Miracle-dz/UniFAR-FTUs huggingface dataset:
A Fully Sensorized Cooperative Robotic System for Surgical Interventions

In this research a fully sensorized cooperative robot system for manipulation of needles is presented. The setup consists of a DLR/KUKA Light Weight Robot III especially designed for safe human/robot interaction, a FD-CT robot-driven angiographic C-arm system, and a navigation camera. Also, new control strategies for robot manipulation in the clinical environment are introduced. A method for fast calibration of the involved components and the preliminary accuracy tests of the whole possible errors chain are presented. Calibration of the robot with the navigation system has a residual error of 0.81 mm (rms) with a standard deviation of ±0.41 mm. The accuracy of the robotic system while targeting fixed points at different positions within the workspace is of 1.2 mm (rms) with a standard deviation of ±0.4 mm. After calibration, and due to close loop control, the absolute positioning accuracy was reduced to the navigation camera accuracy which is of 0.35 mm (rms). The implemented control allows the robot to compensate for small patient movements.
Analysis of Microarray Gene Expression Data Using Machine Learning Techniques

The advent of DNA microarrays has facilitated a fundamental transition from gene science to genome science. By performing massively parallel experiments on thousands of genes at once, scientists have, for the first time, the capability of observing the complex relationships between genes under controlled experimental conditions. However, the immense volume of data being generated by microarray experiments requires sophisticated data processing to match. Machine learning methods are particularly well suited to this task, as the types of reasoning we want to make about DNA microarrays often involves extracting patterns from the data, and discovering meaningful ways to view these patterns. In this paper we demonstrate how machine learning methods can be used to extract biologically significant insights from DNA microarray gene
Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil

Over the last decades, understanding of the effects of plants on soil microbiomes has greatly advanced. However, knowledge on the assembly of rhizospheric communities in aged-contaminated industrial soils is still limited, especially with regard to transcriptionally active microbiomes and their link to the quality or quantity of carbon sources. We compared the short-term (2–10 days) dynamics of bacterial communities and potential PAH-degrading bacteria in bare or ryegrass-planted aged-contaminated soil spiked with phenanthrene, put in relation with dissolved organic carbon (DOC) sources and polycyclic aromatic hydrocarbon (PAH) pollution. Both resident and active bacterial communities (analyzed from DNA and RNA, respectively) showed higher species richness and smaller dispersion between replicates in planted soils. Root development strongly favored the activity of Pseudomonadales within the first 2 days, and of members of Actinobacteria, Caulobacterales, Rhizobiales, and Xanthomonadales within 6–10 days. Plants slowed down the dissipation of phenanthrene, while root exudation provided a cocktail of labile substrates that might preferentially fuel microbial growth. Although the abundance of PAH-degrading genes increased in planted soil, their transcription level stayed similar to bare soil. In addition, network analysis revealed that plants induced an early shift in the identity of potential phenanthrene degraders, which might influence PAH dissipation on the long-term.
Can ChatGPT predict article retraction based on Twitter mentions?

Detecting problematic research articles timely is a vital task. This study explores whether Twitter mentions of retracted articles can signal potential problems with the articles prior to retraction, thereby playing a role in predicting future retraction of problematic articles. A dataset comprising 3,505 retracted articles and their associated Twitter mentions is analyzed, alongside 3,505 non-retracted articles with similar characteristics obtained using the Coarsened Exact Matching method. The effectiveness of Twitter mentions in predicting article retraction is evaluated by four prediction methods, including manual labelling, keyword identification, machine learning models, and ChatGPT. Manual labelling results indicate that there are indeed retracted articles with their Twitter mentions containing recognizable evidence signaling problems before retraction, although they represent only a limited share of all retracted articles with Twitter mention data (approximately 16%). Using the manual labelling results as the baseline, ChatGPT demonstrates superior performance compared to other methods, implying its potential in assisting human judgment for predicting article retraction. This study uncovers both the potential and limitation of social media events as an early warning system for article retraction, shedding light on a potential application of generative artificial intelligence in promoting research integrity.
Evidencia geoarqueológica de la transición Pleistoceno-Holoceno en reparos rocosos de Tandilia oriental (provincia de Buenos Aires)

espanolEn el ambito de Tandilia oriental (provincia de Buenos Aires) existen numerosas evidencias sobre el poblamiento humano a partir de la finalizacion del Pleistoceno tardio. Esto demuestra la utilizacion continua de tales territorios por parte de las sociedades de cazadores-recolectores. Los contextos arqueologicos de estas poblaciones se ubican por encima de una discordancia de erosion/depositacion que implico un cambio en la dinamica sedimentaria observada en este tipo de sitios a escala regional. Esta discordancia es uno de los factores mas recurrentes observado en las matrices de los reparos rocosos. En este trabajo se analizan las implicancias geoarqueologicas y paleoambientales de la transicion Pleistoceno tardio-Holoceno (c. 10.500 anos 14C AP), vinculadas a los procesos de formacion de los sitios. El analisis geoarqueologico de la transicion en secuencias condensadas y expandidas aporta nueva informacion sobre los procesos sedimentarios que operaron en las cavidades y que, en parte, habrian dependido de las condiciones climaticas del exterior. Los cambios ocurridos en el periodo de transicion PleistocenoHoloceno fueron alternantes entre ciclos aridos y ciclos humedos, hasta establecerse un regimen pluviometrico mayor durante el Holoceno temprano. EnglishIn the area of eastern Tandilia (Buenos Aires Province) there is abundant evidence on human settlement since the end of the late Pleistocene, which proves the continuous use of these territories by hunter-gatherer societies. The archaeological contexts of these populations are located above a discordance of erosion/deposition which suggests a change in the sedimentary dynamics observed at regional scale. This boundary is one of most recurrent features observed in the rock shelters. This work analyzes the geoarchaeological and paleoenvironmental record of the Pleistocene-Holocene transition (c. 10,500 14C years BP) linked to the formation processes of the sites. The geoarchaeological analysis of the transition in condensed and expanded sequences provides new information on the sedimentary processes that operated in the cavities and which, in part, would have depended on the climatic conditions. The changes occurred during the Pleistocene-Holocene transition were alternating between arid and wet cycles, until a higher rainfall regime was established during the early Holocene.
Integrated path stability selection

Stability selection is a widely used method for improving the performance of feature selection algorithms. However, stability selection has been found to be highly conservative, resulting in low sensitivity. Further, the theoretical bound on the expected number of false positives, E(FP), is relatively loose, making it difficult to know how many false positives to expect in practice. In this paper, we introduce a novel method for stability selection based on integrating the stability paths rather than maximizing over them. This yields a tighter bound on E(FP), resulting in a feature selection criterion that has higher sensitivity in practice and is better calibrated in terms of matching the target E(FP). Our proposed method requires the same amount of computation as the original stability selection algorithm, and only requires the user to specify one input parameter, a target value for E(FP). We provide theoretical bounds on performance, and demonstrate the method on simulations and real data from cancer gene expression studies.
Data Mixing Laws: Optimizing Data Mixtures by Predicting Language Modeling Performance

Pretraining data of large language models composes multiple domains (e.g., web texts, academic papers, codes), whose mixture proportions crucially impact the competence of outcome models. While existing endeavors rely on heuristics or qualitative strategies to tune the proportions, we discover the quantitative predictability of model performance regarding the mixture proportions in function forms, which we refer to as the data mixing laws. Fitting such functions on sample mixtures unveils model performance on unseen mixtures before actual runs, thus guiding the selection of an ideal data mixture. Furthermore, we propose nested use of the scaling laws of training steps, model sizes, and our data mixing law to enable predicting the performance of large models trained on massive data under various mixtures with only small-scale training. Moreover, experimental results verify that our method effectively optimizes the training mixture of a 1B model trained for 100B tokens in RedPajama, reaching a performance comparable to the one trained for 48% more steps on the default mixture. Extending the application of data mixing laws to continual training accurately predicts the critical mixture proportion that avoids catastrophic forgetting and outlooks the potential for dynamic data schedules
On Some Tighter Inapproximability Results

We give a number of improved inapproximability results, including the best up to date explicit approximation thresholds for bounded occurrence satisfiability problems like MAX-2SAT and E2-LIN-2, and the bounded degree graph problems, like MIS, NodeCover, and MAX CUT. We prove also for the first time inapproximability of the problem of Sorting by Reversals and display an explicit approximation threshold.
Balancing art and money in pursuit of a Kelly-type optimality

We introduce and study a mathematical model of an art collector. In our model, the collector is a rational agent whose actions in the art market are driven by two competing long-term objectives, namely sustainable financial health and maintaining the collection. Mathematically, our model is a two-dimensional random linear dynamical system with transformation matrix of a peculiar type. In some examples we are able to show that within the Kelly-type optimization paradigm, that is optimizing the system’s Lyapunov exponent over a set of policy parameters, the dilemma “art or money” can be successfully resolved, namely the optimal policy creates a coexistence equilibrium where the value of both is increasing over the time
High-order transient multidimensional simulation of a thermo-electro-chemo-mechanical model for Lithium-ion batteries

We build a transient multidimensional multiphysical model based on continuum theories, involving the coupled mechanical, thermal and electrochemical phenomena occurring simultaneously in the discharge or charge of lithium-ion batteries. The process delivers a system of coupled nonlinear partial differential equations. Besides initial and boundary conditions, we highlight the treatment of the electrode-electrolyte interface condition, which corresponds to a Butler-Volmer reaction kinetics equation. We present the derivation of the strong and weak forms of the model, as well as the discretization procedure in space and in time. The discretized model is computationally solved in two dimensions by means of a finite element method that employs $hp$ layered meshes, along with staggered second order semi-implicit time integration. The expected error estimate is of higher order than any other similar work, both in space and in time. A representative battery cell geometry, under distinct operating scenarios, is simulated. The numerical results show that the full model allows for important additional insights to be drawn than when caring only for the electrochemical coupling. Considering the multiphysics becomes more important as the applied current is increased, whether for discharge or for charge. Our full model provides battery design professionals with a valuable tool to optimize designs and advance the energy storage industry.
ELA BOUNDS FOR GRAPH EXPANSIONS VIA ELASTICITY

In two recent papers, one by Friedland and Schneider, the other by Förster and Nagy, the authors used polynomial matrices to study the effect of graph expansions on the spectral radius of the adjacency matrix. Here it is shown that the notion of the elasticity of the entries of a nonnegative matrix coupled with the Variational Principle for Pressure from symbolic dynamics can be used to derive sharper bounds than existing estimates. This is achieved for weighted and unweighted graphs, and the case of equality is characterized. The work is within the framework of studying measured graphs where each edge is assigned a positive length as well as a weight.
Characterization of site-directed mutants in the lac permease of Escherichia coli. 1. Replacement of histidine residues.

Wild-type lac permease from Escherichia coli and two site-directed mutant permeases containing Arg in place of His35 and His39 or His322 were purified and reconstituted into proteoliposomes. H35-39R permease is indistinguishable from wild type with regard to all modes of translocation. In contrast, purified, reconstituted permease with Arg in place of His322 is defective in active transport, efflux, equilibrium exchange, and counterflow but catalyzes downhill influx of lactose without concomitant H+ translocation. Although permease with Arg in place of His205 was thought to be devoid of activity [Padan, E. , Sarkar, H. K. , Viitanen, P. V. , Poonian, M. S. , & Kaback, H. R. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 6765], sequencing of lac Y in pH205R reveals the presence of two additional mutations in the 5' end of the gene, and replacement of this portion of lac Y with a restriction fragment from the wild-type gene yields permease with normal activity. Permeases with Asn, Gln, or Lys in place of His322, like H322R permease, catalyze downhill influx of lactose without H+ translocation but are unable to catalyze active transport, equilibrium exchange, or counterflow. Unlike H322R permease, however, the latter mutants catalyze efflux at rates comparable to that of wild-type permease, although the reaction does not occur in symport with H+. Finally, as evidenced by flow dialysis and photoaffinity labeling experiments, replacement of His322 appears to cause a marked decrease in the affinity of the permease for substrate. The results confirm and extend the contention that His322 is the only His residue in the permease involved in lactose/H+ symport and that an imidazole moiety at position 322 is obligatory. (ABSTRACT TRUNCATED AT 250 WORDS)
Electro-mechanical behaviour of indium tin oxide coated polymer substrates for flexible electronics

Highly conductive (3.0 - 5.0 x 10 \(^{-4}\) \( \Omega\) cm) and transparent (80 – 85% ) ITO films were successfully fabricated on glass and polymer substrates (PET, PEN and PC) by pulsed laser deposition at low temperatures (24 – 150 °C). The influence of deposition conditions on the structural and physical properties of ITO-coated glass substrates was studied. The samples were investigated using Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), X-Ray Diffraction (XRD), the fourpoint probe and a spectrophotometer. Sol-gel derived ITO films dip-coated on glass substrates were also studied. The optimum film obtained at a firing temperature of 600 °C had a resistivity of 1.8 x 10 \(^{-2}\) \( \Omega\) cm, and optical transmittance of 80%. The electro-mechanical behaviour of ITO/polymer systems was investigated under uniaxial tension and controlled buckling in tension and compression. The resistance changes were monitored in situ. Cracking and buckling delamination failure modes were observed for all samples investigated at critical strains raging from 2.8 to 3.4%, and from 7.0 to 8.0%, respectively. The results showed that the dominant critical failure mode depends on the applied stress conditions. The ITO/PEN samples showed high flexibility; the samples were buckled in tension down to a 2.6 mm radius of curvature before cracks start to occur.
Categorising sports injuries in epidemiological studies: the subsequent injury categorisation (SIC) model to address multiple, recurrent and exacerbation of injuries

Objective Sports injuries are often recurrent and there is wide recognition that a subsequent injury (of either the same or a different type) can be strongly influenced by a previous injury. Correctly categorising subsequent injuries (multiple, recurrent, exacerbation or new) requires substantial clinical expertise, but there is also considerable value in combining this expertise with more objective statistical criteria. This paper presents a new model, the subsequent injury categorisation (SIC) model, for categorising subsequent sports injuries that takes into account the need to include both acute and overuse injuries and ten different dependency structures between injury types. Methods The suitability of the SIC model was demonstrated with date ordered sports injury data from a large injury database from community Australian football players over one playing season. A subsequent injury was defined to have occurred in the subset of players with two or more reported injuries. Results 282 players sustained 469 subsequent injuries of which 15.6% were coded to categories representing injuries that were directly related to previous index injuries. This demonstrates that players can sustain a number of injuries over one playing season. Many of these will be unrelated to previous injuries but subsequent injuries that are related to previous injury occurrences are not uncommon. Conclusion The handling of subsequent sports injuries is a substantial challenge for the sports medicine field—both in terms of injury treatment and in epidemiological research to quantify them. Application of the SIC model allows for multiple different injury types and relationships within players, as well as different index injuries.
Social behavioral changes in MPTP-treated monkey model of Parkinson's disease

Parkinsonian patients experience not only the physical discomfort of motor disorders but also the considerable psychological distress caused by cognitive deficits and behavioral disorders. These two factors can result in a disruption of social relationships during the symptomatic and even the presymptomatic motor states of the disease. However, it remains difficult, if not impossible, to evaluate social relationships in presymptomatic patients. The present study focused on the evaluation of social relationships within a group of female long-tailed macaques during presymptomatic and symptomatic motor states induced by Chronic Low-Dose (CLD) and then Chronic High-Dose (CHD) systemic administration of 1-methyl-4-phenyl-l,2,3,6-tetrahydropyridine (MPTP). Dopaminergic denervation within basal ganglia and cortical areas was evaluated using Positron Emission Tomography (PET) scans with 18F-DOPA (6-[18F]-fluoro-L-3,4-dihydroxyphenylalanine) radiotracer. Interestingly, social behavioral changes could be identified in the presymptomatic motor state before any motor and/or cognitive impairment occurred. Stronger effects were observed in subordinate animals compared to dominant animals. From baseline state to CLD-presymptomatic motor state, the frequency of emitted affiliative and aggressive behaviors increased. From CLD-presymptomatic to CHD-presymptomatic motor states, the frequency of the three categories of social behaviors (aggressive, submissive and affiliative) decreased. At this time, quantitative data analysis in PET scans highlighted a dopaminergic denervation in the insula and the posterior caudate nucleus. Finally, the frequency of the three categories of social behaviors decreased during the stable-symptomatic motor state compared to baseline and presymptomatic motor states; this was also associated with motor and cognitive disorders and a dopaminergic denervation in all the evaluated cortical and subcortical structures.
High rates of cervical cancer among HIV-infected women at a referral hospital in Malawi

Cervical cancer is the most common cancer among women in Malawi. National guidelines recommend screening women aged 30–45 years every five years; however, no specific recommendations exist for women with HIV. We aimed to assess the frequency of high-grade dysplasia (CIN 2 or CIN3) and cervical cancer among women in central Malawi and to examine associations with CIN2+ (CIN2/3 or cancer). We extracted cervical Pap smear, biopsy, loop electrosurgical excision procedure and uterine specimen reports from a hospital pathology database from November 2012 to November 2013. We used logistic regression to estimate associations with CIN2+. We reviewed specimens from 824 women; we excluded 194 with unknown HIV status, leaving 630 in the analytic sample. Twelve percent had high-grade dysplasia and 109 women (17%) had cancer. Twenty-five percent of high-grade dysplasia cases and 35% of cancers occurred among women outside recommended screening ages. The odds of having CIN2+ were 6.55 times (95% CI 4.44-9.67) greater for HIV+ women. High-grade dysplasia and cervical cancer are very common among Malawian women, especially HIV+ women. HIV infection was strongly associated with CIN2+. Expanding screening to women not covered by current guidelines could avert a substantial proportion of cervical cancer cases in Malawi.
Understanding TCP fairness over wireless LAN

As local area wireless networks based on the IEEE 802.11 standard see increasing public deployment, it is important to ensure that access to the network by different users remains fair. While fairness issues in 802.11 networks have been studied before, this paper is the first to focus on TCP fairness in 802.11 networks in the presence of both mobile senders and receivers. In this paper, we evaluate extensively through analysis, simulation, and experimentation the interaction between the 802.11 MAC protocol and TCP. We identify four different regions of TCP unfairness that depend on the buffer availability at the base station, with some regions exhibiting significant unfairness of over 10 in terms of throughput ratio between upstream and downstream TCP flows. We also propose a simple solution that can be implemented at the base station above the MAC layer that ensures that different TCP flows share the 802.11 bandwidth equitably irrespective of the buffer availability at the base station.