Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of Vasculogenic Mimicry Formation and CD133 Expression with Poor Prognosis in Ovarian Cancer

Aims: This study was conducted to investigate the association of vasculogenic mimicry (VM) formation and CD133 expression with the clinical outcomes of patients with ovarian cancer. Methods: This retrospective study was performed in 120 ovarian carcinoma samples. VM formation and CD133 expression was identified with CD31/periodic acid-Schiff double-staining and CD133 immunohistochemical staining. Collected clinical and pathological data included age at diagnosis, histologic type, tumor grade, tumor stage, lymph node metastases and response to chemotherapy. The overall survival time was calculated. Results: VM was identified in 52 (43%) of 120 ovarian carcinoma tissues and CD133 expression was found in 56 (47%) cases. Both VM formation and CD133 expression were associated with advanced tumor stage, high-grade carcinoma and non-response to chemotherapy (p < 0.05). They were also associated with shorter overall survival time (p < 0.05) by log-rank test. Combined marker of VM formation and CD133 expression was associated with high-grade ovarian carcinoma, late-stage disease, non-response to chemotherapy and shorter overall survival time (p < 0.05). Conclusions: VM formation and CD133 expression can provide additional prognostic information for patients with ovarian cancer. Combined marker of VM formation and CD133 expression may be a potent predictor for poor prognosis for patients with ovarian cancer.
MicroRNA miR-125a controls hematopoietic stem cell number

MicroRNAs influence hematopoietic differentiation, but little is known about their effects on the stem cell state. Here, we report that the microRNA processing enzyme Dicer is essential for stem cell persistence in vivo and a specific microRNA, miR-125a, controls the size of the stem cell population by regulating hematopoietic stem/progenitor cell (HSPC) apoptosis. Conditional deletion of Dicer revealed an absolute dependence for the multipotent HSPC population in a cell-autonomous manner, with increased HSPC apoptosis in mutant animals. An evolutionarily conserved microRNA cluster containing miR-99b, let-7e, and miR-125a was preferentially expressed in long-term hematopoietic stem cells. MicroRNA miR-125a alone was capable of increasing the number of hematopoietic stem cells in vivo by more than 8-fold. This result was accomplished through a differentiation stage-specific reduction of apoptosis in immature hematopoietic progenitors, possibly through targeting multiple proapoptotic genes. Bak1 was directly down-regulated by miR-125a and expression of a 3′UTR-less Bak1 blocked miR-125a-induced hematopoietic expansion in vivo. These data demonstrate cell-state-specific regulation by microRNA and identify a unique microRNA functioning to regulate the stem cell pool size.
Acellular pertussis vaccination facilitates Bordetella parapertussis infection in a rodent model of bordetellosis

Despite over 50 years of population-wide vaccination, whooping cough incidence is on the rise. Although Bordetella pertussis is considered the main causative agent of whooping cough in humans, Bordetella parapertussis infections are not uncommon. The widely used acellular whooping cough vaccines (aP) are comprised solely of B. pertussis antigens that hold little or no efficacy against B. parapertussis. Here, we ask how aP vaccination affects competitive interactions between Bordetella species within co-infected rodent hosts and thus the aP-driven strength and direction of in-host selection. We show that aP vaccination helped clear B. pertussis but resulted in an approximately 40-fold increase in B. parapertussis lung colony-forming units (CFUs). Such vaccine-mediated facilitation of B. parapertussis did not arise as a result of competitive release; B. parapertussis CFUs were higher in aP-relative to sham-vaccinated hosts regardless of whether infections were single or mixed. Further, we show that aP vaccination impedes host immunity against B. parapertussis—measured as reduced lung inflammatory and neutrophil responses. Thus, we conclude that aP vaccination interferes with the optimal clearance of B. parapertussis and enhances the performance of this pathogen. Our data raise the possibility that widespread aP vaccination can create hosts more susceptible to B. parapertussis infection.
Alpha-2 adrenergic stimulation triggers Achilles tenocyte hypercellularity: Comparison between two model systems

The histopathology of tendons with painful tendinopathy is often tendinosis, a fibrosis‐like condition of unclear pathogenesis characterized by tissue changes including hypercellularity. The primary tendon cells (tenocytes) have been shown to express adrenoreceptors (mainly alpha‐2A) as well as markers of catecholamine production, particularly in tendinosis. It is known that adrenergic stimulation can induce proliferation in other cells. The present study investigated the effects of an exogenously administered alpha‐2 adrenergic agonist in an established in vivo Achilles tendinosis model (rabbit) and also in an in vitro human tendon cell culture model. The catecholamine producing enzyme tyrosine hydroxylase and the alpha‐2A‐adrenoreceptor (α2A AR) were expressed by tenocytes, and alpha‐2 adrenergic stimulation had a proliferative effect on these cells, in both models. The proliferation was inhibited by administration of an α2A AR antagonist, and the in vitro model further showed that the proliferative alpha‐2A effect was mediated via a mitogenic cell signaling pathway involving phosphorylation of extracellular‐signal‐regulated kinases 1 and 2. The results indicate that catecholamines produced by tenocytes in tendinosis might contribute to the proliferative nature of the pathology through stimulation of the α2A AR, pointing to a novel target for future therapies. The study furthermore shows that animal models are not necessarily required for all aspects of this research.
The protected landscape approach : linking nature, culture and community

The traditional patterns of land use that have created many of the worlds cultural landscapes contribute to biodiversity, support ecological processes, provide important environmental services, and have proven sustainable over the centuries. Protected landscapes can serve as living models of sustainable use of land and resources, and offer important lessons for sustainable development. Examples of these landscapes and the diverse strategies needed to maintain this essential relationship between people and the land are provided.
Trade and the Topography of the Spatial Economy

We develop a versatile general equilibrium framework to determine the spatial distribution of economic activity on any surface with (nearly) any geography. Combining the gravity structure of trade with labor mobility, we provide conditions for the existence, uniqueness, and stability of a spatial economic equilibrium and derive a simple set of differential equations which govern the relationship between economic activity and the geography of the surface. We then use the framework to estimate the topography of trade costs, productivities, amenities and the strength of spillovers in the United States. We find that geographic location accounts for 24% of the observed spatial distribution of income. Finally, we calculate that the construction of the interstate highway system increased welfare by 3.47%, roughly twice its cost.
Linking speaking and looking behavior patterns with group composition, perception, and performance

This paper addresses the task of mining typical behavioral patterns from small group face-to-face interactions and linking them to social-psychological group variables. Towards this goal, we define group speaking and looking cues by aggregating automatically extracted cues at the individual and dyadic levels. Then, we define a bag of nonverbal patterns (Bag-of-NVPs) to discretize the group cues. The topics learnt using the Latent Dirichlet Allocation (LDA) topic model are then interpreted by studying the correlations with group variables such as group composition, group interpersonal perception, and group performance. Our results show that both group behavior cues and topics have significant correlations with (and predictive information for) all the above variables. For our study, we use interactions with unacquainted members i.e. newly formed groups.
Climatology of semidiurnal lunar and solar tides at middle and high latitudes: Interhemispheric comparison

The semidiurnal lunar and solar tides obtained from meteor radar measurements spanning from 2009 to 2013 observed at Davis (69°S) and Rio Grande (54°S) are presented and compared to the Northern Hemisphere ones at Andenes (69°N) and Juliusruh (54°N). Mean tidal differences for both intrahemispheric and interhemispheric scenarios are analyzed. Tidal behavior is also compared against numerical simulations during 2009 and 2013 sudden stratospheric warming (SSW) time periods. Possible influences in the Southern Hemisphere from the local stratosphere are also investigated using Modern Era Retrospective analysis for Research and Applications, version 2 (MERRA 2) data sets. The main features of the mean zonal wind are similar in both hemispheres, i.e., stronger amplitudes over midlatitude locations, eastward winds during winter and westward below 90 km with eastward higher up during corresponding summer times. On the other hand, the semidiurnal solar tides observed in the Southern Hemisphere show clear differences when compared to the Northern Hemisphere and between middle‐ and high‐latitude locations at the same hemisphere. These differences are even larger for the semidiurnal lunar tide, which shows stronger amplitudes from October to March and March to October, over Davis and Rio Grande, respectively. Our results indicate that the lunar tides over the Southern Hemisphere midlatitudes are more prone to react to the Northern Hemisphere stratospheric polar vortex influences, in agreement with numerical simulations, particularly for the time of the 2013 SSW.
Transcriptional Attenuation Controls Macrolide Inducible Efflux and Resistance in Streptococcus pneumoniae and in Other Gram-Positive Bacteria Containing mef/mel(msr(D)) Elements

Macrolide resistance, emerging in Streptococcus pneumoniae and other Gram-positive bacteria, is increasingly due to efflux pumps encoded by mef/mel(msr) operons found on discrete mobile genetic elements. The regulation of mef/mel(msr) in these elements is not well understood. We identified the mef(E)/mel transcriptional start, localized the mef(E)/mel promoter, and demonstrated attenuation of transcription as a mechanism of regulation of macrolide-inducible mef-mediated macrolide resistance in S. pneumoniae. The mef(E)/mel transcriptional start site was a guanine 327 bp upstream of mef(E). Consensus pneumococcal promoter -10 (5′-TATACT-3′) and -35 (5′-TTGAAC-3′) boxes separated by 17 bp were identified 7 bp upstream of the start site. Analysis of the predicted secondary structure of the 327 5’ region identified four pairs of inverted repeats R1-R8 predicted to fold into stem-loops, a small leader peptide [MTASMRLR, (Mef(E)L)] required for macrolide induction and a Rho-independent transcription terminator. RNA-seq analyses provided confirmation of transcriptional attenuation. In addition, expression of mef(E)L was also influenced by mef(E)L-dependent mRNA stability. The regulatory region 5’ of mef(E) was highly conserved in other mef/mel(msr)-containing elements including Tn1207.1 and the 5612IQ complex in pneumococci and Tn1207.3 in Group A streptococci, indicating a regulatory mechanism common to a wide variety of Gram-positive bacteria containing mef/mel(msr) elements.
On the overconsumption of food portions : is the problem in the size or the number?

While larger food portions lead to greater consumption, the effect appears to be greater when the larger food portions are created by increasing the size of food units than when created by increasing the number of food units making up the portion. Study 1 shows consumer estimates of food quantities are more sensitive to unit-number information (i.e., the number of units) and less sensitive to unit-size information (i.e., the size of food units). Estimates of the food quantity presented in a portion size are larger when the portion is presented as many, smaller units than when presented as few, larger units. Study 2 demonstrates that participants tend to consume less when a portion is presented as more, smaller units vs. few, larger units. This result along with that of Study 1 suggest the portion-size effect on consumption is inversely related to the portion-size effect on quantity perceptions. When consumers are induced to focus on unit-size rather than unit-number (Study 3), quantity estimates can be made more sensitive to unit-size manipulations. Study 4 extends this finding to show that the portion-size effect on consumption is greatest when quantity estimation is insensitive to portion size change, and mitigated when information focus encourages processing of the relevant information.
p-ISOMAP: An Efficient Parametric Update for ISOMAP for Visual Analytics

One of the most widely-used nonlinear data embedding methods is ISOMAP. Based on a manifold learning framework, ISOMAP has a parameter k or ǫ that controls how many edges a neighborhood graph has. However, a suitable parameter value is often difficult to determine because of a time-consuming optimization process based on certain criteria, which may not be clearly justified. When ISOMAP is used to visualize data, users might want to test different parameter values in order to gain various insights about data, but such interaction between humans and such visualizations requires reasonably efficient updating, even for large-scale data. To tackle these problems, we propose an efficient updating algorithm for ISOMAP with parameter changes, called p-ISOMAP. We present not only a complexity analysis but also an empirical running time comparison, which show the advantage of p-ISOMAP. We also show interesting visualization applications of p-ISOMAP and demonstrate how to discover various characteristics of data through visualizations using different parameter values.
RUN-LENGTH ENCODING FOR VOLUMETRIC TEXTURE

With the dramatic increase of 3D imaging techniques, there is a great demand for new approaches in texture analysis of volumetric data. In this paper, we present a new approach for volumetric texture analysis using a runlength encoding matrix and its texture descriptors. We experiment with our approach on the volumetric data generated from two normal Computed Tomography (CT) studies of the chest and abdomen. Our preliminary results show that there are run-length features calculated from the volumetric run-length matrix that are capable of capturing the texture primitives’ properties for different structures in 3D image data, such as the homogeneous text ure structure of the liver.
The centrality of expressive indices

Abstract 1. Introduction Without exception, the commentaries on my paper help further develop and refine the theory of expressives. They approach the expressive dimension from diverse theoretical perspectives, and they leave us with important new data. There is not space in this reply to do justice to all the points raised, so I instead highlight and reexamine the main themes.
Identification and Characterization of σS, a Novel Component of the Staphylococcus aureus Stress and Virulence Responses

S. aureus is a highly successful pathogen that is speculated to be the most common cause of human disease. The progression of disease in S. aureus is subject to multi-factorial regulation, in response to the environments encountered during growth. This adaptive nature is thought to be central to pathogenesis, and is the result of multiple regulatory mechanisms employed in gene regulation. In this work we describe the existence of a novel S. aureus regulator, an as yet uncharacterized ECF-sigma factor (σS), that appears to be an important component of the stress and pathogenic responses of this organism. Using biochemical approaches we have shown that σS is able to associates with core-RNAP, and initiate transcription from its own coding region. Using a mutant strain we determined that σS is important for S. aureus survival during starvation, extended exposure to elevated growth temperatures, and Triton X-100 induced lysis. Coculture studies reveal that a σS mutant is significantly outcompeted by its parental strain, which is only exacerbated during prolonged growth (7 days), or in the presence of stressor compounds. Interestingly, transcriptional analysis determined that under standard conditions, S. aureus SH1000 does not initiate expression of sigS. Assays performed hourly for 72h revealed expression in typically background ranges. Analysis of a potential anti-sigma factor, encoded downstream of sigS, revealed it to have no obvious role in the upregulation of sigS expression. Using a murine model of septic arthritis, sigS-mutant infected animals lost significantly less weight, developed septic arthritis at significantly lower levels, and had increased survival rates. Studies of mounted immune responses reveal that sigS-mutant infected animals had significantly lower levels of IL-6, indicating only a weak immunological response. Finally, strains of S. aureus lacking sigS were far less able to undergo systemic dissemination, as determined by bacterial loads in the kidneys of infected animals. These results establish that σS is an important component in S. aureus fitness, and in its adaptation to stress. Additionally it appears to have a significant role in its pathogenic nature, and likely represents a key component in the S. aureus regulatory network.
FSHB promoter polymorphism within evolutionary conserved element is associated with serum FSH level in men

BACKGROUND No polymorphisms affecting serum FSH levels have been described in the human FSHB gene. We have identified a potential regulatory single nucleotide polymorphism (SNP, rs10835638; G/T) 211 bp upstream from the FSHB mRNA transcription start-site, located within a highly conserved region among placental mammals. We aimed to determine the correlation of carrier status of rs10835638 alternative alleles with serum FSH level in men, and testicular and hormonal parameters. METHODS A quantitative genetic association study using a cohort of healthy men (n = 554; age 19.2 ± 1.7 years) visiting the Centre of Andrology, Tartu University Hospital, Estonia. RESULTS Rs10835638 (allele frequencies: G 87.6%, T 12.4%) was significantly associated with serum FSH level (analysis of variance: F = 13.0, P = 0.0016, df = 1; regression testing for a linear trend: P = 0.0003). Subjects with the GG genotype exhibited higher FSH levels (3.37 ± 1.79 IU/l, n = 423) compared with heterozygotes (2.84 ± 1.54 IU/l, n = 125) (P = 0.0005), the group of T-allele carriers (GT+TT, 2.78 ± 1.51 IU/l, n = 131) (P = 0.0005) and TT-homozygotes (2.02 ± 0.81 IU/L, n = 6) (P = 0.031). Rs10835638 was also associated with significant (P < 0.05) reduction in free testosterone index and testes volume, but increased semen volume, sex hormone-binding globulin, serum testosterone and estradiol. LH and inhibin-B levels did not differ significantly between groups. CONCLUSIONS The identification of a regulatory SNP in FSHB promoter paves the way to study the effect of constitutively low FSH on male health and fertility. As FSH contributes to follicular development and sex steroid production in women, the role of this FSHB variant in female reproductive success is still to be addressed.
Comparison of plain potassium hydroxide mounts, fungal cultures and nail plate biopsies in the diagnosis of onychomycosis.

OBJECTIVE To compare the relative sensitivity of direct microscopy, fungal culture and nail plate biopsy in the diagnosis of onychomycosis. DESIGN Cross-sectional study. PLACE AND DURATION OF STUDY The Skin Department, Military Hospital, Rawalpindi from February 1998 to February 1999. PATIENTS AND METHODS A total of 50 patients who were suffering from different clinical variants of onychomycosis, irrespective of their age, gender, with or without simultaneous presence of systemic diseases, were subjected to laboratory investigations including direct microscopy with 20% potassium hydroxide (KOH) for fungal hyphae, fungal cultures and nail plate biopsies. These patients were later categorized into two groups based upon the results of nail plate biopsies. RESULTS Of 50 patients, 15 (30%) were positive for fungal elements in direct microscopy, 8 (16%) were positive for fungal culture and 16 (32%) revealed positive results in nail plate biopsies. Amongst nail plate biopsy positive cases, 10 (63%) were positive for direct microscopy and 6 (37.5%) were positive for fungal cultures. In biopsy negative cases, positive results for direct microscopy were seen in 5 (14.7%) patients and positive fungal culture was found in 2 (5.88%) patients. CONCLUSION The clinical impression of onychomycosis is not true in all the cases. Nail scraping for direct microscopy with 20% KOH should be the first line screening test for all patients which should then be supplemented with fungal culture and/ or nail plate biopsy.
Pay‐Back‐Revenue‐Sharing Contract in Coordinating Supply Chains with Random Yield

We consider coordination issues in supply chains where supplier's production process is subject to random yield losses. For a simple supply chain with a single supplier and retailer facing deterministic demand, a pay back contract which has the retailer paying a discount price for the supplier's excess units can provide the right incentive for the supplier to increase his production size and achieve coordination. Building upon this result, we consider coordination issues for two other supply chains: one with competing retailers, the other with stochastic demand. When retailers compete for both demand and supply, they tend to over‐order. We show that a combination of a pay back and revenue sharing mechanism can coordinate the supply chain, with the pay back mechanism correcting the supplier's under‐producing problem and the revenue sharing mechanism correcting the retailers' over‐ordering problem. When demand is stochastic, we consider a modified pay‐back‐revenue‐sharing contract under which the retailer agrees to not only purchase the supplier's excess output (beyond the retailer's order), but also share with the supplier a portion of the revenue made from the sales of the excess output. We show that this contract, by giving the supplier additional incentives in the form of revenue share, can achieve coordination.