Miracle-dz/UniFAR-FTUs huggingface dataset:
Upregulation of transmembrane 4 L6 family member 1 predicts poor prognosis in invasive breast cancer

Abstract Transmembrane 4 L6 family member 1 (TM4SF1) belongs to the 4-transmembrane-domain family and functions as an oncogene in multiple human cancers. In this work, we aim to determine TM4SF1 expression and its prognostic impact on patients with invasive breast cancer. Overall, we enrolled 209 invasive breast cancer patients and immunohistochemically examined the expression of TM4SF1 in tumor specimens. The relationship between TM4SF1 expression and clinicopathological parameter and patient survival of breast cancer patients was analyzed. Among the 209 cases, 137 (65.6%) exhibited high expression of TM4SF1. High TM4SF1 expression was significantly associated with advanced histological grade and negative estrogen receptor and progesterone receptor status. Triple-negative breast cancer (TNBC) tumors were more likely to express high levels of TM4SF1 than non-TNBC cases. Patients with high tumoral expression of TM4SF1 had a significantly shorter disease-free survival (DFS; P = .00) and overall survival (OS; P = .01) than those with low expression of TM4SF1. When survival analysis was restricted to the 167 patients (79.9%) receiving adjuvant chemotherapy, TM4SF1 expression was also correlated with poorer DFS and OS (P = .00). In multiple Cox regression analysis TM4SF1 expression remained an independent prognostic indicator for OS and DFS. TM4SF1 is upregulated and serves as an independent poor prognostic indicator in invasive breast cancer.
Structural Class Classification of 3D Protein Structure Based on Multi-View 2D Images

Computing similarity or dissimilarity between protein structures is an important task in structural biology. A conventional method to compute protein structure dissimilarity requires structural alignment of the proteins. However, defining one best alignment is difficult, especially when the structures are very different. In this paper, we propose a new similarity measure for protein structure comparisons using a set of multi-view 2D images of 3D protein structures. In this approach, each protein structure is represented by a subspace from the image set. The similarity between two protein structures is then characterized by the canonical angles between the two subspaces. The primary advantage of our method is that precise alignment is not needed. We employed Grassmann Discriminant Analysis (GDA) as the subspace-based learning in the classification framework. We applied our method for the classification problem of seven SCOP structural classes of protein 3D structures. The proposed method outperformed the k-nearest neighbor method (k-NN) based on conventional alignment-based methods CE, FATCAT, and TM-align. Our method was also applied to the classification of SCOP folds of membrane proteins, where the proposed method could recognize the fold HEM-binding four-helical bundle (f.21) much better than TM-Align.
A novel microRNAs expression signature for hepatocellular carcinoma diagnosis and prognosis

This study aims to identify prognostic microRNAs (miRNAs) biomarkers for diagnosis and survival of hepatocellular carcinoma (HCC) based on large patients cohort analysis. HCC patient cohort data were downloaded from The Cancer Genome Atlas, including paired HCC and adjacent non-cancer tissues. Receiver operating characteristic curve method was used to classify cancer and non-cancer tissues according to microRNAs expression levels. The aberrant microRNAs expression level were ranked and risked for building a prognostic miRNAs signature model. Kaplan–Meier survival was used to analyze the differences among various risk factors in accordance with miRNAs ranking scores. The study showed 33-miRNA signature, 11 were down-regulated and 22 were up-regulated through comparison between cancer samples and non-cancer samples. The maximum correct classification rate is up to 98.7%. Five microRNAs, hsa-mir-3677, hsa-mir-421, hsa-mir-326, hsa-mir-424 and hsa-mir-511-2, significantly correlated with patient survival. The survival rate and time negatively associated with lowering miRNAs index. In the low risk group, over 70% patients showed 5 years survival, while none patients survived longer than 5 years in the high risk group. MiR-424, miR-326 and miR-511 could be applied for HCC diagnostic biomarkers. These five miRNAs were significantly associated with lysosome pathway and D-Glutamine and D-glutamate metabolism pathway via Kyoto Encyclopedia of Genes and Genomes pathway analysis and Gene Ontology annotation. Conclusively, the five miRNAs expression signature could be used as HCC prognostic and diagnostic biomarkers.
Long-term metabolic cage housing increases anxiety/depression-related behaviours in adult male rats

Abstract There are several reports on unfavourable effects of metabolic cage housing on animal welfare mainly due to the characteristic structures of these cages such as single housing and grid flooring. This study was aimed to compare the effects of long-term metabolic cage housing and conventional housing (normal grouped housing in standard cages) on the anxiety/depression-like behaviours in male rats. Anxiety/depression-related behaviours were evaluated by use of forced swimming test and open field test. Swimming and climbing were significantly lower and immobility duration higher in the metabolic cage group. In the open field test, total distance, mean velocity, time spent in the central area, zone transition, grooming, and rearing scores were significantly lower in the metabolic cage. Moreover, serum corticosterone level was higher in the metabolic cage group. The results of the study indicate that long-term metabolic cage housing may cause an increase in the anxiety- and depression-related behaviours in male rats.
Differential Effects of Parental “drug talk” Styles and Family Communication Environments on Adolescent Substance Use

ABSTRACT The current study examines the relationships among adolescent reports of parent–adolescent drug talk styles, family communication environments (e.g., expressiveness, structural traditionalism, and conflict avoidance), and adolescent substance use. ANCOVAs revealed that the 9th grade adolescents (N = 718) engaged in four styles of “drug talks” with parents (e.g., situated direct, ongoing direct, situated indirect, and ongoing indirect style) and these styles differed in their effect on adolescent substance use. Multiple regression analyses showed that expressiveness and structural traditionalism were negatively related to adolescent substance use, whereas conflict avoidance was positively associated with substance use. When controlling for family communication environments and gender, adolescents with an ongoing indirect style reported the lowest use of substance. The findings suggest implications and future directions for theory and practice.
Effects of a Split Keyboard Design and Wrist Rest on Performance, Posture, and Comfort

The purpose of this study was to examine differences in experienced typists′ performance, posture, and musculoskeletal pain when using a split, adjustable (SA) computer keyboard and when using a standard flat keyboard. In addition, the use of a wrist rest was examined for performance, posture, and musculoskeletal pain effects. Eighteen participants were exposed to the SA keyboard and a flat keyboard in a laboratory study of text typing for four consecutive hours on five days. The results indicated that after just 2 h of orientation and practice, the participants could perform as well on the SA keyboard as on the flat keyboard. The SA keyboard provided advantages for reduced wrist/hand pronation. There was no difference between the keyboards in the level of musculoskeletal pain reported by participants after typing. However, they reported increased pain in the back, neck, shoulders, and wrists from the beginning to the end of each of the experimental periods for both keyboards
Effect of two different commercially available white light LED fixtures on broiler hatchability and chick quality

ABSTRACT 1. The objective of this study was to evaluate the effect of two different spectra of white light on hatchability and chick quality of broiler chickens. 2. A total of 8424 Ross 708 broiler eggs were divided over three light exposure treatments during incubation: No light (DARK), a light emitting diode (LED) light with high levels of blue light (BLUE), or a LED light with high levels of red light (RED). Hatchability, embryo mortality and chick quality were assessed at hatch. 3. DARK had a higher percentage of chicks with unhealed navels (21.1 ± 1.3%) and fewer overall chicks with no defects (77.0 ± 1.2%) compared to both the BLUE (9.9 ± 0.9% and 88.4 ± 1.1%) and RED treatments (7.7 ± 0.8% and 90.2 ± 1.0%). 4. Both the BLUE (80.9 ± 1.0%) and RED treatments (82.9 ± 1.4%) had higher hatchability of fertile eggs than the DARK treatment (76.0 ± 2.2%). 5. These results indicate that either of these LED fixtures could be used to improve hatchability and chick quality in broiler chickens. Utilising these types of lightings in commercial hatcheries will improve the efficiency via increased hatchability and quality of the chicks hatched.
Polylogarithmic Approximation for Minimum Planarization (Almost)

In the minimum planarization} problem, given some n-vertex graph, the goal is to find a set of vertices of minimum cardinality whose removal leaves a planar graph. This is a fundamental problem in topological graph theory. We present a \log^{O(1)} n-approximation algorithm for this problem on general graphs with running time n^{O(\log n/\log\log n)}. We also obtain a O(n^&#x2265;)-approximation with running time n^{O(1/&#x2265;)} for any arbitrarily small constant &#x2265; 0. Prior to our work, no non-trivial algorithm was known for this problem on general graphs, and the best known result even on graphs of bounded degree was a n^{&#x03A9;(1)}-approximation \cite{chekuri2013approximation}. As an immediate corollary, we also obtain improved approximation algorithms for the crossing number problem on graphs of bounded degree. Specifically, we obtain O(n^{1/2+&#x2265;})-approximation and n^{1/2} \log^{O(1)} n-approximation algorithms in time n^{O(1/&#x2265;)} and n^{O(\log n/\log\log n)} respectively. The previously best-known result was a polynomial-time n^{9/10}\log^{O(1)} n-approximation algorithm \cite{DBLP:conf/stoc/Chuzhoy11}. Our algorithm introduces several new tools including an efficient grid-minor construction for apex graphs, and a new method for computing irrelevant vertices. Analogues of these tools were previously available only for exact algorithms. Our work gives efficient implementations of these ideas in the setting of approximation algorithms, which could be of independent interest.
Proximal Femoral Nail Antirotation in Treatment of Intertrochanteric Hip Fractures: a Retrospective Study in 113 Patients

Introduction: The best treatment for intertrochanteric fractures remains controversial. Many methods have been recommended. Aim: We aimed to assess the results of osteosynthesis using the Proximal Femoral Nail Antirotation (PFNA) system. Patients and Methods: We retrospectively analyzed 113 consecutive patients with intertrochanteric fractures treated with PFNA. Fractures were classified in accordance with the AO/OTA classification system into the groups A1, A2 and A3. The postoperative quality of fracture reduction was described as good, acceptable or poor. The location of the blade within the head was recorded as per the Cleveland method. Tip-apex distance (TAD) was used as a method for evaluating screw position. Pre-fracture and postoperative functional level were evaluated by the new mobility score (NMS). Results: The average age at the time of surgery was 75.9 years. The majority, 75 (66.3 %), were unstable fracture types. The reduction was good in 67 (61.4 %) cases. Of the 24 deaths, 19 patients had comorbidities (p < 0.001). The number of deaths in the first 6 months was significantly higher than in the next 6 months (p = 0.001). The mean TAD was 25.6 mm. The Cleveland zone centre-centre was the most common placement of the blade, accounting for 33 (29 %) of the cases. Reoperation was required in four patients. There were four patients with cut-out. The pre-facture mean value NMS was 8.6 (SD 1.1) and the postoperative mean value was 4.3 (SD 3.6). Conclusion: We concluded that PFNA offers biomechanical advantages, but the best position of the blade is still unknown.
Introduction to biosensors

Biosensors are nowadays ubiquitous in biomedical diagnosis as well as a wide range of other areas such as point-of-care monitoring of treatment and disease progression, environmental monitoring, food control, drug discovery, forensics and biomedical research. A wide range of techniques can be used for the development of biosensors. Their coupling with high-affinity biomolecules allows the sensitive and selective detection of a range of analytes. We give a general introduction to biosensors and biosensing technologies, including a brief historical overview, introducing key developments in the field and illustrating the breadth of biomolecular sensing strategies and the expansion of nanotechnological approaches that are now available.
Insulating and Thermally Conductive Composite Filled with Boron Nitride Particles

A new kind of thermally conductive composites reinforced by glass fibers with boron nitride (BN) as thermally conductive filler was prepared in heat press molding. Thermal conductivity of the composites was found to increase with increasing in filler content. But impact strength and flexural strength reach the top point, 385.05KJ/m2 and 912.6481MPa, with content of 50wt% and 20wt% respectively. The thermal conductivity of 0.8385 W/mK was obtained at 50wt% filler content. Experimental dates show that mixed matrix of epoxy (EP) and polyimide (PI) displays high thermal stability and can improve thermal stability compared to pure epoxy obviously at 50wt% PI content. Additionally, the obtained composites possess high surface resistivity and volume resistivity, which are suitable for substrate materials.
Agile Amulet: Real-Time Salient Object Detection with Contextual Attention

This paper proposes an Agile Aggregating Multi-Level feaTure framework (Agile Amulet) for salient object detection. The Agile Amulet builds on previous works to predict saliency maps using multi-level convolutional features. Compared to previous works, Agile Amulet employs some key innovations to improve training and testing speed while also increase prediction accuracy. More specifically, we first introduce a contextual attention module that can rapidly highlight most salient objects or regions with contextual pyramids. Thus, it effectively guides the learning of low-layer convolutional features and tells the backbone network where to look. The contextual attention module is a fully convolutional mechanism that simultaneously learns complementary features and predicts saliency scores at each pixel. In addition, we propose a novel method to aggregate multi-level deep convolutional features. As a result, we are able to use the integrated side-output features of pre-trained convolutional networks alone, which significantly reduces the model parameters leading to a model size of 67 MB, about half of Amulet. Compared to other deep learning based saliency methods, Agile Amulet is of much lighter-weight, runs faster (30 fps in real-time) and achieves higher performance on seven public benchmarks in terms of both quantitative and qualitative evaluation.
Permission Use Analysis for Vetting Undesirable Behaviors in Android Apps

The android platform adopts permissions to protect sensitive resources from untrusted apps. However, after permissions are granted by users at install time, apps could use these permissions (sensitive resources) with no further restrictions. Thus, recent years have witnessed the explosion of undesirable behaviors in Android apps. An important part in the defense is the accurate analysis of Android apps. However, traditional syscall-based analysis techniques are not well-suited for Android, because they could not capture critical interactions between the application and the Android system. This paper presents VetDroid, a dynamic analysis platform for generally analyzing sensitive behaviors in Android apps from a novel permission use perspective. VetDroid proposes a systematic permission use analysis technique to effectively construct permission use behaviors, i.e., how applications use permissions to access (sensitive) system resources, and how these acquired permission-sensitive resources are further utilized by the application. With permission use behaviors, security analysts can easily examine the internal sensitive behaviors of an app. Using real-world Android malware, we show that VetDroid can clearly reconstruct fine-grained malicious behaviors to ease malware analysis. We further apply VetDroid to 1249 top free apps in Google Play. VetDroid can assist in finding more information leaks than TaintDroid, a state-of-the-art technique. In addition, we show how we can use VetDroid to analyze fine-grained causes of information leaks that TaintDroid cannot reveal. Finally, we show that VetDroid can help to identify subtle vulnerabilities in some (top free) applications otherwise hard to detect.
Varying Degrees of Temporoparietal Hypometabolism on FDG-PET Reveal Amyloid-Positive Logopenic Primary Progressive Aphasia is not a Homogeneous Clinical Entity.

BACKGROUND The logopenic variant of primary progressive aphasia (lvPPA) manifests due to a breakdown of the language network with prominent hypometabolism of the left temporoparietal region. LvPPA is strongly associated with amyloid deposition, yet there is question as to whether it is a homogeneous clinical entity. OBJECTIVE This study investigated whether differences in temporoparietal metabolic patterns on 18F fludeoxyglucose positron emission tomography (FDG-PET) could elucidate brain regions preferentially affected in lvPPA. METHOD We used differences in FDG-PET metabolic z-scores relative to controls for means of left lateral temporal, left inferior parietal, and left superior parietal regions to classify 53 amyloid-positive lvPPA patients into temporal, parietal, or temporoparietal predominate groups. Clinical features and FDG-PET regions of hypometabolism outside of the temporoparietal region were then compared across the three groups; the latter using statistical parametric mapping. RESULTS Of the 53 lvPPA patients, 15 were classified as temporal, 14 as temporoparietal, and 22 as parietal predominate. There were no significant differences between the groups on demographic measures, language evaluation, or apolipoprotein E genotype. Compared to the other two groups, individuals with the parietal predominate pattern had extensive hypometabolism in left frontal lobe and the precuneus. Furthermore, this group had greater behavioral dyscontrol and deficits in executive function, visuospatial skills, visual memory retention, working memory, and cognitive flexibility (Bonferronip < 0.05). CONCLUSIONS This study demonstrates that there is clinical heterogeneity within amyloid-positive lvPPA. Patients with lvPPA with predominant parietal hypometabolism, unlike those with temporal or temporoparietal predominant hypometabolism, demonstrated widespread cognitive and behavioral changes.
Routing aware space-time compressive sensing for Wireless Sensor Networks

As the size of Wireless Sensor Networks continues to grow, the amount of data for processing and transmitting becomes enormous. In many practical cases, the wireless sensors are distributed across a physical field to monitor physical phenomena with high space-time correlation. Compressive Sensing is a promising technique to exploit this correlation in order to limit the number of transmission and therefore increase the lifetime of the network. In this paper, we are interested in mesh network topology where the sink node is not in the range of sensors and routing schemes must be applied. We propose a joint Space-Time Compressive Sensing by exploiting jointly inter-sensor and intra-sensor data dependency. Since the routing and the number of retransmission affect significantly the total energy consumption, we introduce the routing in our cost function in order to optimize the selection of transmitting sensors. The simulations show that this method outperforms the existing ones and confirm the validity of our approach.
Rapid progression of a basal cell carcinoma after photodynamic therapy.

Photodynamic therapy (PDT) can be an effective treatment modality for actinic keratoses and some superficial and thin nodular basal cell carcinomas (BCCs). In PDT, a topical or intralesional photosensitizer accumulates in neoplastic cells and is then activated using one of a variety of light sources to generate reactive oxygen species that selectively destroy abnormal cells. Because of the broad therapeutic benefits of PDT, its application in the treatment of neoplastic and non-neoplastic disease is increasing. Although PDT is well tolerated, with minimal associated morbidity, awareness of all potential risks is imperative. We herein report the first case of rapid progression of BCC after PDT.
Age-Related Changes in a Human Cognitive Mapping System: Data from a Computer-Generated Environment

Two studies investigated age-related changes in human spatial cognition. In Study 1, younger and older adults searched computer-generated space, over several trials, for the location of a hidden target. Younger adults, but not older adults, quickly located the target and consistently returned to it. All the younger adults, but few of the older adults, reported using spatial relations among distal cues to navigate the space. In Study 2, young, middle-aged, and older adults performed the same task, but were provided with increased environmental support and pre-task training. The data pattern from Study 1 was replicated, with the performance of middle-aged adults falling between that of young and older adults. Although older adults in Study 2 reported less experience at completing computer-based tasks than did young and middle-aged adults, effects of this differential level of computer experience appeared to diminish over the course of experimental procedures (i.e., group differences that appeared on pre-task non-spatial practice trials were not apparent on a similar post-task trial). Age-related differences in spatial cognition persisted, however. Thus, the current data (a) suggest that a human cognitive mapping system changes over the lifespan, (b) suggest that computer-generated tasks can be sensitive to those changes, and (c) are consistent with a substantial literature investigating age-related changes in human and rodent spatial cognition.
Stochastic performance analysis of visual motion observer and experimental verifications

This paper analyzes an estimation performance of a vision-based observer, presented in one of the authors' antecessors, when a target object 3-D motion includes stochastic factors. We first formulate time evolution of the error between the actual object motion and its estimate, produced by the visual observer, as a stochastic differential equation (SDE) on SE(3). In order to evaluate the error, we first employ the notion of noise-to-state stability (NSS). By using the notion, it is shown that the error is bounded above in a probabilistic sense. However, the analysis remains qualitative and hence we do not explicitly know the bound. Thus, in order to reveal a quantitative property, we further analyze the estimation performance based on the notion of exponential ultimate boundedness in mean square. Finally, we demonstrate the validity of the results through experiment.
Accelerating Particle Filter on FPGA

Particle filters (PFs) are Bayesian based estimation algorithms with attractive theoretical properties for addressingwide range of complex applications that are nonlinear and nonGaussian. However, they are associated with a huge computational demand which limited their application in most realtime systems. To address such a drawback in PFs, this paper presents different approaches for PFs acceleration based on afield programmable gate arrays (FPGAs).