Miracle-dz/UniFAR-FTUs huggingface dataset:
TOPIC 1 - Natural language processing and knowledge management projects

GOAL: This project proposes the use of recently introduced genera�ve language models (h�ps://arxiv.org/pdf/2112.11739v2.pdf) to automa�cally describe surgical videos frames based on ac�on triples (ac�on, tool, anatomy) recognized in the image ( h�ps://github.com/CAMMA-public/cholect45 ). The student is expected to apply these instruments in the surgical domain and evaluate their performance according to standard protocol/metrics. MOTIVATION: The automa�c genera�on of textual descrip�on from opera�ve images using deep learning techniques is a fundamental step towards the automa�c documenta�on of surgical interven�ons. This applica�on is a prerequisite for intra-operave context-aware surgical assistance. For example, the generated natural language sentence can help surgeons to decide how to perform the opera�on based on the current surgical view. It is an essen�al component towards building context aware surgical system, which aims to u�lize available informa�on inside the opera�on room to provide clinicians with contextual support at appropriate �me. Moreover, when on-site mentoring is unavailable or a rare case is detected, providing intra-operave surgical instruc�ons by expert surgeons is impera�ve. However,
S 6 . Additional results S 6 . 1 Impact of encoders

The TR-based deep learning models used in our study have an encoder for extracting features from the given input patches. In other words, an encoder can be seen as a core component of the aforementioned segmentation models. ResNet [1] is currently one of the most popular encoders to address computer vision-related tasks. All models used in our experiments are leveraging ResNet101 as their encoder. For the experiment presented in this section, we selected MP-Net and we performed a comparative evaluation by introducing encoder changes. The results obtained are shown in Figure 1. Five different types of encoders were tested. The number next to each ResNet model refers to the number of stacked residual blocks. As discussed in [1], an increase in the number of stacked residual blocks leads,in general, to a higher effectiveness. Among the encoders presented in Figure 1, ResNet-18 scored the highest in terms of mAccuracy, mRecall, and mIoU. On the other hand, ResNet-34 obtained the highest mPrecision and mF1-score. Compared to ResNet-101, ResNet-34 consistently scored higher for all five metrics. Similarly, ResNet-18 outperforms ResNet-101 for all metrics, with the exception of mPrecision. Our results suggest that MP-Net could be improved further by changing the encoder to ResNet-18 or ResNet-34. However, since the evaluation was performed using only CVF (1) as the validation set and CVF (2), CVF (3), and CVF (4) as the fine-tuning set (see Fine-tuning (1) in Figure 6, the execution of a complete cross-validation is desirable to confirm the obtained levels of effectiveness.
Counterexamples Related to Rotations of Shadows of Convex Bodies

We construct examples of two convex bodies $K,L$ in $\mathbb{R}^n$, such that every projection of $K$ onto a $(n-1)$-dimensional subspace can be rotated to be contained in the corresponding projection of $L$, but $K$ itself cannot be rotated to be contained in $L$. We also find necessary conditions on $K$ and $L$ to ensure that $K$ can be rotated to be contained in $L$ if all the $(n-1)$-dimensional projections have this property.
A multistart weight‐adaptive recursive parameter estimation method

The determination of the parameters for hydrologic models has been the subject of a large number of studies during the last 3 decades. A multitude of methods have been developed for this purpose. Generally, the mismatch between the model simulations and the observations is lumped into an objective function, which is then is optimized by these methods. This can lead to parameter values that result in a good model performance under certain (e.g., low flow) conditions but not under other (e.g., high flow) conditions. The objective of this paper is to demonstrate a calibration algorithm which leads to a good model performance under all boundary conditions. This algorithm is referred to as Multistart Weight‐Adaptive Recursive Parameter Estimation (MWARPE). For this purpose the equations of the Extended Kalman Filter (EKF) have been used recursively in a Monte‐Carlo approach, strongly increasing the chance that a globally optimal parameter set is obtained instead of a local optimum. The method has been applied to a rainfall‐runoff model for the Zwalm catchment in Belgium, using a 1‐year, a 2‐year, and a 3‐year calibration period. The results have been compared to the Shuffled Complex Evolution (SCE)‐UA method. A synthetic study revealed that for narrow parameter limits the SCE‐UA algorithm outperformed MWARPE, while for broad parameter limits the opposite occurred. For the test case using in situ observed data, the SCE‐UA method resulted in slightly lower RMSE values than MWARPE, but MWARPE performed better outside the calibration period. It has been found that MWARPE can bypass local optima in the determination of the final parameter set. Also, the best initial parameter sets (with the lowest RMSE) do not lead to the best final parameter values. To apply the method only four parameters need to be specified, more specifically the number of starting points, the number of iterations per starting point, one parameter used to initialize the model error covariance matrix, and the observation error. For this reason, the method could be a simple alternative to more complex methods if model parameters have to be determined when time and/or computational power are limited.
The VLA/ALMA Nascent Disk and Multiplicity (VANDAM) Survey of Perseus Protostars. VI. Characterizing the Formation Mechanism for Close Multiple Systems

We present Atacama Large Millimeter/submillimeter Array observations of multiple protostar systems in the Perseus molecular cloud, previously detected by the Karl G. Jansky Very Large Array. We observe 17 close (<600 au separation) multiple systems at 1.3 mm in continuum and five molecular lines (i.e., 12CO, C18O, 13CO, H2CO, SO) to characterize the circum-multiple environments in which these systems are forming. We detect at least one component in the continuum for the 17 multiple systems. In three systems one companion is not detected, and for two systems the companions are unresolved at our observed resolution. We also detect circum-multiple dust emission toward eight out of nine Class 0 multiples. Circum-multiple dust emission is not detected toward any of the eight Class I multiples. Twelve systems are detected in the dense gas tracers toward their disks/inner envelopes. For these 12 systems, we use the dense gas observations to characterize their formation mechanism. The velocity gradients in the circum-multiple gas are clearly orthogonal to the outflow directions in eight out of the 12 systems, consistent with disk fragmentation. Moreover, only two systems with separations <200 au are inconsistent with disk fragmentation, in addition to the two widest systems (>500 au). Our results suggest that disk fragmentation via gravitational instability is an important formation mechanism for close multiple systems, but further statistics are needed to better determine the relative fraction formed via this method.
Evaluation of strength statistics of quasibrittle structures based on mean size effect analysis

This paper presents a new method to indirectly determine the probability distribution function of strength of quasibrittle structures. Based on the finite weakest link model, which relates the probability distribution of the structural strength to the size dependence of mean strength, it is shown that that the cumulative distribution function of structural strength can be directly determined from the parameters of the mean size effect curve. A comprehensive experimental set of tests, which includes both strength histograms and mean size effect tests on specimens of asphalt mixture at low temperature, is used to verify the proposed method. The predicted strength histograms obtained with this method are found to be in very good agreement with the experimental histograms of asphalt mixture specimens of different sizes, confirming the validity of the newly proposed formulation.
Reduced effective scanning time in SPECT due to OSEM accelerated reconstruction

We study the increase of image noise which can be observed in images reconstructed with the OSEM algorithm. We argue that the excessive noise is equivalent to shortening scanning time by a factor of 2 or more at high number of subsets (acceleration factors). Therefore, by keeping the number of OSEM subsets low one can significantly reduce image noise, which in turn is equivalent to increasing scanning time or radiation dose. While the OSEM remains a very useful reconstruction method enabling substantial reduction of reconstruction times, it should be used with caution. In particular, high numbers of subsets should be avoided if possible. Whenever the available computing power allows achieving acceptable reconstruction times at lower number of subsets, one can consider reducing scanning time or injected dose, while maintaining the image quality of standard scans reconstructed with higher OSEM acceleration. The recommended maximal "safe" number of subsets, which does not lead to significant increase of image noise, is about 5.
What is the lowest possible reheating temperature

We study models in which the universe exits reheating at temperatures in the MeV regime. By combining light element abundance measurements with cosmic microwave background and large scale structure data we find a fairly robust lower limit on the reheating temperature of T_RH > 4 MeV at 95% C.L. However, if the heavy particle whose decay reheats the universe has a direct decay mode to neutrinos, there are some small islands left in parameter space where a reheating temperature as low as 1 MeV is allowed. The derived lower bound on the reheating temperature also leads to very stringent bounds on models with $n$ large extra dimensions. For n=2 the bound on the compactification scale is M > 2000 TeV, and for n=3 it is 100 TeV. These are currently the strongest available bounds on such models.
Dosimetry for quantitative analysis of low dose ionizing radiation effects on humans in radiation therapy patients

We have successfully developed a practical approach to predicting the location of skin surface dose at potential biopsy sites that receive 1 cGy and 10 cGy, respectively, in support of in vivo biologic dosimetry in humans. This represents a significant technical challenge as the sites lie on the patient surface out side the radiation fields. The PEREGRINE Monte Carlo simulation system was used to model radiation dose delivery and TLDs were used for validation on a phantom and confirmation during patient treatment. In the developmental studies the Monte Carlo simulations consistently underestimated the dose at the biopsy site by approximately 15% for a realistic treatment configuration, most likely due to lack of detail in the simulation of the linear accelerator outside the main beam line. Using a single, thickness-independent correction factor for the clinical calculations, the average of 36 measurements for the predicted 1 cGy point was 0.985 cGy (standard deviation: 0.110 cGy) despite patient breathing motion and other real world challenges. Since the 10 cGy point is situated in the region of high dose gradient at the edge of the field, patient motion had a greater effect and the six measured points averaged 5.90 cGy (standard deviation: 1.01 cGy), more » a difference that is equivalent to approximately a 6 mm shift on the patient's surface. « less
Essentials of k essence

We recently introduced the concept of ``k-essence'' as a dynamical solution for explaining naturally why the universe has entered an epoch of accelerated expansion at a late stage of its evolution. The solution avoids fine-tuning of parameters and anthropic arguments. Instead, k-essence is based on the idea of a dynamical attractor solution which causes it to act as a cosmological constant only at the onset of matter domination. Consequently, k-essence overtakes the matter density and induces cosmic acceleration at about the present epoch. In this paper, we present the basic theory of k-essence and dynamical attractors based on evolving scalar fields with nonlinear kinetic energy terms in the action. We present guidelines for constructing concrete examples and show that there are two classes of solutions, one in which cosmic acceleration continues forever and one in which the acceleration has finite duration.
Blood-Based Transcriptomic and Proteomic Biomarkers of Radiologic Emphysema

Rationale: Emphysema is a key component of COPD with important prognostic implications. Identifying blood-based biomarkers of emphysema will facilitate early diagnosis and possible development of targeted therapies. Objectives: Discover blood transcriptomic and proteomic biomarkers for chest computed tomography-quantified emphysema in smokers and develop predictive biomarker panels. Methods: Emphysema blood biomarker discovery was performed using differential gene expression, alternative splicing, and protein association analyses in a training set of 2,370 COPDGene participants with available whole blood RNA sequencing, plasma SomaScan proteomics, and clinical data. Validation was conducted in a testing set of 1,016 COPDGene subjects. Since body mass index (BMI) and emphysema often co-occur, we performed a mediation analysis to quantify the effect of BMI on gene and protein associations with emphysema. Predictive models were also developed using elastic net to predict quantitative emphysema from cell blood count, RNA sequencing, and proteomic biomarkers. Model accuracy was assessed by area under the receiver-operator-characteristic-curves (AUROC) for subjects stratified into tertiles of emphysema severity. Measurements and Main Results: 4,913 genes, 1,478 isoforms, 386 exons, and 881 proteins were significantly associated with emphysema (FDR 10%). 75% and 77% of genes and proteins, respectively, were mediated by BMI. The significantly enriched biological pathways were involved in inflammation and cell differentiation, differing between the most and least BMI-mediated genes. The cell blood count plus protein model achieved the highest performance with an AUROC of 0.89. Conclusions: Blood transcriptome and proteome-wide analyses reveal key biological pathways of emphysema and enhance the prediction of emphysema.
Dynamic Radiographs in Assessing Stability of Cervical Spine Fractures: A Multicentre Study

Background: In the management of a trauma patient with cervical spine injury, the need for accurate diagnostic imaging is key to ensure correct management. Different classification systems have been developed including the Subaxial Injury Classification (SLIC) system and AO cervical spine fracture classification. Through a multicentre study, we have identified a group of cases where the use of CT alone to classify fractures by either SLIC or AO score may be deficient and the use of dynamic cervical spine radiographs could help identify instability. Methods: Three level 1 trauma centers retrospectively reviewed patients with cervical spine injuries. Cervical spine radiographs (AP and lateral) were undertaken in collar, in all patients with suspected cervical spine injury within 2 weeks, followed by reanalysis of scoring systems. Results: Eleven cases were identified in total, and 72% were male with a mean age of 65 years, with approximately 54% being older than 70 years. All patients reported their pain as severe using the Visual Analogue Scale scale. The predynamic radiograph mean SLIC score was 0.73, which is in contrast to the postdynamic radiograph mean SLIC score of 6. The statistical significance (P = 0.004) was found using the Wilcoxon signed-rank test. Conclusion: Supine imaging eliminates the gravitational loads normally exerted on the c-spine. The cases show assumed cervical stability based on CT, but dynamic c-spine radiographs subsequently demonstrated instability. Therefore, we suggest a combination of SLIC and AO classification using radiologic imaging to classify fracture and correlate clinical symptoms with persistent neck pain, which warrants a Miami-J collar and dynamic c-spine radiograph to assess stability with re-evaluation of scoring.
USING FU ORIONIS OUTBURSTS TO CONSTRAIN SELF-REGULATED PROTOSTELLAR DISK MODELS

One-dimensional, convective, vertical structure models and one dimensional time-dependent, radial diffusion models are combined to create a self-consistent picture in which FU Orionis outbursts occur in young stellar objects (YSOs) as the result of a large-scale, self-regulated, thermal ionization instability in the surrounding protostellar accretion disk. Although active accretion disks have long been postulated to be ubiqitous among low-mass YSOs, few constraints have until now been imposed on physical conditions in these disks. By fitting the results of time-dependent disk models to observed timescales of FU Orionis events, we estimate the magnitude of the effective viscous stress in the inner disk (r approximately less than 1 AU) to be, in accordance with an ad hoc 'alpha' prescription, the product of the local sound speed, pressure scale height, and an efficiency factor alpha of 10(exp -4) where hydrogen is neutral and 10(exp 3) where hydrogen is ionized. We hypothesize that all YSOs receive infall onto their outer disks which is steady (or slowly declining with time) and that FU Orionis outbursts are self-regulated, disk outbursts which occur only in systems which transport matter inward at a rate sufficiently high to cause hydrogen to be ionized in the inner disk. We estimate a critical mass flux of dm(sub crit)/dt = 5 x 10(exp 7) solar mass/yr independent of the magnitude of alpha for systems with one solar mass, three solar radius central objects. Infall accretion rates in the range of dm(sub in)/dt = 1-10) x 10(exp -6) solar mass/yr produce observed FU Orionis timescales consistent with estimates of spherical molecular cloud core collapse rates. Modeled ionization fronts are typically initiated near the inner edge of the disk and propogate out to a distance of several tens of stellar radii. Beyond this region, the disk transports mass steadily inward at the supplied constant infall rate. Mass flowing through the innermost disk annulus is equal to dm(sub in)/dt only in a time-averaged sense and is regulated by the ionization of hydrogen in the inner disk such that long intervals (approximately 1000 yr) of low-mass flux: (1-30) x 10(exp -8) solar mass/yr are punctuated by short intervals (approximately 100 yr) of high-mass flux: (1-30) x 10(exp -5) solar mass/yr. Timescales and mass fluxes derived for quiescent and outburst stages are consistent with estimates from observations of T Tauri and FU Orionis systems, respectively.
Characterization of channel diffusion in a sodium tetrasilicate glass via molecular-dynamics simulations

We study the structural and dynamical characteristics of the sodium atoms inside and outside the ``diffusion channels'' in glassy ${\mathrm{Na}}_{2}\mathrm{O}\ensuremath{-}4{\mathrm{SiO}}_{2}$ (NS4) using classical molecular dynamics. We show that on average neither energetic arguments nor local environment considerations can explain the increased density of sodium atoms inside the subspace made of the channels. Nevertheless, we show that at low temperature the mean-square displacement of the sodium atoms inside this subspace is significantly larger than that of the atoms outside the channels.
Hyposmotic stress causes ATP release in a discrete zone within the outer cortex of rat lens

Purpose Purinergic signaling pathways activated by extracellular ATP have been implicated in the regulation of lens volume and transparency. In this study, we investigated the location of ATP release from whole rat lenses and the mechanism by which osmotic challenge alters such ATP release. Methods Three-week-old rat lenses were cultured for 1 h in isotonic artificial aqueous humor (AAH) with no extracellular Ca2+, hypotonic AAH, or hypertonic AAH. The hypotonic AAH-treated lenses were also cultured in the absence or presence of connexin hemichannels and the pannexin channel blockers carbenoxolone, probenecid, and flufenamic acid. The ATP concentration in the AAH was determined using a Luciferin/luciferase bioluminescence assay. To visualize sites of ATP release induced by hemichannel and/or pannexin opening, the lenses were cultured in different AAH solutions, as described above, and incubated in the presence of Lucifer yellow (MW = 456 Da) and Texas red-dextran (MW = 10 kDa) for 1 h. Then the lenses were fixed, cryosectioned, and imaged using confocal microscopy to visualize areas of dye uptake from the extracellular space. Results The incubation of the rat lenses in the AAH that lacked Ca2+ induced a significant increase in the extracellular ATP concentration. This was associated with an increased uptake of Lucifer yellow but not of Texas red-dextran in a discrete region of the outer cortex of the lens. Hypotonic stress caused a similar increase in ATP release and an increase in the uptake of Lucifer yellow in the outer cortex, which was significantly reduced by probenecid but not by carbenoxolone or flufenamic acid. Conclusions Our data suggest that in response to hypotonic stress, the intact rat lens is capable of releasing ATP. This seems to be mediated via the opening of pannexin channels in a specific zone of the outer cortex of the lens. Our results support the growing evidence that the lens actively regulates its volume and therefore, its optical properties, via puerinergic signaling pathways.
Prevalence of Vitamin D Deficiency in Patients With Charcot Arthropathy: A Single-Center Analysis

Introduction: Vitamin D deficiency may be a potentially modifiable risk factor in patients with orthopaedic conditions including Charcot arthropathy. The purpose of this study was to determine the prevalence of vitamin D deficiency and insufficiency in patients with Charcot arthropathy. Methods: All patients with Charcot arthropathy seen in our foot and ankle surgery clinic from January 2017 through June 2021 were screened for serum 25-hydroxyvitamin D levels. Patients were categorized as sufficient, insufficient, or deficient based on previously accepted guidelines. The prevalence of vitamin D deficiency and insufficiency was calculated. Results: A total of 57 subjects were included in this study after meeting the inclusion criteria. Of these, 27 (47.4%) were found to be deficient in vitamin D, 21 (36.8%) were insufficient in vitamin D, and 9 (15.8%) were sufficient in vitamin D. Overall, 84.2% of the cohort was found to be either insufficient or deficient in vitamin D. Conclusion: Vitamin D insufficiency and deficiency is highly prevalent in patients with Charcot arthropathy. As such, it is possible that this may play a role in the pathogenesis of Charcot arthropathy and may represent a potentially modifiable risk factor that could be optimized during the management of patients with Charcot arthropathy.