Miracle-dz/UniFAR-FTUs huggingface dataset:
CLADISTIC TESTS OF ADAPTATIONAL HYPOTHESES

Abstract— A cladistic viewpoint provides an historical definition of adaptation and an operational ecological test for evolutionary adaptations. Adaptation is apomorphic function promoted by natural selection, as compared with plesiomorphic function. Adaptation is thus a conditional, hierarchical, comparative term, like homology. Hypotheses of adaptation that do not specify levels of apomorphy are weak; they should refer to and explain the function at the level at which it is apomorphic with respect to the plesiomorphic (outgroup) condition. The adaptational hypothesis serves as a prior prediction in the comparison of the apomorphic function of the derived trait with the plesiomorphic function of the plesiomorphic trait serving as the null hypothesis. It is useful to distinguish whether hypotheses about characters identify selection as facilitating: 1) the origin of a character; 2) its maintenance; 3) neither; or 4) both. The latter two are uniformitarian and testable in a strong sense. The former two possibilities use ancillary arguments to protect the hypothesis of the role of natural selection in one way or another, but might still be tested by the weak criterion of plausibility. Given an hypothesis of both origin and maintenance due to selection, the test of adaptation may still be thwarted because only certain kinds of cladistic structure allow feasible tests. Few of the really classic and common examples of supraspecific adaptation survive this kind of cladistic test.
Planning and managing manufacturing capacity when demand is subject to di ! usion e ! ects

When launching a new product, the manufacturing and marketing functions of a "rm are required to jointly take critical decisions concerning the amount of manufacturing capacity to be acquired, and to elaborate policies for managing it over the product's life cycle. The time-varying demand pro"le caused by new-product di! usion phenomena, together with learning e! ects, cause the emergence of critical trade-o! decisions among the options of increasing production capacity, delaying launch, increasing backlog or accepting a signi"cant amount of lost sales. In this paper these trade-o! s are studied by developing a simple Mixed-Integer Linear Programming model and by experimenting upon it with realistic data representing di! erent scenarios. Optimal policies arising from the experiments are then compared and discussed. ( 2000 Elsevier Science B.V. All rights reserved.
A new compact low-pass filter with broad stopband and sharp skirt characteristics

In this paper, we proposed a new compact microstrip low-pass filter with broad stopband and sharp skirt characteristics. The philosophy of the structure behind this novel microstrip low-pass filter is simple as it is composed of a pair of parallel coupled-line and an open-stub. With this configuration, a finite attenuation pole near the stopband cutoff frequency is available, and the notch frequency can be well controlled by adjusting the circuit parameters. The design formulas are derived by using an equivalent-circuit model of a parallel coupled transmission line. In order to validate the feasibility of the proposed design method, a 3-order Chebyshev low-pass filter with 0.01-dB ripple is designed, fabricated, and measured. Experimental results agree well with the simulation and analytical results.
Peripheral T lymphocytes from patients with early systemic sclerosis co‐cultured with autologous fibroblasts undergo an oligoclonal expansion similar to that occurring in the skin

In recent years several reports have suggested that T cells may have a role in systemic sclerosis (SSc). The aim of our study was to investigate the dynamics of T cell repertoire in early SSc disease analysing a target organ, the skin, and the peripheral blood. To date, indeed, it is not clear if T cell expansions found in SSc reflect a general activation or result from specific antigen stimulation in the target organs. This is an important point to assess in order to characterize the role of T cells in the development of SSc. To address these questions we studied T cell repertoire by CDR3 length analysis in skin biopsies and peripheral blood obtained from patients affected by SSc and we found that a skewed T cell repertoire was present only in the biopsies. In order to characterize more effectively the meaning of these data, we performed co‐cultures using fibroblasts and peripheral blood mononuclear cells (PBMCs) obtained from SSc patients. These experiments showed that same T cell expansions were detectable in the skin of SSc patients and in the cultures of PBMCs and autologous fibroblasts of the patients but not in their peripheral blood. Taken together, these data suggest that fibroblasts trigger specific T cell expansions in the early phase of SSc.
"Vulnerabilidad al VIH/Sida: sociabilidad y trayectorias de mujeres jóvenes con prácticas homoeróticas en Rio de Janeiro"

Apoyado en la contribucion de los estudios antropologicos para el analisis de la vulnerabilidad a las ITS/VIH/Sida, este estudio tuvo por objetivo analizar las trayectorias afectivo-sexuales de un grupo de jovenes que se autodenominan lesbianas o bisexuales, frecuentadoras de espacios de sociabilidad nocturna en Rio de Janeiro (Brasil). Con base en observaciones etnograficas y entrevistas en profundidad se caracterizo su nivel socio-educativo, dinamicas de sociabilidad, practicas sexuales y percepcion de riesgo. Los patrones de interaccion sexual del grupo indican que la nocion de riesgo en el ambito homoerotico femenino ha sido poco incorporada. Esta nocion emerge mas claramente en las practicas con parejas de mujeres bisexuales y parejas del sexo opuesto, dado que se reconoce el potencial de transmision del virus del VIH en el contacto directo con las secreciones seminales. No obstante, los relatos sobre practicas sexuales con hombres indican que sus consecuencias son minimizadas debido a la confianza y eventualidad de estos encuentros. La logica de proteccion frente al VIH/Sida basada en la tension conocido-desprevencion y desconocido-alerta y la 'no concordancia' entre practicas e identidades sexuales evidenciadas en este y otros estudios nacionales, imponen desafios en el terreno de las politicas de prevencion dirigidas al universo juvenil. La investigacion forma parte de un proyecto mayor, Relaciones entre „raza‟, sexualidad y genero en diferentes contextos locales y nacionales, coordinado internacionalmente por CLAM-USP-CEBRAP y por la Fundacion Oswaldo Cruz en Rio de Janeiro, Brasil (apoyo Fundacion Ford y CNPq).
Immunosuppression after measles vaccination

The influence of conventional live attenuated measles vaccine on cellular immune responsiveness was investigated in Sweden and Guinea‐Bissau. Sixteen children in a residential area in Bissau and 16 living in southern Stockholm were examined before and 8–10 days after vaccination. Lymphoproliferation was measured to concanavalin A (con‐A), PPD and tetanus toxoid (TT) using a whole‐blood 3H‐thymidine incorporation assay. Stimulation indices were significantly lower after vaccination than before, in the case of con‐A (p= 0.03) and TT (p= 0.01) in the Guinean children and in the case of PPD (p= 0.009) and TT (p= 0.03) in the Swedish children. Stimulation of lymphocytes from measles‐immune children with measles antigens resulted in weak lymphoproliferative responses. These observations may be relevant to the increased mortality found in children immunized with high‐titre measles vaccines, as compared to controls, in recent studies. The study confirms the applicability and usefulness under field conditions of the whole blood version of the thymidine incorporation assay.
Quantifying the impacts of modeling uncertainties on the seismic drift demands and collapse risk of buildings with implications on seismic design checks

Robust estimation of collapse risk should consider the uncertainty in modeling of structures as well as variability in earthquake ground motions. In this paper, we illustrate incorporation of the uncertainty in structural model parameters in nonlinear dynamic analyses to probabilistically assess story drifts and collapse risk of buildings. Monte Carlo simulations with Latin hypercube sampling are performed on ductile and non‐ductile reinforced concrete building archetypes to quantify the influence of modeling uncertainties and how it is affected by the ductility and collapse modes of the structures. Inclusion of modeling uncertainty is shown to increase the mean annual frequency of collapse by approximately 1.8 times, as compared with analyses neglecting modeling uncertainty, for a high‐seismic site. Modeling uncertainty has a smaller effect on drift demands at levels usually considered in building codes; for the same buildings, modeling uncertainty increases the mean annual frequency of exceeding story drift ratios of 0.03 by 1.2 times. A novel method is introduced to relate drift demands at maximum considered earthquake intensities to collapse safety through a joint distribution of deformation demand and capacity. This framework enables linking seismic performance goals specified in building codes to drift limits and other acceptance criteria. The distributions of drift demand at maximum considered earthquake and capacity of selected archetype structures enable comparisons with the proposed seismic criteria for the next edition (2016) of ASCE 7. Subject to the scope of our study, the proposed drift limits are found to be unconservative, relative to the target collapse safety in ASCE 7. Copyright © 2016 John Wiley & Sons, Ltd.
An updated review of antidepressants with marked serotonergic effects in obsessive–compulsive disorder

Introduction: Since the recognition of the effectiveness of clomipramine in treating obsessive–compulsive disorder (OCD), a number of recent empirical studies have confirmed a key role of the serotonergic (5-HT) system in the pathophysiology of OCD. The current study presents a review of the existing double-blind studies testing 5-HT antidepressants in OCD. Areas covered: A systematic review was performed to identify double-blind, placebo-controlled, randomized clinical trials investigating the efficacy of antidepressants with marked 5-HT effects [clomipramine, selective serotonin reuptake inhibitors (SSRIs), venlafaxine, desvenlafaxine, duloxetine, mirtazapine, agomelatine, vortioxetine and vilazodone] in the short-term treatment of OCD. The search provided 29 studies investigating eight different 5-HT antidepressants. While the findings show reliable efficacy of clomipramine and SSRIs in the treatment of OCD symptoms, no double-blind studies were identified investigating the efficacy of desvenlafaxine, duloxetine, mirtazapine, agomelatine, vortioxetine or vilazodone. Expert opinion: While our results support the effectiveness of older antidepressants with marked 5-HT effects in OCD, it also suggests that newer agents should be tested more comprehensively.
The impact of uncertainties in the CT conversion algorithm when predicting proton beam ranges in patients from dose and PET-activity distributions

The advantages of a finite range of proton beams can only be partly exploited in radiation therapy unless the range can be predicted in patient anatomy with <2 mm accuracy (for non-moving targets). Monte Carlo dose calculation aims at 1–2 mm accuracy in dose prediction, and proton-induced PET imaging aims at ∼2 mm accuracy in range verification. The latter is done using Monte Carlo predicted PET images. Monte Carlo methods are based on CT images to describe patient anatomy. The dose calculation algorithm and the CT resolution/artifacts might affect dose calculation accuracy. Additionally, when using Monte Carlo for PET range verification, the biological decay model and the cross sections for positron emitter production affect predicted PET images. The goal of this work is to study the effect of uncertainties in the CT conversion on the proton beam range predicted by Monte Carlo dose calculations and proton-induced PET signals. Conversion schemes to assign density and elemental composition based on a CT image of the patient define a unique Hounsfield unit (HU) to tissue parameters relationship. Uncertainties are introduced because there is no unique relationship between HU and tissue parameters. In this work, different conversion schemes based on a stoichiometric calibration method as well as different numbers of tissue bins were considered in three head and neck patients. For Monte Carlo dose calculation, the results show close to zero (<0.5 mm) differences in range using different conversion schemes. Further, a reduction of the number of bins used to define individual tissues down to 13 did not affect the accuracy. In the case of simulated PET images we found a more pronounced sensitivity on the CT conversion scheme with a mean fall-off position variation of about 1 mm. We conclude that proton dose distributions based on Monte Carlo calculation are only slightly affected by the uncertainty on density and elemental composition introduced by unique assignment to each HU if a stoichiometric calibration is used. Calculated PET images used for range verification are more sensitive to conversion uncertainties causing an intrinsic limitation due to CT conversion alone of at least 1 mm.
Correlation of tumor markers p53, bcl-2, CD34, CD44H, CD44v6, and Ki-67 with survival and metastasis in laryngeal squamous cell carcinoma.

BACKGROUND Recent basic discoveries about the biological significance of nuclear and cell-surface marker proteins have opened new areas of research into head and neck cancer. However, the clinical significance of these markers is not yet understood. OBJECTIVE To perform a historical prospective study of 70 patients with squamous cell carcinoma of the larynx who were treated at our institution between 1979 and 1989 to correlate tumor marker expression with survival and metastasis. DESIGN Archival tissue was immunohistochemically stained for the p53 tumor suppressor gene product, the inhibitor of apoptosis (bcl-2), the stem cell marker CD34, the cell adhesion molecules CD44H and CD44v6, and a marker of cellular proliferation (Ki-67). The slides were examined using a light microscope and scored according to intensity and percentage of cells labeled. The patients were stratified by tumor stage, and survival and metastatic data were correlated with staining scores. RESULTS For the stage IV group, increased expression of p53 and decreased expression of CD44H and CD44v6 correlated with a decreased survival (P = .03, P = .03, and P = .02, respectively), and decreased expression of CD44H correlated with an increase in metastasis (P = .01). For all stages, excluding metastatic cases, increased p53 expression was consistent with a shorter survival (P < .03), while increased CD44v6 expression was consistent with a longer survival (P < .02). CONCLUSIONS The present study suggests that a loss of cell proliferation control implied by overexpression of p53 and loss of cell adhesion implied by decreased expression of CD44 may be determinants of survival in patients with carcinoma of the larynx. The tumor markers bcl-2 and Ki-67 were not prognostic discriminators in this limited series. This study also indicates that the stem cell marker CD34 is rarely expressed by laryngeal carcinoma cells.
A hybrid clustering algorithm for identifying modules in Protein - Protein Interaction networks

Identifying modules in Protein-Protein Interaction (PPI) networks is important to understand the organisation of the cellular processes. In this paper, we present a novel algorithm combining Molecular Complex Detection (MCODE) with Girvan-Newman (GN) to identify modules in PPI networks. Our algorithm can accurately discover denser modules in large-scale protein interaction networks. We applied it to S. cerevisiae PPI networks and obtained high matching rate between the predicted modules and the known protein complexes in Munich Information Center for Protein Sequences (MIPS). The simulation results show that our algorithm provides an effective, reliable and scalable method of identifying modules in PPI networks.
Examining Students' Perceptions of E-Learning in a Women-Only Environment

In terms of achieving growth and profitability, women play an important role in public and private organizations. Despite the increase of women in the workforce, they continue to be underrepresented in managerial positions. Appropriate initiatives need to be implemented in an organization to manage and retain women talent. Online courses catered specifically to women can provide women professionals with relevant development opportunities throughout their career, as these women-only programs allow women to freely discuss their particular issues and concerns in a supportive and safe climate. Apart from being flexible and cost effective, these online women-only courses provide an optimal learning environment for women to share and analyze the unique strengths, weaknesses, challenges, and opportunities facing women in the workplace. Yet, several questions exist concerning the design and delivery of such online courses, particularly from the student’s perspective. In this study, students' perceptions of e-learning in a women-only environment are examined. An exploratory study of female students enrolled in an Executive Certificate of Leadership for Women, which is a customized online program facilitated by international PhD qualified women faculty, is conducted to understand students’ perceptions of the various attributes of a women-only online learning course.
[Effects of apolipoprotein E genetic polymorphism on susceptibility of depression and efficacy of antidepressants].

OBJECTIVE To assess the effects of apolipoprotein E (APOE) polymorphism on the susceptibility of depression and the efficacy of antidepressants. METHODS A total of 275 patients with depression, who met the diagnostic criteria of both CCMD-3 and DSM-4, were randomly assigned into venlafaxine group (n=136)and paroxetine group(n=139). Another 202 healthy subjects were enrolled as the control group. Hamilton Rating Scale for Depression (HAMD)-17 was adopted as the primary rating instrument to evaluate the severity of depression on the baseline and the end of the 1st, 2nd, 4th, 6th week after treatment, respectively. HAMD scores ≤7 was defined as remission, and the reduction of HAMD scores ≥50% was defined as response while <50% was defined as invalid. PCR-restriction fragment length polymorphisms (PCR-RFLP) was applied to detect the genetic polymorphism of the APOE in the case groups and control group. RESULTS In the venlafaxine group, the remission rate was 52.9%(n=72), the response rate was 26.5%(n=36), and the invalid rate was 20.6%(n=28), whereas the corresponding data in the paroxetine group wee 42.4%(n=59), 31.7%(n=44), and 25.9% (n=36), respectively. There were no significant differences in the efficacy between the two groups(p>0.05). In the venlafaxine group, there were no significant differences in the genotypes and the allele distribution frequency of APOEΕ2/Ε3/Ε4 between the remitters, nonremitters, and healthy controls at the end of the 6th week(p>0.05), but there was significant differences in the allele distribution frequency between the nonremitters and healthy controls(p=0.02). In paroxetine group, there were no significant differences in the genotypes and the allele distribution frequency of APOEΕ2/Ε3/Ε4 among the remitters, nonremitters and healthy controls at the end of the 6th week(p>0.05), but there were significant differences in the allele distribution frequency between the nonremitters and healthy controls (p=0.04); in addition, there were also significant differences in Ε2/Ε3 and Ε4 allele between the two groups (p=0.014). CONCLUSIONS The APOE gene may not play a major role in the pathogenesis of major depression. The efficacy of venlafaxine is same as paroxetine after treatment for six weeks. The APOE (Ε2+Ε3) allele may be an indicator of the bad efficacy of paroxetine treatment.
2-Methoxyestradiol Mediates Apoptosis Through Caspase-Dependent and Independent Mechanisms in Ovarian Cancer Cells But Not in Normal Counterparts

Objective: The estrogen metabolite 2-methoxyestradiol has shown antitumorigenic action in some epithelial tumors. In the present work we investigate its effects in ovarian cancer used alone or in combination with other apoptotic-inducing reagents such as tumor necrosis factor-related apoptosis-inducing ligand. Methods: To assess the effect of 2-methoxyestradiol, dose response and time courses in ovarian cancer and normal cells were conducted. Apoptosis was confirmed through DNA laddering, by flow cytometry, and Western blotting of proteins involved in the apoptotic cascade. Results: 2-Methoxyestradiol induced apoptosis in ovarian cancer cells but not in normal counterparts. 2-Methoxyestradiol activates both the intrinsic and extrinsic apoptotic pathways. 2-Methoxyestradiol—mediated apoptosis involves reactive oxygen species generation and caspase-dependent and caspase-independent mechanisms. We also demonstrate that 2-methoxyestradiol selectively induces an additive/synergistic apoptotic response in ovarian cancer cells when used in combination with tumor necrosis factor-related apoptosis-inducing ligand. Conclusions: 2-Methoxyestradiol, alone or in combination with tumor necrosis factor-related apoptosis-inducing ligand, should be considered as a potential treatment for ovarian cancer.
A vertebrate gene related to orthodenticle contains a homeodomain of the bicoid class and demarcates anterior neuroectoderm in the gastrulating mouse embryo.

We studied the expression of two vertebrate homeobox genes, Otx1 and Otx2, related to orthodenticle, a gene expressed in the developing head of Drosophila. Both genes are expressed in restricted regions of the developing rostral brain including the presumptive cerebral cortex and olfactory bulbs. The expression patterns of the two genes in diencephalon suggest that they both have a role in establishing the boundary between presumptive dorsal and ventral thalamus. They are also expressed in regions of the developing olfactory, auricolar and ocular system, including the covering of the optic nerve. Otx1 expression is detectable from day 8 of gestation in telencephalic, diencephalic and mesencephalic regions. From day 10.5 of gestation its expression extends to some metencephalic areas. Otx2 appears to be already expressed in the epiblast of prestreak embryos. It persists in the entire embryonic ectoderm for some time after the onset of gastrulation. In midstreak embryos its expression appears progressively restricted to the anterior embryonic ectoderm corresponding to presumptive fore‐ and mid‐brain. In early midgestation embryos it is expressed in telencephalic, diencephalic and mesencephalic regions but from day 11.75 of gestation its expression disappears from dorsal telencephalon and is confined to diencephalic and mesencephalic regions. Otx2 is one of the earliest genes expressed in the epiblast and immediately afterwards is expressed in anterior neuroectoderm, demarcating rostral brain regions even before headfold formation. Its gene product contains a homeodomain of the bicoid class and is able to recognize and transactivate a bicoid target sequence.
The 18-kilodalton antigen secreted by Aspergillus fumigatus

One of the major antigens secreted in vitro by Aspergillus fumigatus is an 18-kDa basic protein which has been purified by cation-exchange chromatography. It is recognized by sera from aspergilloma patients. It is also the major circulating antigen found in urine of patients with invasive aspergillosis. Our results indicated that this antigen has potential for the diagnosis of both aspergilloma and invasive aspergillosis.