Miracle-dz/UniFAR-FTUs huggingface dataset:
"Pregnant Victims of Domestic Violence in Puerto Rico: The Lived Experience"

Domestic violence is defined as a pattern of assaultive and coercive behaviors that includes the threat or infliction of physical, sexual, or psychological abuse that is used by perpetrators for the purpose of intimidation and control over the victim. This study describes pregnant women’s lived experience of domestic violence and examines the factors influencing the process of disclosure of domestic violence among pregnant women in the southern region of Puerto Rico. A phenomenological method was used where women who had experienced domestic violence during pregnancy were invited to participate in online semi structured interviews. Data analysis included qualitative coding of the interview identifying emergent themes. In order to ensure trustworthiness and accurate representation of the text the use of a second reader was employed in the thematic analysis. The main themes identified included lack of direct questions from providers, isolation, worsening of abuse by pregnancy, physical, psychological and sexual abuse; support from family, friends and shelter; lack of police support and economic dependence. Implications for nursing are discussed
Structure of the 12-Subunit RNA Polymerase II Refined with the Aid of Anomalous Diffraction Data*

RNA polymerase II (Pol II) is the central enzyme of eukaryotic gene expression machinery. Complete definition of the three-dimensional structure of Pol II is essential for understanding the mechanisms that regulate transcription via protein-protein interactions within the Pol II apparatus. To date a series of Pol II-related crystal structures have been reported. However, certain peptide regions, including several that are implicated to interact with regulatory factors, remain obscure. Here we describe conformations for two such regions that are close to the Pol II surface and assume seemingly flexible loop structures. One is located in the TFIIF-interacting Protrusion domain, whereas the other is in the TFIIE-interacting Clamp domain. This structural definition was aided by the application of an advanced crystallographic refinement approach that utilizes the single anomalous diffraction (SAD) from zinc ions bound intrinsically in Pol II. The SAD-based strategy allowed the 12-subunit Pol II model to be fully refined up to 3.8 Å with excellent stereochemical properties, demonstrating the effectiveness of the SAD approach for the refinement of large structures at low-to-moderate resolutions. Our results also define additional components of the free Pol II, including the functionally critical Fork Loop-1 and Fork Loop-2 elements. As such, this refined Pol II model provides the most complete structural reference for future analyses of complex structures formed between Pol II and its regulatory factors.
Changes in Human Immunodeficiency Virus Type 1 Gag at Positions L449 and P453 Are Linked to I50V Protease Mutants In Vivo and Cause Reduction of Sensitivity to Amprenavir and Improved Viral Fitness In Vitro

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) Gag protease cleavage sites (CS) undergo sequence changes during the development of resistance to several protease inhibitors (PIs). We have analyzed the association of sequence variation at the p7/p1 and p1/p6 CS in conjunction with amprenavir (APV)-specific protease mutations following PI combination therapy with APV. Querying a central resistance data repository resulted in the detection of significant associations (P < 0.001) between the presence of APV protease signature mutations and Gag L449F (p1/p6 LP1′F) and P453L (p1/p6 PP5′L) CS changes. In population-based sequence analyses the I50V mutant was invariably linked to either L449F or P453L. Clonal analysis revealed that both CS mutations were never present in the same genome. Sequential plasma samples from one patient revealed a transition from I50V M46L P453L viruses at early time points to I50V M46I L449F viruses in later samples. Various combinations of the protease and Gag mutations were introduced into the HXB2 laboratory strain of HIV-1. In both single- and multiple-cycle assay systems and in the context of I50V, the L449F and P453L changes consistently increased the 50% inhibitory concentration of APV, while the CS changes alone had no measurable effect on inhibitor sensitivity. The decreased in vitro fitness of the I50V mutant was only partially improved by addition of either CS change (I50V M46I L449F mutant replicative capacity ≈ 16% of that of wild-type virus). Western blot analysis of Pr55 Gag precursor cleavage products from infected-cell cultures indicated accumulation of uncleaved Gag p1-p6 in all I50V viruses without coexisting CS changes. Purified I50V protease catalyzed cleavage of decapeptides incorporating the L449F or P453L change 10-fold and 22-fold more efficiently than cleavage of the wild-type substrate, respectively. HIV-1 protease CS changes are selected during PI therapy and can have effects on both viral fitness and phenotypic resistance to PIs.
Tissue array analysis of expression microarray candidates identifies markers associated with tumor grade and outcome in serous epithelial ovarian cancer

Molecular profiling is a powerful approach to identify potential clinical markers for diagnosis and prognosis as well as providing a better understanding of the biology of epithelial ovarian cancer. On the basis of the analysis of HuFL expression data, we have previously identified genes that distinguish low malignant potential and invasive serous epithelial ovarian tumors. In this study, we used immunohistochemistry to monitor a subset of differently expressed candidates (Ahr, Paep, Madh3, Ran, Met, Mek1, Ccne1, Ccd20, Cks1 and Cas). A tissue array composed of 244 serous tumors of different grades (0–3) and stages (I–IV) was used in this analysis. All markers assayed presented differential protein expression between serous tumors of low and high grade. Significant differences in Ccne1 and Ran expression were observed in a comparison of low malignant potential and grade 1 tumor samples (p < 0.01). In addition, irrespective of the grade, Ccne1, Ran, Cdc20 and Cks1 showed significant differences of expression in association with the clinical stage of disease. While high level of Ccne1 have previously been associated with poor outcomes, here we found that high level of either Ran or Cdc20 appear to be more tightly associated with a poor prognosis (p < 0.001, 0.03, respectively). The application of these biomarkers in both the initial diagnosis and prognostic attributes of patients with epithelial ovarian tumors should prove to be useful in patient management. © 2006 Wiley‐Liss, Inc.
Comparison of electronic volume and forward scatter principles of cell selection using flow cytometry for the evaluation of acrosome and plasma membrane integrity of bull spermatozoa

The objective of the study was to compare two different flow cytometers to reveal if there are differences between them and to find the most suitable protocol for analysis of spermatozoa. These two flow cytometers; Cell Lab Quanta™ and Coulter Epics XL, have different principles to calculate cell size, electric volume, and forward scatter (FS), respectively. Flow cytometry is a valuable tool to assess various spermatozoa quality traits simultaneously, such as plasma membrane and acrosome integrity. A double‐ and triple‐stain combination was performed to compare evaluation of these two parameters by both flow cytometers and to assess the need of a fluorescent probe to identify the spermatozoa. Propidium iodide was used to assess the proportion of dead spermatozoa, whereas Alexa Fluor® 488 conjugated peanut agglutinin (PNA‐ Alexa 488) was used to evaluate the percentage of acrosome intact and acrosome–reacted cells or degenerated cells. In the triple‐stain protocol, MitoTracker® Orange (MO) was included to test the capacity of this probe to discriminate spermatozoa from egg yolk and debris particles present in the semen sample. Cryopreserved semen from 13 Norwegian Red bulls was included in the study and the semen was evaluated immediately after thawing and after 3 hr incubation at 37°C. The results show that there is good agreement between the instruments. Nevertheless, a significant difference was found in percentages of acrosome intact live spermatozoa (% AIL) when including MO as a spermatozoa identification probe, compared to assessment without MO, with the Coulter Epics XL, while no significant difference was found when including the probe with the Cell Lab Quanta. In conclusion, the results show that cell size measurement based on electronic volume used by the Cell Lab Quanta flow cytometer is more accurate than FS used by the Coulter Epics XL flow cytometer in identification of spermatozoa. © 2014 International Society for Advancement of Cytometry
Relationships between tumor-associated macrophages and clinicopathological factors in patients with colorectal cancer.

BACKGROUND As macrophages have both tumor promoting and inhibiting effects, tumor-associated macrophages (TAM) play a complex role in the regulation of cancer progression and tumor growth. The clinicopathological significance of TAMs in human colorectal cancer remains unclear. MATERIALS AND METHODS We investigated the relationships between TAM IF (invasive front), TAM TS (tumor stroma), prognosis and clinicopathological factors in 30 patients with colorectal cancer. Moreover, MVD (microvessel density) was examined for correlation with these factors. TAMs were detected by immunohistochemistry using the anti-CD68 antigen, KP1 mouse monoclonal antibody. MVD was determined by counting the number of CD34-positive vessels. RESULTS Low TAM IF and TAM TS tended to occur with more advanced colorectal cancer, although this finding was not statistically significant. High TAM IF tended to be found in patients with a good prognosis or those with less recurrence or worsening of their condition. MVD was significantly higher in patients with lymph node metastasis, lymphatic invasion or more advanced tumors than stage III (TNM). Although the correlation between TAM IF, TAM TS and MVD was not statistically significant, the correlation between TAM IF and TAM TS was statistically significant. CONCLUSION These results suggest that TAMs may act as one line of defence against malignant cells in patients with colorectal cancer.
Use of Cotton Rats to Evaluate the Efficacy of Antivirals in Treatment of Measles Virus Infections

ABSTRACT No practical animal models for the testing of chemotherapeutic or biologic agents identified in cell culture assays as being active against measles virus (MV) are currently available. Cotton rats may serve this purpose. To evaluate this possibility, 5-ethynyl-1-β-d-ribofuranosylimidazole-4-carboxamide (EICAR) and poly(acrylamidomethyl propanesulfonate) (PAMPS), two compounds that have been reported to inhibit MV in vitro, and ribavirin, an established antiviral drug with MV-inhibitory activity, were evaluated for their antiviral activities against MV and respiratory syncytial virus (RSV) in tissue culture and in hispid cotton rats. A single administration of PAMPS markedly inhibited pulmonary RSV or MV replication (>3 log10 reduction in pulmonary titer compared to that for controls), but only if this compound was administered intranasally at about the time of virus inoculation. Both EICAR and ribavirin exhibited therapeutic activity against RSV and MV in cotton rats when they were administered parenterally. However, both of these compounds were less effective against MV. On the basis of the pulmonary virus titers on day 4 after virus inoculation, the minimal efficacious dose of EICAR against MV (120 mg/kg of body weight/day when delivered intraperitoneally twice daily) appeared to be three times lower against this virus than that of ribavirin delivered at a similar dose (i.e., 360 mg/kg/day). These findings correlated with those obtained in vitro. The data obtained suggest that cotton rats may indeed be useful for the initial evaluation of the activities of antiviral agents against MV.
Long-term survival and functional status in the elderly after cardiac surgery.

BACKGROUND Hospital mortality and morbidity of cardiac surgery have been well described in the elderly, but there is a paucity of data regarding long-term functional status. OBJECTIVE To evaluate long-term survival and functional status of patients aged 70 years or older after cardiac surgery. DESIGN Retrospective observational study. SETTING University-affiliated tertiary care hospital. PATIENTS Three hundred and twenty-nine consecutive patients aged 70 or older who had undergone cardiac surgery from January 1990 to December 1993. INTERVENTIONS Besides postoperative mortality and morbidity, data regarding long-term survival and functional status and preoperative variables affecting these outcomes were analyzed. MAIN RESULTS Mean age at surgery was 73.9 +/- 2.9 years, and 70.2% of the procedures were performed on an urgent basis. Postoperative mortality was 9.4%. Five-year Kaplan-Meier survival in postoperative survivors was 85.9% and is comparable with the survival of the general sex- and age-matched Quebec population. Preoperative variables affecting long-term survival were atrial fibrillation (RR 3.8; 95% CI 1.4 to 10.0), smoking status on admission (RR 3.6; CI 1.6 to 8.1), peripheral vascular disease (RR 2.9; CI 1.4 to 6.2) and low creatinine clearance (RR 1.4; CI 1.1 to 1.7). Functional status evaluated by the Karnofsky score showed a successful functional outcome in 84.6% of patients at follow-up (mean 2.6 +/- 1.1 years). Preoperative variables unfavourably influencing a successful functional outcome were hypertension (OR 0.34; CI 0.15 to 0.76), cerebrovascular disease (OR 0.35; CI 0.15 to 0.87) and low creatinine clearance (OR 0.73; CI 0.55 to 0.96). CONCLUSIONS Despite severe cardiovascular and often urgent conditions, sustained functional improvement and good long term survival can be objectively documented in most elderly patients after cardiac surgery.
Effects of non-steroidal antiinflammatory drugs and dexamethasone on the activity and expression of matrix metalloproteinase-1, matrix metalloproteinase-3 and tissue inhibitor of metalloproteinases-1 by bovine articular chondrocytes.

OBJECTIVE To determine the in-vitro effects of several non-steroidal antiinflammatory drugs and the glucocorticoid dexamethasone on the IL-1 altered expression and activity of MMP-1, MMP-3 and TIMP-1 by bovine articular chondrocytes. DESIGN Bovine chondrocytes were cultured in alginate gel beads. Cells were treated with IL-1alpha in the presence of vehicle or drugs at various concentrations. After 48 h mRNA expression of MMP-1, MMP-3, and of the tissue inhibitor of metalloproteinases (TIMP-1) was analysed by RT-PCR-ELISA. The protein synthesis of TIMP-1 and MMP-3 was determined by immunoprecipitation. The activity of enzymes and inhibitors was measured by functional assays. RESULTS IL-1 increased the expression and activity of MMPs. In contrast, TIMP activity remained unchanged although TIMP-1 expression was down-regulated. All tested NSAIDs and dexamethasone inhibited collagenase activity induced by IL-1. Transcript levels of MMP-1, however, were only reduced by indomethacin, meloxicam, naproxen and dexamethasone. Proteoglycanase activity was only reduced by indomethacin, meloxicam and dexamethasone. These effects were pre-translational as confirmed by immunoprecipitation. The IL-1 decreased expression of TIMP-1 was further reduced by dexamethasone, which resulted in a significant loss of TIMP activity. No effects on TIMP activity or TIMP-1 biosynthesis were observed after treatment of chondrocytes with NSAIDs. CONCLUSION Our studies clearly demonstrate that marked differences exist between individual NSAIDs with respect to their ability to modulate the imbalance between proteases and inhibitors during OA and RA, suggesting that the respective modes of action are independent of the inhibition of cyclooxygenases. Due to their co-regulation of MMPs and TIMP(s) glucocorticoids should be carefully studied for their overall effect on ECM proteolysis.
Combination use of medicines from two classes of renin–angiotensin system blocking agents: risk of hyperkalemia, hypotension, and impaired renal function

European and United States regulatory agencies recently issued warnings against the use of dual renin–angiotensin system (RAS) blockade therapy through the combined use of angiotensin-converting enzyme inhibitors (ACEIs), angiotensin II receptor blockers (ARBs) or aliskiren in any patient, based on absence of benefit for most patients and increased risk of hyperkalemia, hypotension, and renal failure. Special emphasis was made not to use these combinations in patients with diabetic nephropathy. The door was left open to therapy individualization, especially for patients with heart failure, when the combined use of an ARB and ACEI is considered absolutely essential, although renal function, electrolytes and blood pressure should be closely monitored. Mineralocorticoid receptor antagonists were not affected by this warning despite increased risk of hyperkalemia. We now critically review the risks associated with dual RAS blockade and answer the following questions: What safety issues are associated with dual RAS blockade? Can the safety record of dual RAS blockade be improved? Is it worth trying to improve the safety record of dual RAS blockade based on the potential benefits of the combination? Is dual RAS blockade dead? What is the role of mineralocorticoid antagonists in combination with other RAS blocking agents: RAAS blockade?
Involvement of different mesotocin (oxytocin homologue) populations in sexual and aggressive behaviours of the brown anole

The oxytocin (OT) family of neuropeptides are known to modulate social behaviours and anxiety in mammals and birds. We investigated cell numbers and neural activity, assessed as Fos induction, within magnocellular and parvocellular populations of neurons producing the OT homologue mesotocin (MT, Ile8-oxytocin). This was conducted within the male brown anole lizard, Anolis sagrei, following agonistic or courtship encounters with a conspecific. Both neurons colocalizing and not colocalizing corticotropin-releasing factor (CRF) were examined. Parvocellular neurons of the paraventricular nucleus exhibited a positive correlation between courtship frequency and Fos colocalization, regardless of whether they produce just MT or MT + CRF. Magnocellular populations showed only trends towards positive relationships with courtship and no cell populations showed aggression-related Fos induction. These findings are novel because they demonstrate the involvement of MT neurons in male social behaviour, especially in reptiles for whom the involvement of MT in social behaviour was previously unknown.
Breast Cancer in Surat Thani, a Province in Southern Thailand: Analysis of 2004-2012 Incidence and Future Trends.

BACKGROUND With the recent epidemiologic transition in Thailand, featuring decreasing incidences of infectious diseases along with increasing rates of chronic conditions, cancer is becoming a serious problem for the country. Breast cancer has the highest incidence rates among females, not only in the southern regions, but throughout Thailand. Surat Thani is a province in the upper part of Southern Thailand. A study was needed to identify the current burden, and the future trends of breast cancer. MATERIALS AND METHODS Here we used cancer incidence data from the Surat Thani Cancer Registry to characterize the incidences of breast cancer. Joinpoint analysis was used to investigate the incidences in the province from 2004 to 2012 and to project future trends from 2013 to 2030. RESULTS Age-standardized incidence rates (world) of breast cancer in the upper parts of Southern Thailand increased from 35.1 to 59.2 cases per 100,000 female population, which is equivalent to an annual percentage change of 4.5-4.8%. Linear drift effects played a role in shaping the increase of incidence. Joinpoint projection suggested that incidence rates would continue to increase in the future with incidence for women aged 50 and above, at a higher rate than for women below the age of 50. CONCLUSIONS The current early detection measures increase detection rates of early disease. Preparation of a budget for treatment facilities and human resources, both in surgical and medical oncology, is essential.
Procedural Treatments for Acne Vulgaris

BACKGROUND Simple procedural treatments such as comedone extraction and intralesional steroids have been utilized for many years as adjunctive therapy for acne. In the past 5 years, new technologies and procedures have become available that present new options for the treatment of acne. OBJECTIVES The objective was to review, summarize, and evaluate the key studies of procedural therapies for the treatment of acne as well as place them in perspective with current clinical practice. METHODS Studies selected for evaluation had at least 10 patients and clear statements of purpose, acne severity, patient selection, follow-up evaluations, previous and concurrent medications, treatment parameters, methods for evaluating results, and adverse effects. All studies were complete and published (in English) in peer-reviewed journals. RESULTS AND CONCLUSIONS Earlier procedural therapies were adjunctive to medical therapy, such as intralesional steroids, chemical peels, and microdermabrasion. Newer methods include radiofrequency, light or laser, and photodynamic therapy that represent treatment alternatives for systemic medications. Still early in their development, these new procedures provide an important, novel set of options for the treatment of acne. The most developed and studied therapies are blue or blue/red light combinations, 1,450-nm diode laser, and photodynamic therapy with 5-aminolevulinic acid or indocyanine green. Review of the literature of more up-to-date physical procedures provides a starting point for physicians seeking to treat their acne patients safely and effectively with these new methods.
Refined structure of chicken skeletal muscle troponin C in the two-calcium state at 2-A resolution.

The structure of troponin C has been refined at 2A resolution to an R value of 0.172 using a total of 8,100 reflections. Troponin C has an unusual dumbbell shape with only the two C-domain high affinity sites III and IV occupied with metals, while the pair of N-domain low affinity sites I and II are devoid of metals. The coordination of the Ca2+ approaches seven with the last glutamic acid residue in each site forming an asymmetric bidentate ligand. The flanking helices in the metal-bound EF hands are in similar orientation (both 113 degrees) while in the apo sites they are more obtuse (134 and 149 degrees). The EF hands of holo sites III and IV are similar while the apo sites I and II are less similar (rms for backbone atoms, 0.78 and 1.44). The half-loops of the 12-residue holo and apo sites show better agreement than the full loops themselves, suggesting a hinge motion at the midpoint of the loops. The long central helix is stabilized by electrostatic interactions and salt bridges between charged side chains spaced at 3 or 4 residues along the helix. A cluster of water molecules encircle the long helix and hydrogen bond to the backbone carbonyls. At the beginning of the B-helix, a water molecule is interposed at each of two consecutive backbone NH.OC hydrogen bonds. The terminal pair of helices A/D (apo) match with E/H (holo), and the internal pair of helices B/C (apo) match with F/G (holo). Thus, muscle contraction may be triggered by Ca2+ binding to loops I and II which results in a concerted rearrangement of residues in the loops, including the essential Gly at position 6 in each loop. This rearrangement than causes a reorientation of helices B and C along with the BC linker.