELO penalized least squares procedure is shown to consistently select the correct model and is asymptotically normal, provided the number of variables grows more slowly than the number of observations. SELO is efficiently implemented using a coordinate descent algorithm. Since tuning parameter selection is crucial to the performance of the SELO procedure, we propose a BIC-like tuning parameter selection method for SELO, and show that it consistently identifies the correct model while allowing the number of variables to diverge. Simulation results show that the SELO procedure with BIC tuning parameter selection performs well in a variety of settings – outperforming other popular penalized least squares procedures by a substantial margin. Using SELO, we analyze a publicly available HIV drug resistance and mutation dataset and obtain interpretable results.
Synchronization in chaotic systems.

Chaotic systems would seem to be dynamical systems that defy synchronization. Two identical autonomous chaotic systems started at nearly the same initial points in phase space have trajectories which quickly become uncorrelated, even though each maps out the same attractor in phase space. It is thus a practical impossibility to construct identical, chaotic, synchronized systems in the laboratory. This chapter describes the linking of two chaotic systems with a common signal or signals. It highlights that when the signs of the Lyapunov exponents for the subsystems are all negative the systems are synchronized. By synchronize it means that the trajectories of one of the systems converge to the same values as the other and they remain in step with each other. The synchronization appears to be structurally stable.
Intuitive or idiomatic: An interdisciplinary study of child‐tablet computer interaction

Using Luhmann's communication framework, we examine the interaction implications for kindergarten to Grade 2 students using mathematics applications on four types of tablet computers. Research questions included what content is communicated between the child and the tablet computer and how engaged are children in the interaction. We found that mathematics applications developers have focused on creating applications for the practice of a priori knowledge, rather than on creating instructional applications. Results show preliminary evidence that child‐tablet communication is generally successful, but this success comes at the cost of richer, multimodal interactions. Tablet computer application developers are being cautious in offering a variety of options for children to interact with the devices, and we suggest that there is scope for a broadening of communicative interaction modes.
Clinical inquiries. How effective are lifestyle changes for controlling hypertension?

Lifestyle modifications plus drug therapy is the best treatment for patients with hypertension Most Americans with hypertension are not at their goal blood pressure, so the value of lifestyle modifications cannot be ignored. While some clinicians argue that these modifications are unreliable, this review should serve to reinforce the substantial impact of lifestyle modifications. Clinicians should remember that drug therapy is the only treatment modality proven to lower blood pressure and cardiovascular morbidity and mortality due to hypertension, based on evidence from outcome-based studies. Reducing cardiovascular morbidity and mortality is the ultimate goal of treating hypertension. Therefore, lifestyle modifications with antihypertensive drug therapy are the best treatments to reduce cardiovascular risk and attain goal blood pressure values for patients with hypertension.
The Anti-HIV-1 Editing Enzyme APOBEC3G Binds HIV-1 RNA and Messenger RNAs That Shuttle between Polysomes and Stress Granules*

Deoxycytidine deaminases APOBEC3G (A3G) and APOBEC3F (A3F) (members of the apolipoprotein B mRNA-editing catalytic polypeptide 3 family) have RNA-binding motifs, invade assembling human immunodeficiency virus (HIV-1), and hypermutate reverse transcripts. Antagonistically, HIV-1 viral infectivity factor degrades these enzymes. A3G is enzymatically inhibited by binding RNA within an unidentified large cytosolic ribonucleoprotein, implying that RNA degradation during reverse transcription may activate intravirion A3G at the necessary moment. We purified a biologically active tandem affinity-tagged A3G from human HEK293T cells. Mass spectrometry and coimmunoprecipitation from HEK293T and T lymphocyte extracts identified many RNA-binding proteins specifically associated with A3G and A3F, including poly(A)-binding proteins (PABPs), YB-1, Ro-La, RNA helicases, ribosomal proteins, and Staufen1. Most strikingly, nearly all A3G-associated proteins were known to bind exclusively or intermittently to translating and/or dormant mRNAs. Accordingly, A3G in HEK293T and T lymphocyte extracts was almost completely in A3G-mRNA-PABP complexes that shifted reversibly between polysomes and dormant pools in response to translational inhibitors. For example arsenite, which inhibits 5′-cap-dependent translational initiation, shifted mRNA-A3G-PABP from polysomes into stress granules in a manner that was blocked and reversed by the elongation inhibitor cycloheximide. Immunofluorescence microscopy showed A3G-mRNA-PABP stress granules only partially overlapping with Staufen1. A3G coimmunoprecipitated HIV-1 RNA and many mRNAs. Ribonuclease released nearly all A3G-associated proteins, including A3G homo-oligomers and A3G-A3F hetero-oligomers, but the viral infectivity factor remained bound. Many proteins and RNAs associated with A3G are excluded from A3G-containing virions, implying that A3G competitively partitions into virions based on affinity for HIV-1 RNA.
Allelic association patterns for a dense SNP map

A dense set of 5,000 SNPs on a 10‐Mb region of human chromosome 20 has been typed on samples of African Americans, East Asians, and United Kingdom Caucasians. There are departures from Hardy‐Weinberg equilibrium beyond the level at which markers are often discarded because of possible genotyping errors. The observation that markers showing such departures are often close together on the chromosome confirms the result that Hardy‐Weinberg tests at two loci are correlated to an extent that depends on the linkage disequilibrium between those two markers. Linkage disequilibrium can be described by the composite linkage disequilibrium coefficient, the parameter that determines the behavior of case‐control allelic tests of association. A useful preliminary investigation of datasets of this type is provided by counting the numbers of distinct multi‐locus genotypes in windows of a few markers. Genet. Epidemiol. © 2004 Wiley‐Liss, Inc.
EXPRESSION OF THE INSULIN-LIKE GROWTH FACTOR RECEPTOR 1 DURING HUMAN EMBRYOGENESIS

Insulin-like growth factor 1 and its receptor (IGF-1/IGF-2) may play important roles in the development of human fetal tissue, and its ligands IGF-1 and IGF-2 have been found in fetuses older than 3 months. Our objective was to study the immunohistochemical distribution of IGF 1-R in tissues obtained from human normal embryos following abortion or natural termination of pregnancy. Immunohistochemical staining was performed on autostainer, using an anti-IGF1-R rabbit polyclonal antibody (dilution 1:75), and the avidin-biotin peroxidase complex method. The embryos ranged between 28 days to 8 weeks gestation. Fully 3 cases were 28 days old, 1 case 32 days old, 2 cases 6 weeks old and 2 cases 8 weeks old. The IGF1-R stain decorated the surface ectoderm, the optic cup, and the lens placode, pharynx, respiratory diverticulum, foregut, liver cords, mesonephros, and metanephric blastema. Mesodermal structures, including limb mesoderm, and neural crest derivatives were IGF-1R negative. On study shows the preferential IGF-1R immunolocalizatrion in specific areas of the developing embryo, suggesting a role of IGF1-R for the optimal maturation of those areas, during developing human embryos.
Use of a synthetic prostaglandin analogue for synchronization of oestrus in heifers.

Abstract Extract Following the initial report of synchronization of oestrus by intra-uterine infusion of prostaglandin F2α (PGF2α; Rowson et al, 1972), a large amount of data has been published on the effects of dose rate and route of administration of PGF2α on the effectiveness of oestrus synchronization. The most convenient method of administration is the intramuscular route; however, owing to the rapidrate of metabolism of PGF2α (Piper et al., 1970) very large doses are needed to achieve consistent effects. The recent development of potent synthetic analogues of prostaglandin has further stimulated research on oestrus control by this method of administration (Tervit et al., 1973; Cooper, 1974; Nancarrow and Hearnshaw, 1974).
Isolation and characterization of a putative liver progenitor population after treatment of fetal rat hepatocytes with TGF‐Beta

The “in vitro” establishment of a physiological model of bipotential liver progenitors would be useful for analyzing the molecular mechanisms involved in regulating growth and differentiation, as well as studying their potential role/s in liver physiology and pathology. The transforming growth factor‐beta (TGF‐β) induces de‐differentiation of fetal rat hepatocytes (FH), concomitant with changes in morphology. The aim of this work was to isolate and characterize this population of TGF‐β‐treated fetal hepatocytes (TβT‐FH) and test whether they can behave as liver progenitors. The TβT‐FH isolated cell lines show high expression of Thy‐1 and low expression of c‐Kit. They express liver‐specific proteins, such as albumin and alpha‐fetoprotein, and mesenchymal markers, such as vimentin. TβT‐FH maintain expression of the hnf3β gene, but lose expression of hnf1β, hnf4, and hnf6. They express c‐met and show an increase in proliferation in response to HGF. Interestingly, the transdifferentiation process is coincident with changes in the expression of genes related to the oxidative metabolism. TβT‐FH cultured in the presence of EGF + DMSO change morphology, towards epithelial cells, gaining expression of CK19 and c‐Kit, markers found in hepatoblasts and bile duct cells. Furthermore, TβT‐FH form duct‐like structures when cultured on Matrigel. TβT‐FH show also potential to revert to an hepatocyte phenotype when submitted to a long‐term “in vitro” differentiation protocol towards hepatocytic lineage. In summary, our results support the hypothesis that hepatocytes can function as facultative liver stem cells and demonstrate that TGF‐β might play an essential role in the transdifferentiation process. J. Cell. Physiol. 215: 846–855, 2008. © 2008 Wiley‐Liss, Inc.
Author ' s personal copy Time-varying market integration and stock and bond return concordance in emerging markets q

We investigate the extent to which emerging stock market integration affects the joint behavior of stock and bond returns using a two-stage semi-parametric approach. Using a sample of 18 emerging markets, we find an unambiguous and robust link between emerging stock market integration and stock–bond return decoupling. We explain this with a decline in the segmentation risk premia in equities modeled by De Jong and De Roon [De Jong, F. , De Roon, F.A. , 2005. Time-varying market integration and expected returns in emerging markets. Journal of Financial Economics 78, 583–613] that leads to increased demand for stocks and reduced or unchanged demand for bonds. Our findings deliver new insights into the financial liberalization and stock–bond comovement literatures. 2008 Elsevier B.V. All rights reserved.
Advances in Brief 3 p 14 and 9 p 21 Loss Is a Simple Tool for Predicting Second Oral Malignancy at Previously Treated Oral Cancer Sites 1

Treatment induces reactive changes that often resemble low-grade dysplasia at former oral cancer sites, complicating histopathological assessment. We tested a set of microsatellite markers shown previously to be predictive of progression for oral premalignant lesions for the ability to predict development of second oral malignancy (SOM). Sixty-eight oral leukoplakia at former cancer sites (with known outcome, 36 progressed to SOM) were evaluated for loss of heterozygosity at 19 loci on seven chromosome arms. 3p and/or 9p loss in these posttreatment leukoplakia was associated with a 26.3-fold increase in risk of developing SOM compared with those that retained both of these arms (P < 0.001), with 60% of cases with loss of heterozygosity developing SOM in 2 years. In contrast, histological diagnosis (moderate or severe dysplasia versus hyperplasia or mild dysplasia) had only a 1.7-fold increase in risk (P 0.11). The identification of 3p and 9p loss in posttreatment lesions could serve as a simple and direct test for stratifying risk of SOM development.
Field experience with a single intravenous injection of marbofloxacin 16% in lactating dairy cows with acute clinical mastitis

SUMMARY In a non-controlled multicentre field trial conducted on commercial farms in France and Germany, local and general tolerance of marbofloxacin (Forcyl ® , Vetoquinol SA) was evaluated after intravenous administration to 100 lactating dairy cows suffering from acute clinical mastitis. Clinical signs, concomitant therapy, disease evolution and bacteriological analysis of milk at inclusion were also monitored. All the 100 included cows presented local and general signs of acute clinical mastitis, involving one or two quarters. They were treated once with marbofloxacin (Forcyl ® ) at the dose rate of 10 mg/kg ( i.e. 10 ml/160kg) by intravenous injection. Most of the included cows (83%) received a concomitant treatment. A clinical examination was performed before and immediately following treatment with the study product and 1, 2-3 and 7 days after this treatment, with some cases up to 14 days later (40%). Milk was sampled for microbiological examination before treatment in 81% of the cases. The time course of the target disease showed a rapid decrease of mean rectal temperature as well as mean score of all the local and general clinical parameters, whether the cows received concomitant therapy (83 cows) or not (17 cows). However, 8 cows were given a new treatment for mastitis during the study. The two main pathogens isolated before treatment were Escherichia coli and Streptococcus uberis. The most frequent side effects observed after injection were moderate and transient local reactions (swelling, slight pain at injection, hematoma). Diarrhoea was observed both before treatment and within the first days following treatment. Tremors, lameness and nervousness were also observed on rare occasions within the first days following injection. Intravenous administration of a high dose of marbofloxacin (Forcyl ® ) was efficacious and safe in cows suffering from acute clinical mastitis, in combination with various concomitant treatments (83% of the included animals) or alone (17%).
Gingival crevicular fluid matrix metalloproteinase (MMP)-7, extracellular MMP inducer, and tissue inhibitor of MMP-1 levels in periodontal disease.

BACKGROUND During periodontal inflammation, matrix metalloproteinases (MMPs) are under the control of several regulatory mechanisms including the upregulation of expression by inducers and downregulation by inhibitors. Our study aimed to examine the levels and molecular forms of MMP-7, tissue inhibitor of MMP (TIMP)-1, and extracellular matrix metalloproteinase inducer (EMMPRIN) in gingival crevicular fluid (GCF) from patients with different periodontal diseases. METHODS A total of 80 subjects (20 patients with generalized aggressive periodontitis [GAgP], 20 with chronic periodontitis [CP], 20 with gingivitis, and 20 periodontally healthy subjects) were included in this study. Periodontal status was evaluated by measuring probing depth, clinical attachment loss, presence of bleeding on probing, and plaque. GCF MMP-7, TIMP-1, and EMMPRIN levels and molecular forms were analyzed by enzyme-linked immunosorbent assay (ELISA) and Western immunoblot techniques using specific antibodies. RESULTS Total amounts of GCF MMP-7 were found to be similar between the study groups. GAgP, CP, and gingivitis groups had significantly higher total amounts of GCF EMMPRIN compared to healthy subjects (P <0.008). Among the patient groups, the GAgP group had the highest total amount of GCF EMMPRIN relative to the gingivitis group (P = 0.0004). Soluble EMMPRIN existed in GCF in multiple molecular-weight species especially in periodontitis-affected GCF under non-reducing conditions, i.e., 30-, 55-, 100-, 180-, and 200-kDa species. All patient groups had significantly elevated total amounts of GCF TIMP-1 relative to the healthy group (P <0.0001). GAgP and CP groups also had a higher total amount of GCF TIMP-1 compared to the gingivitis group (P <0.0001 and P <0.0001, respectively). The GAgP group had higher GCF TIMP-1 and EMMPRIN levels compared to the CP group, but this elevation did not reach statistical significance. CONCLUSIONS Our data indicate that MMP-7 is associated with the innate host defense in periodontal tissues. Increased EMMPRIN and TIMP-1 levels in GCF are associated with the enhanced severity of periodontal inflammation, indicating that these molecules can participate in the regulation of progression of periodontal diseases. To our knowledge, the present study demonstrated the presence of soluble forms of EMMPRIN in GCF of patients with different periodontal diseases for the first time.
Use of sodium Hypochlorite in root canal irrigation. Opinion survey and concentration in commercial products

Objective: To determine hypochlorite concentration of solutions used for root canal irrigation and compare them with concentrations deemed as “ideal” in scientific literature ( 5.25% and 2.5% (w / v)) Methods Opinion survey among endodontic specialists to ascertain sodium hypochlorite commercial brand most used in root canals irrigation. Iodometric titration to determine solution concentrations. Clorox Regular Bleach ( Oakland, California) commercial brand most referred to in literature. Mean comparison of different commercial brands and lots. Concentrations deemed ideal 5.25% and 2.5% (w / v). Results Commercial brands of sodium hypochlorite most used by 192 endodontic specialists were as follows: Cloralex ( 43.2%), Concentrated Clorox (30.2%), Viarzoni-t (16.7%), Great Value ( 1.0%), “Los Patitos” (0.5%) and other brands ( 8.3%). Concentration ( mean IC 95%) of Clorox Regular Bleach (6.34%, 6.32 – 6.36) Concentrated Clorox ( 5.43%, 5.42-5.45%), Cloralex (5.40%, %.38-5.41), Great Value ( 6.21% 6.19-6.23) and “ Los Patitos” ( 5.82%, 5.80-5.83) exceeded a 5.25% sodium hypochlorite concentration. Viarzone-T ( 2.86%, 2.85-2.87) rated above the 2.5% hypochlorite concentration. There were statistically significant differences (p≤0.001) among averages of different commercial brands and lots, with respect to concentrations deemed as ideal (5.25% and 2.5% (w/ v ). Conclusion Hypochlorite concentrations in commonly used commercial products are not the concentration recommended in scientific literature ( 5.25% w/v and 2.5 % w/v). This can cause tissue damage in cases when hypochlorite solutions are improperly used without field isolation
Association of Periodontal Diseases with Genetic Polymorphisms

Periodontal diseases are multifactorial in nature. While microbial and other environmental factors are believed to initiate and modulate periodontal disease progression, there now exist strong supporting data that genetic polymorphis ms play a role in the predisposition to and progression of periodontal diseases. Variat ions in any number or combination of genes that control the development of the periodontal tissues or the competency of the cellular and humoral immune systems could affect an individual's risk fo r d isease. A corollary of this realization is that if the genetic basis of periodontal disease susceptibility can be understood, such information may have diagnostic and therapeutic value. This review aims to update the clin ician about various genetic polymorphis ms associated with periodontal diseases to aid in a better approach to the condition in the future.
Clinical and microbiological benefits of strict supragingival plaque control as part of the active phase of periodontal therapy.

AIM To compare the clinical and microbiological effects of scaling and root planing (SRP) alone or combined with mechanical [professional plaque control (PPC)] or chemical [chlorhexidine rinsing (CHX)] control of supragingival plaque in the treatment of chronic periodontitis. MATERIAL AND METHODS Sixty subjects were randomly assigned to receive SRP alone or combined with PPC (twice a week) or with CHX rinsing (twice a day). The adjunctive treatments began with SRP and were continued for 42 days. Clinical and microbiological examinations were performed at baseline, 2 and 6 months post-therapy. Subgingival plaque samples were analysed for 38 bacterial species by checkerboard DNA-DNA hybridization. RESULTS The two test treatments were more effective in improving probing depth and clinical attachment level (CAL) than SRP alone, even in intermediate and deep sites. CAL gain was better maintained in the CHX group. The most beneficial microbiological changes were observed in CHX-treated subjects, who showed a significant reduction in the proportions of red and orange complexes, as well as an increase in the proportions of the host-compatible bacterial species. CONCLUSION Strict plaque control performed during and after SRP improves periodontal treatment outcomes. The greatest microbiological and clinical benefits were observed with the use of CHX rinsing.
An intronic polymorphism in GRP78 improves chemotherapeutic prediction in non-small cell lung cancer.

BACKGROUND Glucose-regulated protein 78 (GRP78) is involved in not only the progression of non-small cell lung cancer (NSCLC) but also chemotherapeutic effects. We hypothesized that an intronic polymorphism (rs430397G>A) in GRP78 affects survival among patients with NSCLC treated with platinum-based chemotherapy. METHODS Blood samples of patients with advanced NSCLC (IIIB/IV) were maintained in our specimen bank between 2001 and 2006. Genomic DNA was genotyped for rs430397. Associations between rs430397 and platinum-based treatment response, overall survival (OS), NSCLC-related survival, progression-free survival (PFS), and relapses were evaluated. GRP78 RNA and protein in NSCLC tissues were tested by real-time polymerase chain reaction and immunohistochemistry. RESULTS The AA genotype is significantly associated with platinum-based chemoresistance (P = .019) and NSCLC-related death (P = .022). OS, NSCLC-related survival, and PFS of the AA genotype group are decreased compared with the GG and AG genotype groups (log-rank P < .05, respectively). The AA group showed a higher prevalence of early NSCLC relapses than the AG and GG group (P = .030). In addition, the AA genotype showed a significantly increased risk for OS (hazard ratio, 1.95) and PFS (hazard ratio, 1.80) compared with the GG group. Functional analysis showed that NSCLC tissues with genotype AA have higher GRP78 RNA and protein expression compared with those carrying GG at rs430397. CONCLUSIONS The rs430397 AA genotype of GRP78 is associated with reduced survival and higher prevalence of early relapses in patients with advanced NSCLC treated with platinum-based chemotherapy.