Miracle-dz/UniFAR-FTUs huggingface dataset:
Tumor‐associated macrophages correlate with response to epidermal growth factor receptor‐tyrosine kinase inhibitors in advanced non‐small cell lung cancer

Our study investigated whether tumor‐associated macrophages (TAMs) in advanced non‐small cell lung cancer (NSCLC) are related to treatment response to epidermal growth factor receptor‐tyrosine kinase inhibitors (EGFR‐TKIs) and may be a predictor of survival. Of 206 advanced NSCLC patients treated (first‐line) with an EGFR‐TKI at the study hospital from 2006 to 2009, 107 with adequate specimens for assessing CD68 immunohistochemistry as a marker of TAMs were assessed. After EGFR‐TKI treatment, response was observed in 55 (51%) patients, and the median follow‐up period was 13.5 months. Most TAMs were located in the tumor stroma (>95%) and positively costained with the M2 marker CD163. TAM counts were significantly higher in patients with progressive disease than in those without (p < 0.0001), a trend that remained in patients with known EGFR mutation status (n = 59) and those with wild‐type EGFR (n = 20). High TAM counts, among other factors (e.g., wild‐type EGFR), were significantly related to poor progression‐free survival (PFS) and overall survival (OS) (all p < 0.0001 for TAMs). Multivariate Cox analyses showed that high TAM counts and EGFR mutations were both independent factors associated with PFS [odds ratio (OR), 8.0; 95% confidence interval (CI), 2.87–22.4; p = 0.0001 and OR, 0.03; 95% CI, 0.003–0.31; p = 0.003, respectively] and OS (OR, 2.641; 95% CI, 1.08–6.5; p = 0.03 and OR, 0.14; 95% CI, 0.03–0.56; p = 0.006, respectively). TAMs are related to treatment response irrespective of EGFR mutation and can independently predict survival in advanced NSCLC treated with an EGFR‐TKI.
Transit Times and Rapid Chemical Equilibrium Explain Chemostasis in Glacial Meltwater Streams in the McMurdo Dry Valleys, Antarctica

Fluid transit time is understood to be an important control on the shape of concentration‐discharge (C‐q) relationships, yet empirical evidence supporting this linkage is limited. We investigated C‐q relationships for weathering‐derived solutes across seven Antarctic glacial meltwater streams. We hypothesized that (H1) solute fluxes in McMurdo Dry Valley streams are reaction limited so that C‐q relationships are characterized by dilution and that (H2) transit time explains between‐stream variability in the degree of C‐q dilution. Results show that C‐q relationships are chemostatic because solute equilibrium times are shorter than stream corridor fluid transit times. Between‐stream variability in the efficiency of solute production is positively correlated with transit time, suggesting that transit time is an important control on the solute export regime. These results provide empirical evidence for the controls on weathering‐derived C‐q relationships and have important implications for Antarctic ecosystems and solute export regimes of watersheds worldwide.
A lysine substitution in the ATP-binding site of eucaryotic initiation factor 4A abrogates nucleotide-binding activity

Eucaryotic initiation factor 4A (eIF-4A) is a member of a family of proteins believed to be involved in the ATP-dependent melting of RNA secondary structure. These proteins contain a derivative of the consensus ATP-binding site AXXGXGKT. To assess the importance of the consensus amino acid sequence in eIF-4A for ATP binding, we mutated the consensus amino-proximal glycine and lysine to isoleucine and asparagine, respectively. The effect of the mutations was examined by UV-induced cross-linking of [alpha-32P]dATP to eIF-4A. Mutation of the lysine residue (but not of the glycine residue) resulted in the loss of [alpha-32P]dATP cross-linking to eIF-4A, suggesting that the lysine is an important determinant in ATP binding to eIF-4A.
Approximately dual frames in Hilbert spaces and applications to Gabor frames

Approximately dual frames are studied in the Hilbert space setting. Approximate duals are easier to construct than classical dual frames, and can be tailored to yield almost perfect reconstruction. Bounds on the deviation from perfect reconstruction are obtained for approximately dual frames constructed via perturbation theory. An alternative bound is derived for the rich class of Gabor frames, by using the Walnut representation of the frame operator to estimate the deviation from equality in the duality conditions. To illustrate these results, we construct explicit approximate duals of Gabor frames generated by the Gaussian; these approximate duals yield almost perfect reconstruction. Surprisingly, the method applies also to certain Gabor frames that are far from being tight.
Platelet Function Predicts Myocardial Damage in Patients With Acute Myocardial Infarction

Background—Platelet activation is a hallmark of acute coronary syndromes. Numerous lines of evidence suggest a mechanistic link between von Willebrand factor or platelet hyperfunction and myocardial damage in patients with acute coronary syndromes. Thus, we assessed whether platelet function under high shear rates (collagen adenosine diphosphate closure times [CADP-CTs]) measured with the platelet function analyzer (PFA-100) may be enhanced in patients with myocardial infarction (MI) and whether it may predict the extent of myocardial damage as measured by creatine kinase (CK-MB) or troponin T (TnT) levels. Methods and Results—Patients with acute chest pain or symptoms suggestive of acute coronary syndromes (n=216) were prospectively examined at an emergency department. CADP-CT was significantly shorter in patients with MI, particularly in those with an ST-segment-elevation MI (STEMI) compared with the other patient groups (unstable angina, stable coronary artery disease, or controls). Furthermore, CADP-CT and collagen epinephrine–CT at presentation were independent predictors of myocardial damage as measured by CK-MB or TnT. Patients with MI whose CADP-CT values fell in the first quartile had 3-fold higher CK-MB and TnT levels than those in the fourth quartile. Conclusions—Patients with STEMI have significantly enhanced platelet function when measured under high shear rates. CADP-CT is an independent predictor of the severity of MI, as measured by markers of cardiac necrosis. Measurement of platelet function with the PFA-100 may help in the risk stratification of patients presenting with MI.
Remembrance of Cases Past: Who Remembers What, When Confronting Critical Flight Events?

Recent “naturalistic” theories of decision making emphasize the role of stored prior experiences or cases as a guide to current action. However, there is little empirical evidence on the role that case-based remindings play in real-life decision making. The present study utilized a Web-based survey to collect data about the role of prior cases in pilot decision making about critical flight events. Results showed that more than half of the 1081 pilots who responded could provide details about utilizing a previous case in responding to a critical flight event. These events were most likely to involve weather or equipment failure. The cases were found to be useful in situational assessment rather than option evaluation. The use of cases increased with age and experience. Data obtained from a concurrent conventional survey showed broadly similar results. The implications of these results are that case-based remindings play an important role in expert pilot decision making and that a training system that incorporates case-based learning would be a potentially useful means of improving pilot decision making. Actual or potential applications of this research include the development of case-based training systems to enhance flight training.
ON THE OCCURRENCE OF SEVENGILL AND SIXGILL SHARKS (HEXANCHIFORMES: HEXANCHIDAE) OFF CEARÁ STATE, BRAZIL, WESTERN EqUATORIAL ATLANTIC

This study reports the first occurrence of Hexanchiformes sharks off Ceara State, Brazil. Captures of sharks of this order were recorded during research cruises and surveillance of landings from small-scale and commercial fisheries, making up thirteen individuals out of a total of 1,937. The sampling effort covered an area corresponding with the continental shelf and upper slope, in depths from 10 to 350 meters. These are the first data gathered on the occurrence of sharks in the mesopelagic zone of Ceara State. This study extends the known distribution range of hexanchiformes in Brazil. The observed depth stratification pattern of hexanchiform shark occurrences off Ceara State underscores the need for thorough deep-sea research surveys in order to obtain a more complete assessment of the region’s elasmobranch fauna.
Is All Face Processing Holistic ?

There has been a great deal of progress, as well as controversy, in understanding how complex objects, in particular, human faces, are processed by the cortex. At the same time, sophisticated neural network models have been developed that do many of the same tasks required by these cortical areas. Such simplifying models allow us to explore hypotheses concerning relatively complex domains such as face processing. In this chapter, we give a somewhat idiosyncratic history of the development of neural network models of face processing, concentrating on work at UCSD, and show how these models have led to a novel hypothesis concerning processing of facial expression. While our models have suggested a role for holistic representations of faces in identi cation, general local features appear to be important in recognition of expression. Is all face processing holistic? 3
Exploring brain network oscillations during seizures in drug-naïve patients with juvenile absence epilepsy

Objective We aimed to investigate the brain network activity during seizures in patients with untreated juvenile absence epilepsy. Methods Thirty-six juvenile absence epilepsy (JAE) patients with a current high frequency of seizures (more than five seizures during a 2 h EEG examination) were included. Each participant underwent a 2 h video EEG examination. Five 10 s EEG epochs for inter-ictal, pre-ictal, and post-ictal, and five 5 s EEG epochs for ictal states were extracted. Five 10 s resting-state EEG epochs for each participant from a sex- and age-matched healthy control (HC) were enrolled. The topological parameters of the brain networks were calculated using a graph theory analysis. Results Compared with the resting state of the HC group, the global efficiency, local efficiency, and clustering coefficients of the JAE group decreased in the inter-ictal state. In addition, the ictal state showed significantly increased global and local efficiency and clustering coefficients (p < 0.05) and a decreased small-world index and the shortest path length (p < 0.05) in the theta and alpha bands, compared to the remaining states within the JAE group. Moreover, subgroup analysis revealed that those JAE patients with typical 3 Hz discharges had upgraded global efficiency, local efficiency, and clustering coefficients in both delta and beta1 bands, compared to those JAE patients with non-3 Hz discharges during seizures. Conclusion The present study supported the idea that the changes in the EEG brain networks in JAE patients are characterized by decreased global and local efficiency and clustering coefficient in the alpha band. Moreover, the onset of seizures is accompanied by excessively enhanced network efficiency. JAE patients with different ictal discharge patterns may have different functional network oscillations.
Effects of pCO2 and iron on the elemental composition and cell geometry of the marine diatom Pseudo‐nitzschia pseudodelicatissima (Bacillariophyceae)1

Partial pressure of CO2 (pCO2) and iron availability in seawater show corresponding changes due to biological and anthropogenic activities. The simultaneous change in these factors precludes an understanding of their independent effects on the ecophysiology of phytoplankton. In addition, there is a lack of data regarding the interactive effects of these factors on phytoplankton cellular stoichiometry, which is a key driving factor for the biogeochemical cycling of oceanic nutrients. Here, we investigated the effects of pCO2 and iron availability on the elemental composition (C, N, P, and Si) of the diatom Pseudo‐nitzschia pseudodelicatissima (Hasle) Hasle by dilute batch cultures under 4 pCO2 (~200, ~380, ~600, and ~800 μatm) and five dissolved inorganic iron (Fe′; ~5, ~10, ~20, ~50, and ~100 pmol · L−1) conditions. Our experimental procedure successfully overcame the problems associated with simultaneous changes in pCO2 and Fe′ by independently manipulating carbonate chemistry and iron speciation, which allowed us to evaluate the individual effects of pCO2 and iron availability. We found that the C:N ratio decreased significantly only with an increase in Fe′, whereas the C:P ratio increased significantly only with an increase in pCO2. Both Si:C and Si:N ratios decreased with increasing pCO2 and Fe′. Our results indicate that changes in pCO2 and iron availability could influence the biogeochemical cycling of nutrients in future oceans with high‐ CO2 levels, and, similarly, during the time course of phytoplankton blooms. Moreover, pCO2 and iron availability may also have affected oceanic nutrient biogeochemistry in the past, as these conditions have changed markedly over the Earth's history.
CAD-HOC: a CAD-Like tool for generating mobility benchmarks in ad-hoc networks

The paper addresses the problem of using unrealistic mobility scenarios for simulation of ad-hoc routing protocols. We present CAD-HOC, a cousin tool to Network Simulator (ns), which allows ad-hoc networking experimentation to be performed under visually realistic scenarios such as an airport or a bus terminal, buildings, highways and other facilities. CAD-HOC focuses on capturing the visual scenario and transforming it into mobility and connection benchmarks, which are subsequently fed to ns to drive simulation experiments. Generation of mobility and connection benchmarks is facilitated by allowing the users to choose from Brownian, Column, Pursue, and Nomadic models, or to specify user-defined movements. The tool also provides online analyses on ad-hoc mobility, ad-hoc connectivity and message complexity, which give an estimate of the overall ns simulation complexity, as the mobility scenario is built. Comparative simulation based on CAD-HOC generated scenarios raise several questions about the reliability of ns simulation results of ad-hoc routing protocols based on random, nonrealistic scenarios.
Stromal cell‐derived factor‐1/CXCR4 promotes IL‐6 production in human synovial fibroblasts

The production of chemokine stromal cell‐derived factor (SDF)‐1 is significantly higher in synovial fluid of patients with osteoarthritis (OA). IL‐6 is a multifunctional cytokine that plays a central role in both OA and rheumatoid arthritis. However, the effects of SDF‐1α on human synovial fibroblasts are largely unknown. In this study, we investigated the intracellular signaling pathway involved in SDF‐1α‐induced IL‐6 production in human synovial fibroblast cells. SDF‐1α caused concentration‐ and time‐dependent increases in IL‐6 production. SDF‐1α also increased the mRNA and surface expression of CXCR4 receptor in human synovial fibroblasts. CXCR4‐neutralizing antibody, CXCR4‐specific inhibitor (AMD3100), or small interfering RNA against CXCR4 inhibited the SDF‐1α‐induced increase of IL‐6 expression. The transcriptional regulation of IL‐6 by SDF‐1α was mediated by phosphorylation of phosphatidylinositol 3‐kinase (PI3K)/Akt and activation of the activator protein (AP)‐1 component of c‐Jun. The binding of c‐Jun to the AP‐1 element on the IL‐6 promoter and the increase in AP‐1 luciferase activity was enhanced by SDF‐1α. Co‐transfection with CXCR4, PI3K, Akt, and c‐Jun mutants or siRNA inhibited the potentiating action of SDF‐1α on AP‐1 promoter activity. Taken together, our results suggest that SDF‐1α‐increased IL‐6 production in human synovial fibroblasts via the CXCR4 receptor, PI3K, Akt, c‐Jun, and AP‐1 signaling pathways. J. Cell. Biochem. 112: 1219–1227, 2011. © 2011 Wiley‐Liss, Inc.
The pressure disturbance of a nonlinear internal wave train

Observations from a lander fixed to the seafloor over the continental shelf in 124 m of water provide highly resolved velocity measurements through nonlinear internal waves of elevation. From these measurements we determine, for the first time, the non-hydrostatic pressure disturbance ($p_{nh}$) in nonlinear internal waves. For near-bottom waves of elevation ranging in amplitude, $a$, from 12 to 33 m, the value of $p_{nh}$ evaluated at the seafloor changes sign from $\,{>}\,0$ to $\,{<}\,0$ and back in accordance with weakly nonlinear theory; peak values of $\vert p_{nh}\vert$ range from 25 to 90 N m$^{-2}$. The external hydrostatic pressure disturbance due to the surface displacement ($\eta_H$) is inferred from horizontal accelerations. For elevation waves, $\eta_H\,{<}\,0$; peak values range from 0.1 to 9 mm (1 to 90 N m$^{-2}$). The internal hydrostatic pressure perturbation ($p_{Wh}$), caused by isopycnal displacement, is inferred from measured streamlines and an ambient density profile. Its value at the seafloor is $\,{>}\,0$ for elevation waves; peak values range from 100 to 300 N m$^{-2}$. $\vert\eta_H\vert$ and seafloor values of $\vert p_{nh}\vert$, $p_{Wh}$ all increase monotonically with $a$. Since $\vert p_{nh}\vert$ and $p_{Wh}$ increase at roughly the same rate with $a$, no clear trend arises in the degree to which waves become more or less non-hydrostatic as $a$ changes. A distinct bottom pressure signature is determined for bottom-trapped nonlinear waves of elevation, a wave train consisting of a sequence of positive pressure perturbations (dominated by $p_{Wh}$). By inference, a train of surface-trapped nonlinear internal waves of depression will consist of a sequence of negative pressure perturbations. A result of this analysis is that significant properties of the waves can be discerned from a simple adequately resolved bottom pressure measurement.
Using Chunked Extendible Array for Physical Storage of Scientific Datasets

The data model found to be most appropriate for scientific databases is the array-oriented data model. This also forms the basis of storing and accessing the database onto and from physical storage. Such storage systems are exemplified by the hierarchical data format(HDF/HDF5), the network common data format (NetCDF) and recently the SciDB. Given that the array is mapped onto linear locations in a file, i.e., a representation of an array file, in either row-major or column-major order, a fundamental feature of the representation is that they should be allowed to grow to massively large sizes by gradual expansions of the array bounds. In both the row-major and column-major order of array elements, extendibility is allowed in one dimension only. We present an approach of storing multi-dimensional dense array on physical storage devices, that allows arbitrary extensions of any of the array bounds, without reorganising previously allocated array elements. For a k-dimensional N-element array, the organisation allows an element to be accessed in time O(k +log N) using O(k2N1/k) additional space. By chunking the array to size Noc chunks, the time and space requirements reduce to O(k + log Noc) and O(k2Nc1/k ).
Increasing Availability of Exposure Therapy Through Intensive Group Treatment for Childhood Anxiety and OCD

Archival data were used to examine the feasibility of a 5-day, clinic-based, intensive exposure–based cognitive-behavioral group therapy for childhood anxiety disorders (CADs) and obsessive-compulsive disorder (OCD). Participants were 143 children (82 girls) aged 6 to 19 years (M = 13.93 years, SD = 2.9 years) with CADs or OCD (or both) in 28 consecutive groups. Repeated-measures ANOVA in the subsample (n = 57) with complete treatment data indicated positive change on all variables from pretreatment to posttreatment with few differences between CADs and OCD patients. Effect sizes were moderate to large for anxiety symptoms (parent reported = 0.74, child reported = 0.65) and impairment (parent reported = 1.02, child reported = 0.69). The intensive group protocol required fewer sessions and 36% fewer therapist-hours per patient than the individually administered protocol. The program increased treatment availability for families from diverse geographic areas (M distance traveled to clinic = 407 miles, SD = 786.4 miles). These findings support further, well-controlled examination of the 5-day intensive group treatment protocol’s efficacy and potential to increase availability of evidence-based exposure therapy.
Finding a needle in a haystack of reviews: cold start context-based hotel recommender system

Online hotel searching is a daunting task due to the wealth of online information. Reviews written by other travelers replace the word-of-mouth, yet turn the search into a time consuming task. Users do not rate enough hotels to enable a collaborative filtering based recommendation. Thus, a cold start recommender system is needed. In this work we design a cold start hotel recommender system, which uses the text of the reviews as its main data. We define context groups based on reviews extracted from TripAdvisor.com and Venere.com. We introduce a novel weighted algorithm for text mining. Our algorithm imitates a user that favors reviews written with the same trip intent and from people of similar background (nationality) and with similar preferences for hotel aspects, which are our defined context groups. Our approach combines numerous elements, including unsupervised clustering to build a vocabulary for hotel aspects, semantic analysis to understand sentiment towards hotel features, and the profiling of intent and nationality groups. We implemented our system which was used by the public to conduct 150 trip planning experiments. We compare our solution to the top suggestions of the mentioned web services and show that users were, on average, 20% more satisfied with our hotel recommendations. We outperform these web services even more in cities where hotel prices are high.
Comparative Analysis of Cytomegalovirus Gastrointestinal Disease in Immunocompetent and Immunocompromised Patients

Background: Cytomegalovirus (CMV) gastrointestinal (GI) diseases impact both immunocompromised and immunocompetent individuals, yet comprehensive studies highlighting the differences between these groups are lacking. Methods: In this retrospective study (January 2000 to July 2022) of 401 patients with confirmed CMV GI diseases, we categorized them based on immunological status and compared manifestations, treatments, outcomes, and prognostic factors. Results: The immunocompromised patients (n = 193) showed older age, severe illnesses, and higher comorbidity rates. GI bleeding, the predominant manifestation, occurred more in the immunocompetent group (92.6% vs. 63.6%, p = 0.009). Despite longer antiviral therapy, the immunocompromised patients had higher in-hospital (32.2% vs. 18.9%, p = 0.034) and overall mortality rates (91.1% vs. 43.4%, p < 0.001). The independent factors influencing in-hospital mortality in the immunocompromised patients included GI bleeding (OR 5.782, 95% CI 1.257–26.599, p = 0.024) and antiviral therapy ≥ 14 days (OR 0.232, 95% CI 0.059–0.911, p = 0.036). In the immunocompetent patients, age (OR 1.08, 95% CI 1.006–1.159, p = 0.032), GI bleeding (OR 10.036, 95% CI 1.183–85.133, p = 0.035), and time to diagnosis (OR 1.029, 95% CI 1.004–1.055, p = 0.021) were significant prognostic factors, with the age and diagnosis time cut-offs for survival being 70 years and 31.5 days, respectively. Conclusions: GI bleeding is the most common manifestation and prognostic factor in both groups. Early diagnosis and effective antiviral therapy can significantly reduce in-hospital mortality.