Miracle-dz/UniFAR-FTUs huggingface dataset:
Galaxy-Targeting Approach Optimized for Finding the Radio Afterglows of Gravitational Wave Sources

Kilonovae and radio afterglows of neutron star merger events have been identified as the two most promising counterparts, of these gravitational wave sources, that can provide arcsecond localization. While several new and existing optical search facilities have been dedicated to finding kilonovae, factors such as dust obscuration and the daytime sky may thwart these searches in a significant fraction of gavitational wave events. Radio-only searches, being almost immune to these factors, are equally capable of finding the counterparts and in fact offer a complementary discovery approach, despite the modest fields of view for many of the present-day radio interferometers. Such interferometers will be able to carry out competitive searches for the electromagnetic counterparts through the galaxy targeting approach. Adapting and improving on an existing algorithm by Rana et al. 2017. we present here a method that optimizes the placement of radio antenna pointings, integration time, and antenna slew. We simulate 3D gravitational wave localizations to find the efficacy of our algorithm; with substantial improvements in slew overhead and containment probability coverage, our algorithm performs significantly better than simple galaxy-rank-ordered observations. We propose that telescopes such as the Very Large Array, MeerKAT, Australia Telescope Compact Array and the Gaint Meterwave Radio Telescope, having fields of view $\lesssim$1 deg$^2$ and searching for the counterparts of nearby GW events over tens of square degrees or larger, will especially benefit from this optimized galaxy-targeting approach for electromagnetic counterpart searches.
Blind Quantum Computing with Decoy States

In this paper, we study the Universal Blind Quantum Computing (UBQC) protocol, which allows a client to perform quantum computation on a remote quantum server and the Remote Blind qubit state Preparation (RBSP) protocol which allows the client to prepare single qubits on the server's location with week coherent pulses. This RBSP protocol is inefficient for small $ T $, because the required number of pulses for generating one single qubit scales as $ \mbox{O}(1/T^4) $, where $ T $ is the transmittance of the quantum channe between the client and the server. Our contribution in this paper is a modified RBSP protocol with decoy states. This new protocol allows us to generate $ S $ single qubits simultaneously in a single instance. With our new rotocol, we are able to reduce the number of weak coherent pulses required for generating one single qubit from $ \mbox{O}(1/T^4) $ to nearly $ \mbox{O}(1/T) $, significantly increasing the efficiency. For a 100 km standard telecom fiber of loss 0.2 dB/km, our method gives a six orders of magnitude improvement in the speed, which is very significant.
The SOPHIE search for northern extrasolar planets - II. A multiple planet system around HD 9446

We report the discovery of a planetary system around HD 9446, performed from radial velocity measurements secured with the spectrograph SOPHIE at the 193-cm telescope of the Haute-Provence Observatory for more than two years. At least two planets orbit this G5V, active star: HD 9446b has a minimum mass of 0.7 MJup and a slightly eccentric orbit with a period of 30 days, whereas HD 9446c has a minimum mass of 1.8 MJup and a circular orbit with a period of 193 days. As for most of the known multiple planet systems, the HD 9446-system presents a hierarchical disposition with a massive outer planet and a lighter inner planet.
Capped Lp approximations for the composite L0 regularization problem

The composite L0 function serves as a sparse regularizer in many applications. The algorithmic difficulty caused by the composite L0 regularization (the L0 norm composed with a linear mapping) is usually bypassed through approximating the L0 norm. We consider in this paper capped Lp approximations with $p>0$ for the composite L0 regularization problem. For each $p>0$, the capped Lp function converges to the L0 norm pointwisely as the approximation parameter tends to infinity. We point out that the capped Lp approximation problem is essentially a penalty method with an Lp penalty function for the composite L0 problem from the viewpoint of numerical optimization. Our theoretical results stated below may shed a new light on the penalty methods for solving the composite L0 problem and help the design of innovative numerical algorithms. We first establish the existence of optimal solutions to the composite L0 regularization problem and its capped Lp approximation problem under conditions that the data fitting function is asymptotically level stable and bounded below. Asymptotically level stable functions cover a rich class of data fitting functions encountered in practice. We then prove that the capped Lp problem asymptotically approximates the composite L0 problem if the data fitting function is a level bounded function composed with a linear mapping. We further show that if the data fitting function is the indicator function on an asymptotically linear set or the L0 norm composed with an affine mapping, then the composite L0 problem and its capped Lp approximation problem share the same optimal solution set provided that the approximation parameter is large enough.
Multivariate Feedback Particle Filter via F-divergence and the Well-posedness of its Admissible Control Input

In this paper, we shall first derive the admissible control input of the multivariate feedback particle filter (FPF) by minimizing the f-divergence of the posterior conditional density function and the empirical conditional density of the controlled particles. On the contrast, in the original derivation \cite{YMM}, a special f-divergence, Kullback-Leibler (K-L) divergence, is used in the 1-dimensional nonlinear filtering problems. We show that the control input is invariant under the f-divergence class. That is, the control input satisfies exactly the same equations as those obtained by minimizing K-L divergence, no matter what f-divergence in use. In the latter half of this paper, we show the existence and uniqueness of the control input under suitable regular conditions. We confirm that the explicit expression of the control input given in \cite{YLMM} is the only admissible one.
Fourier Series and Transforms in Grand Lebesgue Spaces As an particular case - exponential Orlicz spaces

In this article we investigate the Fourier series and transforms for the functions defined on the [-pi, pi]^ d or on the R^d and belonging to the (Bilateral) Grand Lebesgue Spaces. As a particular case we obtain some results about Fourier's transform in the so-called exponential Orlicz spaces. We construct also several examples to show the exactness of offered estimations.
Comparative Transcriptome Analysis of Hypocotyls During the Developmental Transition of C3 cotyledons to C4 Leaves in Halimocnemis mollissima Bunge

Identification of signaling pathways that control C4 photosynthesis development is essential for introducing the C4 pathway into C3 crops. Species with dual photosynthesis in their life cycle are interesting models to study such regulatory mechanisms. The species used here Halimocnemis mollissima Bunge, belonging to the Caroxyleae tribe, displays C3 photosynthesis in its cotyledons and a NAD-ME subtype of C4 photosynthesis in the First leaves (FLs) onwards. We explored the long-distance signaling pathways that are probably implicated in the shoot-root coordination associated with the manifestation of the C4 traits, including efficient resource usage by comparing the mRNA content of hypocotyls before and after the C4 first leave’s formation. Histological examination showed the presence of C3 anatomy in cotyledons and C4 anatomy in the FLs. Our transcriptome analyses verified the performance of the NAD-ME subtype of C4 in FLs and revealed differential transcript abundance of several potential mobile regulators and their associated receptors or transporters in two developmentally different hypocotyls of H. mollissima Bunge. These differentially expressed genes (DEGs) belong to diverse functional groups, including various transcription factor (TF) families, phytohormones metabolism, and signaling peptides, part of which could be related to hypocotyl development. Our findings support the higher nitrogen and water use efficiency associated with C4 photosynthetic and provide insights into the coordinated above- and under-ground tissue communication during the developmental transition of C3 to C4 photosynthesis in this species.
Separable approximation to two-body matrix elements

Two-body matrix elements of arbitrary local interactions are written as the sum of separable terms in a way that is well suited for the exchange and pairing channels present in mean-field calculations. The expansion relies on the transformation to center of mass and relative coordinate (in the spirit of Talmi's method) and therefore it is only useful (finite number of expansion terms) for harmonic oscillator single particle states. The converge of the expansion with the number of terms retained is studied for a Gaussian two body interaction. The limit of a contact (delta) force is also considered. Ways to handle the general case are also discussed.
Dysfunction of the Visual Sensory Thalamus in Developmental Dyslexia

Developmental dyslexia (DD) is a reading disorder with a prevalence of 5-10%. Neuroscientific research has typically focused on explaining DD symptoms based on pathophysiological changes in the cerebral cortex. However, DD might also be associated with alterations in sensory thalami – central subcortical stations of sensory pathways. A post-mortem study on the visual sensory thalamus (lateral geniculate nucleus, LGN) showed histopathological changes in the magnocellular (M-LGN), but not in the parvocellular (P-LGN), subdivisions. M-LGN and P-LGN have different functional properties and belong to two different visual systems. Whether M-LGN alterations also exist in DD in-vivo is unclear. Also, the potential relevance of M-LGN alterations to DD symptoms is unknown. This lack of knowledge is partly due to considerable technical challenges in investigating LGN subdivisions non-invasively in humans. Here, we employed recent advances in high-field 7 Tesla functional magnetic resonance imaging (fMRI) to map the M- and P-LGN in-vivo in DD adults (n=26) and matched controls (n=28). We show that (i) M-LGN responses differ between DD and control participants, (ii) these differences are more pronounced in male than in female DD participants, and (iii) M-LGN alterations predict a core symptom of DD in male DD participants only, i.e., rapid naming ability. Our results provide a first functional interpretation of M-LGN changes in DD and support DD theories that propose a direct relevance of sensory thalamus alterations for DD symptoms. In addition, the sex-specific behavioral relevance of M-LGN alterations within DD calls for taking sex differences into account when planning brain-based therapeutic interventions. Significance Statement Developmental dyslexia (DD) is one of the most common learning disorders affecting millions of children and adults world-wide. Several decades ago, pioneering research in five DD post-mortem brains suggested that DD is characterized not only by alterations of the cerebral cortex, but also by changes in a subsection of the visual sensory thalamus – the so-called M-LGN. The relevance of these findings for DD remained highly controversial. Using recent developments in high-resolution functional neuroimaging, we now discovered that M-LGN alterations are present also in DD in-vivo and predict a core symptom of DD in males. Our results provide a first functional interpretation of M-LGN alterations in DD and provide a basis for better understanding sex-specific differences in DD.
Emergent Electrical Activity, Tissue Heterogeneity, and Robustness in a Calcium Feedback Regulatory Model of the Sinoatrial Node

The sinoatrial node (SAN) is the primary pacemaker of the heart. SAN activity emerges at an early point in life and maintains a steady rhythm for the lifetime of the organism. The ion channel composition and currents of SAN cells can be influenced by a variety of factors. Therefore, the emergent activity and long-term stability imply some form of dynamical feedback control of SAN activity. We adapt a recent feedback model - previously utilized to describedion conductances in neurons - to a model of SAN cells and tissue. The model describes a minimal regulatory mechanism of ion channel conductances via feedback between intracellular calcium and an intrinsic target calcium level. By coupling a SAN cell to the calcium feedback model, we show that spontaneous electrical activity emerges from quiescence and is maintained at steady-state. In a 2D SAN tissue, spatial variability in intracellular calcium targets lead to significant, self-organized heterogeneous ion channel expression and calcium transients throughout the tissue. Further, multiple pacemaking regions appear, which interact and lead to time-varying cycle length, demonstrating that variability in heart rate is an emergent property of the feedback model. Finally, we demonstrate that the SAN tissue is robust to the silencing of leading cells or ion channel knockouts. Thus, the calcium feedback model can reproduce and explain many fundamental emergent properties of activity in the SAN that have been observed experimentally based on a minimal description of intracellular calcium and ion channel regulatory networks. Key Points Summary The robust function of the sinoatrial node (SAN) is reproduced in an intracellular calcium feedback model governing ion channel conductances The feedback model predicts the emergence and long-term maintenance of spontaneous oscillatory electrical activity Integrating the feedback model into a 2D SAN tissue leads to emergent spatial heterogeneity, multiple pacemaking regions, and variable cycle length SAN cells and tissue with feedback are robust to cell injury and channel knock-outs
Elimusertib outperforms standard of care chemotherapy in preclinical patient-derived pediatric solid tumor models

The small molecule inhibitor of ataxia telangiectasia and Rad3-related protein (ATR), elimusertib, is currently being tested clinically in various cancer entities in adults and children. Its preclinical anti-tumor activity in pediatric malignancies, however, is largely unknown. We here assessed the preclinical activity of elimusertib in >40 cell lines and >30 patient-derived xenograft (PDX) models derived from common pediatric solid tumor entities. Detailed in vitro and in vivo molecular characterization of the treated models enabled the evaluation of response biomarkers. Pronounced objective response rates were observed for elimusertib monotherapy in PDX, when treated with a regimen currently used in clinical trials. Strikingly, elimusertib outperformed standard of care chemotherapies, particularly in alveolar rhabdomysarcoma PDX. Thus, elimusertib has strong preclinical anti-tumor activity in pediatric solid tumor models, which may translate to clinically meaningful responses in patients. Statement of translational relevance Elimusertib is a small molecule inhibitor of ATR. ATR inhibitors have shown promising results as anticancer agents in adult cancers, but there is limited information on their effectiveness in pediatric solid tumors. Using a cohort of 32 patient-derived xenografts from pediatric solid tumors, we here evaluated the therapeutic potential of elimusertib in vivo. Elimusertib reduced tumor volume growth in all samples. Elimusertib had very limited toxicity and was potent even in tumors with preexisting chemoresistance. Our preclinical data indicates that elimusertib is a safe and potent therapeutic option for pediatric solid tumors. This data may serve as a rationale for the development of pediatric clinical trials for ATR inhibitors.
Neuroelectrophysiology-Compatible Electrolytic Lesioning

Lesion studies have historically been instrumental for establishing causal connections between brain and behavior. They stand to provide additional insight if integrated with multielectrode techniques common in systems neuroscience. Here we present and test a platform for creating electrolytic lesions through chronically implanted, intracortical multielectrode probes without compromising the ability to acquire neuroelectrophysiology. A custom-built current source provides stable current and allows for controlled, repeatable lesions in awake-behaving animals. Performance of this novel lesioning technique was validated using histology from ex vivo and in vivo testing, current and voltage traces from the device, and measurements of spiking activity before and after lesioning. This electrolytic lesioning method avoids disruptive procedures, provides millimeter precision over the extent and submilimeter precision over the location of the injury, and permits electrophysiological recording of single-unit activity from the remaining neuronal population after lesioning. This technique can be used in many areas of cortex, in several species, and theoretically with any multielectrode probe. The low-cost, external lesioning device can also easily be adopted into an existing electrophysiology recording setup. This technique is expected to enable future causal investigations of the recorded neuronal population’s role in neuronal circuit function, while simultaneously providing new insight into local reorganization after neuron loss.
Biomimetic microstimulation of sensory cortices

Background Intracortical microstimulation (ICMS) is an emerging approach to restore sensation to people with neurological injury or disease. Biomimetic microstimulation, or stimulus trains that mimic neural activity in the brain through encoding of onset and offset transients, could improve the utility of ICMS for BCI applications, but how biomimetic microstimulation affects neural activation is not understood. Stimulus induced depression of neural activity (decreases in evoked intensity over time) is also a potential barrier to clinical implementation of sensory feedback, and biomimetic microstimulation may reduce this effect. Objective We evaluated how biomimetic trains change the calcium response, spatial distribution, and depression of neurons in the somatosensory and visual cortices. Methods Calcium responses of neurons were measured in Layer 2/3 of visual and somatosensory cortices of anesthetized GCaMP6s mice in response to ICMS trains with fixed amplitude and frequency (Fixed) and three biomimetic ICMS trains that increased the stimulation intensity during the onset and offset of stimulation by modulating the amplitude (BioAmp), frequency (BioFreq), or amplitude and frequency (BioBoth). ICMS was provided for either 1-s with 4-s breaks (Short) or for 30-s with 15-s breaks (Long). Results BioAmp and BioBoth trains evoked distinct onset and offset transients in recruited neural populations, while BioFreq trains evoked population activity similar to Fixed trains. Individual neurons had heterogeneous responses primarily based on how quickly they depressed to ICMS, where neurons farther from the electrode depressed faster and a small subpopulation (1-5%) were modulated by BioFreq trains. Neurons that depressed to Short trains were also more likely to depress to Long trains, but Long trains induced more depression overall due to the increased stimulation length. Increasing the amplitude during the hold phase resulted in an increase in recruitment and intensity which resulted in more depression and reduced offset responses. Biomimetic amplitude modulation reduced stimulation induced depression by 14.6±0.3% for Short and 36.1±0.6% for Long trains. Ideal observers were 0.031±0.009 s faster for onset detection and 1.33±0.21 s faster for offset detection with biomimetic amplitude encoding. Conclusions Biomimetic amplitude modulation evokes distinct onset and offset transients, reduces depression of neural calcium activity, and decreases total charge injection for sensory feedback in brain-computer interfaces by lowering recruitment of neurons during long maintained periods of ICMS. In contrast, biomimetic frequency modulation evokes distinct onset and offset transients in a small subpopulation of neurons but also reduces depression in recruited neurons by reducing the rate of activation.
Generative modeling of short, disordered proteins with homogeneous sequence composition

Protein design has seen remarkable progress in the past decade, with numerous examples of de novo proteins with novel topologies and functions being successfully synthesized. Computational tools have played a large role in the ability to rationally design proteins. Recently, there have been numerous successes applying deep learning techniques to protein design that have demonstrated comparable or significantly improved performance over traditional energy-based approaches. However, the protein design problem has been less well explored for disordered proteins or, more generally, proteins with conformational heterogeneity. In this work, we demonstrate that if one approximates the spatial output of a coarse-grained molecular dynamics simulation as a multivariate normal distribution parameterized by a mean vector (representing an ensemble-averaged pairwise distance map) and covariance matrix, one can train a generative model to learn the distribution of these parameters across a set of sequences. Specifically, we encoded the mean vector and covariance matrix for each sequence in a low-dimensional space via a fixed linear transformation and trained a masked auto-encoder to accurately learn the distribution of this low-dimensional output. Furthermore, by sampling from the masked auto-encoder and transforming the generated samples back into their original high-dimensional space, one can generate realistic, ensemble-averaged pairwise distance maps. These results were demonstrated on coarse-grained simulation data derived from approximately 2000 distinct sequences, each sequence being 24 residues in length and consisting exclusively of glycine, serine, glutamate, and lysine. Though this set of sequences is relatively homogeneous in composition, we speculate our approach can be applied to disordered sequences of longer length and more heterogeneous composition, given the appropriate training set.