Miracle-dz/UniFAR-FTUs huggingface dataset:
Lung Manifestation in Asymptomatic Patients with Primary Sjögren Syndrome: Assessment with High Resolution CT and Pulmonary Function Tests

The authors studied 37 consecutive patients with primary Sjögren syndrome and normal chest radiographs. Thin-section CT images were analyzed using a semiquantitative grading system. The presence, distribution, and severity of 9 morphologic parameters were assessed. In 34 patients, CT findings were correlated to pulmonary function tests (PFTs). Abnormal high resolution CT (HRCT) findings were seen in 24 of 37 patients (65%): interlobular septal thickening, n = 9; micronodules, n = 9; ground glass attenuation n = 4; parenchymal cysts, n = 5. Intralobular opacities, honey combing, bronchial wall thickening, bronchiectasis, and pleural irregularities were less frequent. Both HRCT and PFTs were normal in 10 patients. Computed tomography was normal in four patients with PFTs that indicated the presence of small airway disease. High resolution CT abnormalities were found in seven patients with normal PFT. The overall correlation between HRCT and PFTs was poor. High resolution CT and PFTs appear to be sensitive for both the early detection of parenchymal abnormalities and a decreases in lung function in asymptomatic patients with primary Sjögren syndrome. However, abnormal HRCT findings do not necessarily indicate a substantial alteration in PFTs.
Human T-cell leukemia virus type 1 Tax transactivates the human proliferating cell nuclear antigen promoter

The human T-cell leukemia virus type 1 (HTLV-1) transforming protein, Tax, is a potent transactivator of both viral and cellular gene expression. The ability of Tax to transform cells is believed to depend on its transactivation of cellular-growth-regulatory genes. Expression of proliferating cell nuclear antigen (PCNA) is intimately linked to cell growth and DNA replication and repair. By testing a series of PCNA promoter deletion constructs, we have demonstrated that the PCNA promoter can be transactivated by Tax. The smallest construct that was activated did not include the ATF/CRE binding site at nucleotide -50, and mutations in the ATF/CRE element in the context of a larger promoter were still activated by Tax. In addition, a Tax mutant that is defective for activation of the CRE pathway retained the ability to activate the -397 promoter construct. When a series of linker scanner mutations that span the region from nucleotide -45 to -7 were assayed, mutations in and around a repeat sequence were found to abolish Tax transactivation. Multimerized copies of either half of the repeat were Tax responsive. A single protein complex was shown to bind specifically to the Tax-responsive region, and the binding of this complex was enhanced in the presence of Tax. These results demonstrate that the PCNA promoter contains a Tax-responsive element located between nucleotides -45 and -7 whose sequence is different from those of other, previously identified Tax-responsive elements. The ability of Tax to activate the PCNA promoter may play an important role in cellular transformation by HTLV-1.
Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer.

BACKGROUND Oncogenic fusion genes consisting of EML4 and anaplastic lymphoma kinase (ALK) are present in a subgroup of non-small-cell lung cancers, representing 2 to 7% of such tumors. We explored the therapeutic efficacy of inhibiting ALK in such tumors in an early-phase clinical trial of crizotinib (PF-02341066), an orally available small-molecule inhibitor of the ALK tyrosine kinase. METHODS After screening tumor samples from approximately 1500 patients with non-small-cell lung cancer for the presence of ALK rearrangements, we identified 82 patients with advanced ALK-positive disease who were eligible for the clinical trial. Most of the patients had received previous treatment. These patients were enrolled in an expanded cohort study instituted after phase 1 dose escalation had established a recommended crizotinib dose of 250 mg twice daily in 28-day cycles. Patients were assessed for adverse events and response to therapy. RESULTS Patients with ALK rearrangements tended to be younger than those without the rearrangements, and most of the patients had little or no exposure to tobacco and had adenocarcinomas. At a mean treatment duration of 6.4 months, the overall response rate was 57% (47 of 82 patients, with 46 confirmed partial responses and 1 confirmed complete response); 27 patients (33%) had stable disease. A total of 63 of 82 patients (77%) were continuing to receive crizotinib at the time of data cutoff, and the estimated probability of 6-month progression-free survival was 72%, with no median for the study reached. The drug resulted in grade 1 or 2 (mild) gastrointestinal side effects. CONCLUSIONS The inhibition of ALK in lung tumors with the ALK rearrangement resulted in tumor shrinkage or stable disease in most patients. (Funded by Pfizer and others; ClinicalTrials.gov number, NCT00585195.).
The Dutch ‘Dialogue and Dissent’ framework to support civic space in Zimbabwe

The ‘Dialogue and Dissent’ programme represents the Netherlands government’s guiding principles in supporting Civil Society Organisations (CSOs) in the Global South. The frame-work envisages strengthening the capacity of civil society organizations in lobbying and advocacy as comparatively more transformative than support for service delivery initiatives. Here I investigate how the policy framework engages with civic space (limitations) under restrictive environments and with a particular focus on Zimbabwe. The policy script provides an outline involving international advocacy pathways as well as localized efforts embedded within the activities of partners. However, a qualitative interviewing process involving the Netherlands Ministry of Foreign Affairs, it’s embassy in Zimbabwe, Dutch NGOs and a selection of Zimbabwean civil society actors, established that not everything within the script contributes to the cause and is reflective of the practice in Zimbabwe. Some of the pathways construed to be addressing the closing space do not necessarily do so but rather simply represent the partners’ resilience or ways of surviving in an unfavorable environment, and this perhaps explains the Dutch government’s own admission that the situation is actually getting much worse in many of those areas in which the policy framework is being implemented. I come to a cautious conclusion that the policy in its current state is yet to illustrate a convincing means to counter the threats to civic space in Zimbabwe and that this gap between the script and the empirics mirror structural policy oversights on the underlying assumptions and particularly the working environment under authoritarian regimes.
Crystal structure of an enzyme-substrate complex provides insight into the interaction between human arylsulfatase A and its substrates during catalysis.

Arylsulfatase A (ASA) belongs to the sulfatase family whose members carry a C(alpha)-formylglycine that is post-translationally generated by oxidation of a conserved cysteine or serine residue. The crystal structures of two arylsulfatases, ASA and ASB, and kinetic studies on ASA mutants led to different proposals for the catalytic mechanism in the hydrolysis of sulfate esters. The structures of two ASA mutants that lack the functional C(alpha)-formylglycine residue 69, in complex with a synthetic substrate, have been determined in order to unravel the reaction mechanism. The crystal structure of the inactive mutant C69A-ASA in complex with p-nitrocatechol sulfate (pNCS) mimics a reaction intermediate during sulfate ester hydrolysis by the active enzyme, without the covalent bond to the key side-chain FGly69. The structure shows that the side-chains of lysine 123, lysine 302, serine 150, histidine 229, the main-chain of the key residue 69 and the divalent cation in the active center are involved in sulfate binding. It is proposed that histidine 229 protonates the leaving alcoholate after hydrolysis.C69S-ASA is able to bind covalently to the substrate and hydrolyze it, but is unable to release the resulting sulfate. Nevertheless, the resulting sulfation is low. The structure of C69S-ASA shows the serine side-chain in a single conformation, turned away from the position a substrate occupies in the complex. This suggests that the double conformation observed in the structure of wild-type ASA is more likely to correspond to a formylglycine hydrate than to a twofold disordered aldehyde oxo group, and accounts for the relative inertness of the C69S-ASA mutant. In the C69S-ASA-pNCS complex, the substrate occupies the same position as in the C69A-ASA-pNCS complex, which corresponds to the non-covalently bonded substrate. Based on the structural data, a detailed mechanism for sulfate ester cleavage is proposed, involving an aldehyde hydrate as the functional group.
Calcium-induced calcium release and calcium buffering in retinal horizontal cells

Calcium plays an integral role in intracellular signaling and process control in neurons. In the outer retina, it is a key component to the phototransduction cycle and neurotransmitter release in photoreceptor and bipolar cell terminals. It also contributes to the responses of horizontal and bipolar cells. In the dark, horizontal cells are depolarized and calcium enters via calcium permeant AMPA receptors and voltage-activated calcium channels. As a result, horizontal cells must be capable of handling high calcium loads without sustaining damage. The aim of this study was to examine the components determining the intracellular calcium levels in H2 horizontal cells in the retina of white bass. Calcium responses were evoked in isolated cells by depolarizing voltage steps and monitored by conventional imaging techniques. The responses consisted of two components: calcium entry through voltage-gated calcium channels and subsequent release from intracellular stores by calcium-induced calcium release (CICR). Under control conditions, changes in calcium levels reached 541 nM on average from a basal level of 60 nM. When release from CICR stores was blocked with ryanodine or dantrolene, calcium levels barely reached 180 nM. The threshold level needed to trigger CICR was dependent on the duration of the applied depolarization and increased in response to shorter pulses.
Distribution and development of glutamic acid decarboxylase immunoreactivity in the spinal cord of the dogfish Scyliorhinus canicula (elasmobranchs)

The adult distribution and development of γ‐aminobutyric acid (GABA)‐synthesizing cells and fibers in the spinal cord of the lesser spotted dogfish (Scyliorhinus canicula L.) was studied by means of immunohistochemistry using antibodies against glutamic acid decarboxylase (GAD). Complementary immunostaining with antibodies against GABA, tyrosine hydroxylase (TH), and HuC/HuD (members of the Hu/Elav family of RNA‐associated proteins) and staining with a reduced silver procedure (“en bloc” Bielschowski method), Nissl, and hematoxylin were also used. In adults, GAD‐immunoreactive (GAD‐ir) cells were observed in the ventral horns, in the spinal nucleus of the dorsal horn, at the base of the dorsal horns, and around the central canal, where some GAD‐ir cells were cerebrospinal fluid‐contacting (CSF‐c). In addition, a few GAD‐ir cells were observed in the lateral funiculus between the ventral horn and the marginal nucleus. The adult spinal cord was richly innervated by GAD‐ir fibers. Large numbers of GAD‐ir fibers and boutons were observed in the dorsal and ventral horns and also interstitially in the dorsal, lateral, and ventral funiculi. In addition, a rich GAD‐ir innervation was observed in the marginal nucleus of the spinal cord. In the embryonic spinal cord, GAD‐ir cells develop very early: The earliest cells were observed in the very thin mantle/marginal layer of stage 22 embryos in a short length of the spinal cord. At stages 25 and 26, several types of GAD‐ir cells (commissural and noncommissural) were distinguished, and two of these cells were of CSF‐c type. At stages 28, 30, and 31, the GAD‐ir populations exhibited a marked longitudinal columnar organization. Double‐immunolabeling experiments in embryos showed the presence of two different GAD‐ir CSF‐c cell populations, one ventral that is simultaneously TH‐ir and other more dorsal that is TH‐negative. By stage 33 (prehatching), GAD‐expressing cells are present in virtually all loci, as in adults, especially in the ventral horn and base of the dorsal horn. The present results for the lesser spotted dogfish suggest an important role for γ‐aminobutyric acid in sensory and motor circuits of the spinal cord. J. Comp. Neurol. 478:189–206, 2004. © 2004 Wiley‐Liss, Inc.
Retinoic Acid Regulation of Cdx1: an Indirect Mechanism for Retinoids and Vertebral Specification

ABSTRACT Retinoic acid (RA) is required for diverse developmental programs, including vertebral specification. Both RA receptor disruption and excess RA result in homeotic transformations of the axial skeleton. These effects are believed to occur through altered expression ofHox genes, several of which have been demonstrated to be direct RA targets. Members of the cdx (caudal) homeobox gene family are also implicated in regulating Hoxexpression. Disruption of cdx1 results in vertebral homeotic transformations and alteration of Hox expression boundaries; similar homeosis is also observed in cdx2heterozygotes. In Xenopus, gain or loss of Cdx function affects vertebral morphogenesis through a mechanism that also correlates with altered Hox expression. Taken together with the finding of putative Cdx binding motifs in several Hoxpromoters, these data strongly support a role for Cdx members in direct regulation of expression of at least some Hox genes. Most retinoid-responsive Hox genes have not been demonstrated to be direct RA targets, suggesting that intermediaries are involved. Based on these findings, we hypothesized that one or morecdx members may transduce the effects of RA onHox transcription. Consistent with this, we present evidence that cdx1 is a direct RA target gene, suggesting an additional pathway for retinoid-dependent vertebral specification.
Cdk5: A New Player in Pain Signaling

Cyclin-dependent kinase 5 (Cdk5) is predominantly active in postmitotic neurons.Despite its structural homology with other cyclin-dependent kinases, Cdk5 is apparentlynot involved in the cell cycle process. The monomeric form of Cdk5 is inactive andrequires the association of p35 or p39 in order to perform its kinase activity. This kinaseis essential for normal brain development and function, but uncontrolled activity of Cdk5may lead to numerous neurodegenerative processes. Although Cdk5 activity has beenimplicated in several neuronal functions, but its precise role in the peripheral nervoussystem has not been determined. Recently we reported for the first time the essential rolefor Cdk5 in pain signaling (Pareek et al., PNAS 2006). Altered nociceptive responses tobasal thermal noxious stimuli in p35 knockout (p35-/-) and p35-overexpresing transgenicmice (Tgp35) have established the important role of this gene in the nociceptive process.Here, we report that Cdk5 regulates mitogen-activated protein kinase kinase1/2(MEK1/2) activity through a negative feedback loop during the peripheral inflammatoryresponse. Moreover a differential nociceptive response after chronic morphine exposurein p35-/- and Tgp35 mice suggests that Cdk5 activity is important for opioid tolerance.In conclusion, our data indicate important molecular roles for Cdk5 in pain signaling andopioid tolerance, which makes it a potential target for analgesic drug development.
Genome-wide analysis of DNA binding and transcriptional regulation by the mammalian Doublesex homolog DMRT1 in the juvenile testis

The DM domain proteins Doublesex- and MAB-3–related transcription factors (DMRTs) are widely conserved in metazoan sex determination and sexual differentiation. One of these proteins, DMRT1, plays diverse and essential roles in development of the vertebrate testis. In mammals DMRT1 is expressed and required in both germ cells and their supporting Sertoli cells. Despite its critical role in testicular development, little is known about how DMRT1 functions as a transcription factor or what genes it binds and regulates. We combined ChIP methods with conditional gene targeting and mRNA expression analysis and identified almost 1,400 promoter-proximal regions bound by DMRT1 in the juvenile mouse testis and determined how expression of the associated mRNAs is affected when Dmrt1 is selectively mutated in germ cells or Sertoli cells. These analyses revealed that DMRT1 is a bifunctional transcriptional regulator, activating some genes and repressing others. ChIP analysis using conditional mutant testes showed that DNA binding and transcriptional regulation of individual target genes can differ between germ cells and Sertoli cells. Genes bound by DMRT1 in vivo were enriched for a motif closely resembling the sequence DMRT1 prefers in vitro. Differential response of genes to loss of DMRT1 corresponded to differences in the enriched motif, suggesting that other transacting factors may modulate DMRT1 activity. DMRT1 bound its own promoter and those of six other Dmrt genes, indicating auto- and cross-regulation of these genes. Many of the DMRT1 target genes identified here are known to be important for a variety of functions in testicular development; the others are candidates for further investigation.
Application of a Novel Method for Assessing Cumulative Risk Burden by County

The purpose of this study is to apply the Human Security Index (HSI) as a tool to detect social and economic cumulative risk burden at a county-level in the state of Texas. The HSI is an index comprising a network of three sub-components or “fabrics”; the Economic, Environmental, and Social Fabrics. We hypothesized that the HSI will be a useful instrument for identifying and analyzing socioeconomic conditions that contribute to cumulative risk burden in vulnerable counties. We expected to identify statistical associations between cumulative risk burden and (a) ethnic concentration and (b) geographic proximity to the Texas-Mexico border. Findings from this study indicate that the Texas-Mexico border region did not have consistently higher total or individual fabric scores as would be suggested by the high disease burden and low income in this region. While the Economic, Environmental, Social Fabrics (including the Health subfabric) were highly associated with Hispanic ethnic concentration, the overall HSI and the Crime subfabric were not. In addition, the Education, Health and Crime subfabrics were associated with African American racial composition, while Environment, Economic and Social Fabrics were not. Application of the HSI to Texas counties provides a fuller and more nuanced understanding of socioeconomic and environmental conditions, and increases awareness of the role played by environmental, economic, and social factors in observed health disparities by race/ethnicity and geographic region.
Peripheral blood mononuclear cell human immunodeficiency virus type 1 proviral DNA quantification by polymerase chain reaction: relationship to immunodeficiency and drug effect

Human immunodeficiency virus type 1 (HIV-1) proviral DNA from peripheral blood mononuclear cells (PBMCs) was quantitated in 61 HIV-1-seropositive individuals by a nonisotopic polymerase chain reaction assay. Primers from the gag region (SK38, SK39) were used to determine the log10 HIV-1 proviral copy number per 10(6) CD4+ T lymphocytes (peripheral blood proviral load). A standard curve was generated for each assay by using ACH-2 cell DNA. The peripheral blood proviral load was followed in 15 individuals in a longitudinal study and was measured in 45 individuals in a cross-sectional analysis. Three of four untreated patients who were followed for 14 months had stable PBMC proviral loads and CD4+ T lymphocyte counts; one untreated patient had a sustained increase in PBMC proviral load followed 5 months later by a significant decline in the CD4+ T lymphocyte count. Eleven previously untreated individuals were monitored for 1 year following initiation of zidovudine and/or 2',3'-dideoxyinosine therapy. The mean log10 number of proviral HIV-1 copies per 10(6) CD4+ T cells decreased from 4.3 +/- 0.4 at the baseline to 3.5 +/- 0.6 after 2 to 4 months of therapy (P < 0.01). This initial 0.8 log10 fall in the PBMC proviral load after the initiation of therapy was followed by a rise in the PBMC proviral load by the sixth month of therapy. The PBMC proviral load in 45 subjects, both treated (n = 25) and untreated (n = 20), correlated inversely with the CD4+ T lymphocyte count (P < 0.01, R = 0.49). PBMC proviral DNA quantification by a nonisotopic polymerase chain reaction assay correlates with HIV-1 disease progression and could be used to monitor the effect of antiretroviral therapy.
Characterization of the Taxol Binding Site on the Microtubule

Photoaffinity labeling methods are being used to define the molecular contacts between taxol and its target protein, tubulin. Our laboratory has demonstrated previously that [3H]3′-(p-azidobenzamido)taxol photolabels the N-terminal 31 amino acids of β-tubulin (Rao, S., Krauss, N. E., Heerding, J. M., Swindell, C. S., Ringel, I., Orr, G. A., and Horwitz, S. B.(1994) J. Biol. Chem. 269, 3132-3134). The interaction of a second photoaffinity analogue of taxol, [3H]2-(m-azidobenzoyl)taxol, with tubulin has been investigated. This analogue specifically photolabels β-tubulin and the photolabeling is competed by both taxol and unlabeled 2-(m-azidobenzoyl)taxol indicating a common binding domain. To identify the site(s) of photoincorporation, [3H]2-(m-azidobenzoyl)taxol-photolabeled β-tubulin was subjected to sequential cyanogen bromide and tryptic digestions. Radiolabeled peptides were purified by reverse phase high performance liquid chromatography, and amino acid sequencing studies identified a peptide containing amino acid residues 217-231 of β-tubulin as the major photolabeled domain.
The helix‐loop‐helix transcription factor SEF‐2 regulates the activity of a novel initiator element in the promoter of the human somatostatin receptor II gene.

The effects of somatostatin hormones are mediated by a family of five different seven‐helix transmembrane spanning receptors (SSTR1–5). The expression of the five different SSTR subtypes displays a complex temporal‐ and tissue‐specific pattern. To investigate the molecular mechanisms controlling the different expression patterns of the SSTRs, we cloned the 5′‐flanking region of the human SSTR2 gene. Characterization of the SSTR2 promoter resulted in the identification of a novel initiator element (SSTR2inr). Transcriptional activity of the SSTR2inr is dependent on the presence of a binding site (E‐box) for basic helix‐loop‐helix (bHLH) transcription factors. By screening a mouse brain cDNA expression library we isolated a cDNA coding for the bHLH transcription factor SEF‐2. SEF‐2 binds to the E‐box present in the SSTR2inr, both in vitro and in vivo and activates transcription from the SSTR2inr. A single point mutation within the E‐box eliminates binding of SEF‐2 and results in a complete loss of transcriptional activity of the SSTR2inr. Furthermore, DNA binding studies demonstrate that the basal transcription factor TFIIB can be tethered to the SSTR2inr through physical interaction with SEF‐2. In summary, the SSTR2inr represents a novel type of initiator element that confers gene expression in the absence of a TATA‐box or binding sites for other known initiator factors, like YY‐1 or USF.