Miracle-dz/UniFAR-FTUs huggingface dataset:
synergistic locoregional chemoradiotherapy using a composite liposome-in-gel system as an injectable drug depot

: The use of radiosensitizers in clinical radiotherapy is limited by systemic toxicity. The biopolymeric, biodegradable, injectable liposome-in-gel-paclitaxel (LG-PTX) system was developed for regional delivery of the radiosensitizer paclitaxel (PTX), and its efficacy was evaluated with concurrent fractionated radiation. LG-PTX is composed of nano-sized drug-loaded fluid-izing liposomes, which are incorporated into a porous biodegradable gellan hydrogel. This allows enhanced drug permeation while maintaining a localization of the drug depot. LG-PTX had an IC 50 of 325 ± 117 nM in B16F10 melanoma cells, and cytotoxicity with concurrent doses of fractionated radiation showed significant increase in apoptotic cells (75%) compared to radiation (39%) or LG-PTX (43%) alone. Peri-tumoral injection in tumor-bearing mice showed PTX localization in the tumor 2 hours after administration, with no drug detected in plasma or other organs. LG-PTX administration with doses of focal radiation (5 × 3 Gy) significantly reduced tumor volumes compared to control (6.4 times) and radiation alone (1.6 times) and improved animal survival. LG-PTX thus efficiently localizes the drug at the tumor site and synergistically enhances the effect of concurrent radiotherapy. This novel liposome-in-gel system can potentially be used as a platform technology for the delivery of radiosensitizing drugs to enhance the efficacy of chemoradiotherapy.
XL-AOF: lightweight aspects for space-based computing

Space-based computing is a powerful model of abstraction for distributed application development. Although such applications solve a high number of cross-cutting concerns, there is no aspect-oriented environment available at the moment which supports the space-based communication paradigm. This paper describes XL-AOF, an extensible lightweight aspect-oriented framework, whose main focus is to allow for easy development of space-based applications.
finite element model using a unified formulation for the analysis of viscoelastic sandwich laminates

Recognizing emotions in non-verbal audio tracks requires a deep understanding of their underlying features. Traditional classifiers relying on excitation, prosodic, and vocal traction features are not always capable of effectively generalizing across speakers’ genders. In the ComParE 2022 vocalisation sub-challenge we explore the use of a Transformer architecture trained on contrastive audio examples. We leverage augmented data to learn robust non-verbal emotion classifiers. We also investigate the impact of different audio transformations, including neural voice conversion, on the classifier capability to generalize across speakers’ genders. The empirical findings indicate that neural voice conversion is beneficial in the pretraining phase, yielding an improved model generality, whereas is harmful at the finetuning stage as hinders model specialization for the task of non-verbal emotion recognition.
Role of breastfeeding cessation in mediating the relationship between maternal HIV disease stage and increased child mortality among HIV-exposed uninfected children.

BACKGROUND Maternal CD4 count predicts child mortality in HIV-uninfected children born to HIV-infected women. METHODS To explore the mediating role of breastfeeding cessation in this relationship, we compared marginal structural models of maternal CD4 count on child death with and without adjustment for breastfeeding. RESULTS In crude analyses, children of mothers with CD4<200 during pregnancy were 3.2 times more likely to die by 18 months (CI 1.3-8.1) as children whose mothers had CD4>500. Earlier breastfeeding cessation was also associated with low CD4 (HR 1.8; CI 1.2-2.7). After adjusting for breastfeeding and low birth weight using a marginal structural model, the low CD4 count-child mortality association through 18 months was reduced 17%. The change was overestimated using a traditional Cox proportional hazards model (35% reduction in HR from 3.4 to 2.5). CONCLUSIONS Our analysis suggests that only a small part of the effect of low vs high CD4 count on child mortality through 18 months is mediated through breastfeeding cessation. Our results must be taken into account when deciding whether or not to recommend breastfeeding for infants of HIV-infected mothers.
Deep-SDM: A Uniﬁed Computational Framework for Sequential Data Modeling Using Deep Learning Models

: Deep-SDM is a uniﬁed layer framework built on TensorFlow/Keras and written in Python 3.12. The framework aligns with the modular engineering principles for the design and development strategy. Transparency, reproducibility, and recombinability are the framework’s primary design criteria. The platform can extract valuable insights from numerical and text data and utilize them to predict future values by implementing long short-term memory (LSTM), gated recurrent unit (GRU), and convolution neural network (CNN). Its end-to-end machine learning pipeline involves a sequence of tasks, including data exploration, input preparation, model construction, hyperparameter tuning, performance evaluations, visualization of results, and statistical analysis. The complete process is systematic and carefully organized, from data import to model selection, encapsulating it into a uniﬁed whole. The multiple subroutines work together to provide a user-friendly and conducive pipeline that is easy to use. We utilized the Deep-SDM framework to predict the Nepal Stock Exchange (NEPSE) index to validate its reproducibility and robustness and observed impressive results.
Palmitate-induced changes in

: Mitochondrial dysfunction has been associated with obesity-related muscle insulin resistance, but the causality of this association is controversial. The notion that mitochondrial oxidative capacity may be insufficient to deal appropriately with excessive nutrient loads is for example disputed. Effective mitochondrial capacity is indirectly, but largely determined by ATP-consuming processes because skeletal muscle energy metabolism is mostly controlled by ATP demand. Probing the bioenergetics of rat and human myoblasts in real time we show here that the saturated fatty acid palmitate lowers the rate and coupling efficiency of oxidative phosphorylation under conditions it causes insulin resistance. Stearate affects the bioenergetic parameters similarly, whereas oleate and linoleate tend to decrease the rate but not the efficiency of ATP synthesis. Importantly, we reveal that palmitate influences how oxidative ATP supply is used to fuel ATP-consuming processes. Direct measurement of newly made protein demonstrates that palmitate lowers the rate of de novo protein synthesis by more than 30%. The anticipated decrease of energy demand linked to protein synthesis is confirmed by attenuated cycloheximide-sensitivity of mitochondrial respiratory activity used to make ATP. This indirect measure of ATP turnover indicates that palmitate lowers ATP supply reserved for protein synthesis by at least 40%. This decrease is also provoked by stearate, oleate and linoleate, albeit to a lesser extent. Moreover, palmitate lowers ATP supply for sodium pump activity by 60-70% and, in human cells, decreases ATP supply for DNA/RNA synthesis by almost three-quarters. These novel fatty acid effects on energy expenditure inform the „mitochondrial insufficiency‟ debate.
Unsupervised pattern recognition: An introduction to the whys and wherefores of clustering microarray data

Clustering has become an integral part of microarray data analysis and interpretation. The algorithmic basis of clustering -- the application of unsupervised machine-learning techniques to identify the patterns inherent in a data set -- is well established. This review discusses the biological motivations for and applications of these techniques to integrating gene expression data with other biological information, such as functional annotation, promoter data and proteomic data.
Event-Oriented Focal Weight-Based Clustering for Environmental Wireless Sensor Networks

Recent trend to steer Wireless Sensor Networks towards a broad outdoor environment allows to monitor harsh areas and prevent a disaster situation. To guarantee an extensive work of the system and smooth cooperation among involved devices a new clustering approach needs to be found. In this paper, we present a new algorithm for an Event-oriented Focal Weight-based clustering for Wireless Sensor Network which will be able to monitor various parameters (physical, biological, and chemical) of the outdoor environment and signal the current situation further to the network. Shown results demonstrate the applicability of the algorithm for the large amount of nodes with various power levels. The use of a dual-band transceiver and advanced processing elements allow to accommodate new features in the nodes and guarantee a high performance with the low power consumption which is crucial for the outdoor system with no human attendance.
A global assessment of the oesophageal adenocarcinoma epidemic

Objective About 20 years ago, the scientific community was first alerted to an enigmatic increase of oesophageal adenocarcinomas in the UK and USA. Subsequently, a virtual epidemic—still unexplained—was confirmed in several western countries. Detailed descriptive data might provide clues to its causes. Design We collected data on incident cases of oesophageal adenocarcinoma from population-based cancer registries in Australia, Europe, North America and Asia. We calculated age-standardised incidence rates and fitted log-linear Poisson models to assess annual rate of increase and to disentangle age-period-cohort effects, linear spine models to estimate rate of increase since 1985, and Joinpoint models to identify possible inflection points. Results With considerable between-registry variation in magnitude and timing, we found a consistent dramatic increase in incidence with an observed or estimated start between 1960 and 1990. The average annual increase ranged from 3.5% in Scotland to 8.1% in Hawaii with similar proportional increase among men and women in most registries and a maintained three to sixfold higher incidence among men. Generally, calendar period was a more important determinant of incidence trends than birth cohort. Where possible to conduct, Joinpoint analyses indicated that the onset of the epidemic varied considerably even between neighbouring countries. Conclusions Given the preponderant period effect and the abrupt onset observed or inferred in most populations, the epidemic appears to be caused by some exposure that was first introduced around 1950. At least 30 years' variation in estimated time of onset opens prospects for hypothesis-generating ecological analyses.
Electronic questionnaires for measuring parent satisfaction and as a basis for quality improvement.

BACKGROUND Using paper questionnaires to measure quality of care from the perspective of the patient is a time consuming procedure resulting in very slow feedback. Response rates are low and patients who cannot read the local language are usually excluded. OBJECTIVE To investigate the applicability of an electronic questionnaire by evaluating the response rate. To study whether computer-based continuous monitoring could elucidate reasons for parents being less satisfied with care and treatment and to compare parent satisfaction with the results of a study performed in 2003. METHODS Parents were asked to assess the quality of care and treatment by answering questions on a touch-screen computer. The questions, which were translated into seven languages, corresponded to the indicators selected by the department for monitoring parents' satisfaction. The system was developed in cooperation with a software company. RESULTS A total of 780 parents answered (69%). Of these, 2% parents answered in a foreign language. The main reasons for being less satisfied were perceived difficulties in getting in contact with the staff, having experienced unnecessary long waiting time and having the impression that the nurses did not have enough time. Significant improvements in satisfaction had occurred as compared to a study from 2003. CONCLUSION By using electronic questionnaires, it was possible to focus on the small percentage of parents not satisfied, to identify reasons for being less satisfied and to respond immediately to the feedback from the parents. Electronic surveys produce a satisfactory response rates.
Gaussian ﬂuctuations of spatially inhomogeneous polymers

Inhomogeneous polymers, such as partially ligand-bound DNA or partially coﬁlin-bound actin ﬁlaments, play an important role in various cellular processes, both in nature and in biotechnological/therapeutic applications. At ﬁnite temperatures, inhomogeneous polymers exhibit non-trivial thermal ﬂuctuations. In a broader context, these are relatively simple examples for ﬂuctuations in spatially inhomogeneous systems, which are less understood compared to their homogeneous counterparts. Here we develop a statistical theory of torsional, extensional and bending Gaussian ﬂuctuations of inhomogeneous polymers (chains), where the inhomogeneity takes the form of an inclusion of variable size and mechanical properties, using both continuum and discrete approaches. First, we analytically calculate the complete eigenvalues and eigenmodes spectrum of the inhomogeneous polymer within a continuum ﬁeld theory. In particular, we show that the wavenumber inside and outside of the inclusion is nearly linear in the eigenvalue index, with a nontrivial coeﬃcient. Second, we solve the corresponding discrete problem, and highlight fundamental diﬀerences between the continuum and discrete spectra of eigenvalues/eigenmodes. In particular, we demonstrate that above a certain wavenumber the discrete spectrum changes qualitatively and discrete evanescent eigenmodes, that do not have continuum counterparts, emerge. The statistical thermodynamic implications of these diﬀerences are then explored by calculating ﬂuctuation-induced forces associated with free-energy variations with either the properties of the inclusion (e.g. inhomogeneity formed by adsorbing molecules) or with an external geometric constraint. The former, which is the ﬂuctuation-induced contribution to the adsorbing molecules binding force, is shown to be aﬀected by short wavelengths and thus cannot be calculated using the continuum approach. The latter, on the other hand, is shown to be dominated by long wavelength shape ﬂuctuations and hence is properly described by the continuum theory.
Mathematical Model of the Impulses Transformation Processes in Natural Neurons for Biologically Inspired Control Systems Development

One of the trends in the development of control systems for autonomous mobile robots is the approach of using neural networks with biologically plausible architecture. Formal neurons do not take into account some important properties of a biological neuron, which are necessary for this task. Namely a consideration of the dynamics of data changing in neural networks; difficulties in describing the structure of the network, which cannot be reduced to the known regular architectures; as well as difficulties in the implementation of biologically plausible learning algorithms for such networks. Existing neurophysiological models of neurons describe chemical processes occurring in a cell, which is too low level of abstraction. The paper proposes a neuron’s model, which is devoid of disadvantages described above. The feature of this model is description cell possibility with treestructured architecture dendrites. All functional changes are formed by modifying structural organization of membrane and synapses instead of parametric tuning. The paper also contains some examples of neural structures for motion control based on this model of a neuron and similar to biological structures of the peripheral nervous system.
First-Year Report of ARL Director’s Strategic Initiative (FY20 ‒ 23): Artificial Intelligence (AI) for Command and Control (C2) of Multi-Domain Operations (MDO)

14. ABSTRACT This report describes efforts conducted in fiscal year 2020 under the US Army Combat Capabilities Development Command Army Research Laboratory’s Director’s Strategic Initiative (DSI) project “Artificial Intelligence (AI) for Command and Control (C2) of Multi-Domain Operations (MDO)”. The speed and complexity of MDO against a near-peer adversary in hyperactive environments calls for high-speed decision-making and execution that may often exceed human cognitive ability. Recently, emerging AI techniques such as deep reinforcement learning (DRL) have outperformed human world champions in complex, relatively unstructured, partial-information, strategic games such as Dota 2 and StarCraft II. This suggests the potential of such AI to contribute to C2 of MDO. However, many questions about the behaviors and limits of such new AI techniques remain unanswered. As part of this DSI, we are investigating whether DRL might support future agile and adaptive C2 of multi-domain forces that would enable the commander and staff to exploit rapidly and effectively fleeting windows of superiority. In our first year, we have developed two novel C2 testbeds and DRL-based learning within these testbeds. This report includes an overview of the project and demonstrates preliminary research results where an “artificial commander” executes an integrated planning-execution process in a simulated brigade-scale battle.
Fog detection from camera images

Fog is one of the most dangerous weather types with more fatalities than winter storms. It is in the interest of general public that a precise, predictive and accurate fog density map with high spatial resolution can be created. Currently, the definition of fog as used by national weather services is so detailed and technical that the fog can be identified only at a few locations by means of the prescribed light scattering experiments. With the rising availability of cameras in public places such as airports, streets and highways, a large amount of data on the occurrence of fog becomes available to researchers. In this article we describe methods for determining not necessary only the existence of fog, but sometimes a visibility distance - a type of optical penetration length - as well. We will show that digital cameras can be a reliable alternative or complementary method for creating fog visibility maps when processing of image data is used.
ClearStamp: A Human-Visible and Robust Model-Ownership Proof based on Transposed Model Training

Due to costly efforts during data acquisition and model training, Deep Neural Networks (DNNs) belong to the intellectual property of the model creator. Hence, unauthorized use, theft, or modification may lead to legal repercussions. Existing DNN watermarking methods for ownership proof are often non-intuitive, embed human-invisible marks, require trust in algorithmic assessment that lacks human-understandable attributes, and rely on rigid thresholds, making it susceptible to failure in cases of partial watermark erasure. This paper introduces ClearStamp, the first DNN watermarking method designed for intuitive human assessment. ClearStamp embeds visible watermarks, enabling human decision-making without rigid value thresholds while allowing technology-assisted evaluations. ClearStamp defines a transposed model architecture allowing to use of the model in a backward fashion to interwove the watermark with the main task within all model parameters. Compared to existing watermarking methods, ClearStamp produces visual watermarks that are easy for humans to understand without requiring complex verification algorithms or strict thresholds. The watermark is embedded within all model parameters and entangled with the main task, exhibiting superior robustness. It shows an 8,544-bit watermark capacity comparable to the strongest existing work. Crucially, ClearStamp’s effectiveness is model and dataset-agnostic, and resilient against adversarial model manipulations, as demonstrated in a comprehensive study performed with four datasets and seven architectures.
Short‐term calorie restriction ameliorates genomewide, age‐related alterations in DNA methylation

DNA methylation plays major roles in many biological processes, including aging, carcinogenesis, and development. Analyses of DNA methylation using next‐generation sequencing offer a new way to profile and compare methylomes across the genome in the context of aging. We explored genomewide DNA methylation and the effects of short‐term calorie restriction (CR) on the methylome of aged rat kidney. Whole‐genome methylation of kidney in young (6 months old), old (25 months old), and OCR (old with 4‐week, short‐term CR) rats was analyzed by methylated DNA immunoprecipitation and next‐generation sequencing (MeDIP‐Seq). CpG islands and repetitive regions were hypomethylated, but 5′‐UTR, exon, and 3′‐UTR hypermethylated in old and OCR rats. The methylation in the promoter and intron regions was decreased in old rats, but increased in OCR rats. Pathway enrichment analysis showed that the hypermethylated promoters in old rats were associated with degenerative phenotypes such as cancer and diabetes. The hypomethylated promoters in old rats related significantly to the chemokine signaling pathway. However, the pathways significantly enriched in old rats were not observed from the differentially methylated promoters in OCR rats. Thus, these findings suggest that short‐term CR could partially ameliorate age‐related methylation changes in promoters in old rats. From the epigenomic data, we propose that the hypermethylation found in the promoter regions of disease‐related genes during aging may indicate increases in susceptibility to age‐related diseases. Therefore, the CR‐induced epigenetic changes that ameliorate age‐dependent aberrant methylation may be important to CR's health‐ and life‐prolonging effects.
Index calculus in the trace zero variety

We discuss how to apply Gaudry's index calculus algorithm for abelian varieties to solve the discrete logarithm problem in the trace zero variety of an elliptic curve. We treat in particular the practically relevant cases of field extensions of degree 3 or 5. Our theoretical analysis is compared to other algorithms present in the literature, and is complemented by results from a prototype implementation.
TWENTY-EIGHT GOLDBACH VARIATIONS

We give twenty eight diverse proofs of the fundamental Euler sum identity ζ(2, 1) = ζ(3) = 8 ζ(2, 1). We also discuss various generalizations for multiple harmonic (Euler) sums and some of their many connections, thereby illustrating the wide variety of techniques fruitfully used to study such sums and the attraction of their study.
Sound gradual typing is nominally alive and well

Recent research has identified significant performance hurdles that sound gradual typing needs to overcome. These performance hurdles stem from the fact that the run-time checks gradual type systems insert into code can cause significant overhead. We propose that designing a type system for a gradually typed language hand in hand with its implementation from scratch is a possible way around these and several other hurdles on the way to efficient sound gradual typing. Such a design process also highlights the type-system restrictions required for efficient composition with gradual typing. We formalize the core of a nominal object-oriented language that fulfills a variety of desirable properties for gradually typed languages, and present evidence that an implementation of this language suffers minimal overhead even in adversarial benchmarks identified in earlier work.