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Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question-answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images. The code and datasets for running all the analyses reported in this paper can be found at https://github.com/sammarfy/VLM4Bio., Comment: 36 pages, 37 figures, 7 tables

This article presents constraints on dark-matter-electron interactions obtained from the first underground data-taking campaign with multiple SuperCDMS HVeV detectors operated in the same housing. An exposure of 7.63 g-days is used to set upper limits on the dark-matter-electron scattering cross section for dark matter masses between 0.5 and 1000 MeV/$c^2$, as well as upper limits on dark photon kinetic mixing and axion-like particle axioelectric coupling for masses between 1.2 and 23.3 eV/$c^2$. Compared to an earlier HVeV search, sensitivity was improved as a result of an increased overburden of 225 meters of water equivalent, an anticoincidence event selection, and better pile-up rejection. In the case of dark-matter-electron scattering via a heavy mediator, an improvement by up to a factor of 25 in cross-section sensitivity was achieved., Comment: 7 pages + title and references, 4 figures, and 1 table

Fishes are integral to both ecological systems and economic sectors, and studying fish traits is crucial for understanding biodiversity patterns and macro-evolution trends. To enable the analysis of visual traits from fish images, we introduce the Fish-Visual Trait Analysis (Fish-Vista) dataset - a large, annotated collection of about 60K fish images spanning 1900 different species, supporting several challenging and biologically relevant tasks including species classification, trait identification, and trait segmentation. These images have been curated through a sophisticated data processing pipeline applied to a cumulative set of images obtained from various museum collections. Fish-Vista provides fine-grained labels of various visual traits present in each image. It also offers pixel-level annotations of 9 different traits for 2427 fish images, facilitating additional trait segmentation and localization tasks. The ultimate goal of Fish-Vista is to provide a clean, carefully curated, high-resolution dataset that can serve as a foundation for accelerating biological discoveries using advances in AI. Finally, we provide a comprehensive analysis of state-of-the-art deep learning techniques on Fish-Vista.

During epithelial-mesenchymal transition (EMT), epithelial cells change their morphology, disperse, and gain mesenchymal-like characteristics. Usually, cells are categorized into discrete cell types or states based on gene expression and other cellular features. Subsequently, EMT is investigated as a dynamical process where cells jump from one discrete state to another. In the current work, we moved away from this idea of discrete state transition and investigated EMT dynamics in a continuous phenotypic space. We used morphology to define the phenotype of a cell. We used the data from quantitative image analysis of MDA-MB-468 cells undergoing EGF-induced EMT. We defined the morphological state space or 'morphospace' using the morphological features extracted through image analysis. During EMT, as the morphology changed, the distribution of cells in the morphospace also changed. However, this morphospace had a very high dimension. We reduced it to a 2-dimensional "reduced morphospace" and investigated the temporal change in the spatial distribution of cells in this reduced space. We used proper orthogonal decomposition to find dominant dynamical features of this spatio-temporal data. The modal analysis detected key features of EMT in this experimental system - reversible transition, distinct paths of phenotypic transition during induction and reversal of EMT, and enhanced diversity of cells during reversal of EMT. We also provide some intuitive physical meaning of the spatial modes and connect them to the key molecular event during EMT., Comment: 33 pages, 8 figures

The phonon-mediated hybrid detector is made out of a monolithic silicon crystal characterized by two interconnected regions linked through a narrow neck. Operating solely on phonon signal measurements, the hybrid design facilitates the differentiation between electron recoil and nuclear recoil events, effectively discerning two types of interaction down to low energy levels. With a newly implemented software triggering technique (SWT), low-energy nuclear recoil events of approximately $500~eV_{ee}$ have been measured. In addition to this, an electron recoil background reduction of up to $95\%$ has been successfully demonstrated.

We measured the nuclear--recoil ionization yield in silicon with a cryogenic phonon-sensitive gram-scale detector. Neutrons from a mono-energetic beam scatter off of the silicon nuclei at angles corresponding to energy depositions from 4\,keV down to 100\,eV, the lowest energy probed so far. The results show no sign of an ionization production threshold above 100\,eV. These results call for further investigation of the ionization yield theory and a comprehensive determination of the detector response function at energies below the keV scale.

We present a new analysis of previously published of SuperCDMS data using a profile likelihood framework to search for sub-GeV dark matter (DM) particles through two inelastic scattering channels: bremsstrahlung radiation and the Migdal effect. By considering these possible inelastic scattering channels, experimental sensitivity can be extended to DM masses that are undetectable through the DM-nucleon elastic scattering channel, given the energy threshold of current experiments. We exclude DM masses down to $220~\textrm{MeV}/c^2$ at $2.7 \times 10^{-30}~\textrm{cm}^2$ via the bremsstrahlung channel. The Migdal channel search provides overall considerably more stringent limits and excludes DM masses down to $30~\textrm{MeV}/c^2$ at $5.0 \times 10^{-30}~\textrm{cm}^2$., Comment: Submitted to PRD

CDMSlite Run 2 was a search for weakly interacting massive particles (WIMPs) with a cryogenic 600 g Ge detector operated in a high-voltage mode to optimize sensitivity to WIMPs of relatively low mass from 2 - 20 GeV/$c^2$. In this article, we present an effective field theory (EFT) analysis of the CDMSlite Run 2 data using an extended energy range and a comprehensive treatment of the expected background. A binned likelihood Bayesian analysis was performed on the recoil energy data, taking into account the parameters of the EFT interactions and optimizing the data selection with respect to the dominant background components. Energy regions within 5$\sigma$ of known activation peaks were removed from the analysis. The Bayesian evidences resulting from the different operator hypotheses show that the CDMSlite Run 2 data are consistent with the background-only models and do not allow for a signal interpretation assuming any additional EFT interaction. Consequently, upper limits on the WIMP mass and coupling-coefficient amplitudes and phases are presented for each EFT operator. These limits improve previous CDMSlite Run 2 bounds for WIMP masses above 5 GeV/$c^2$., Comment: 16 pages, 8 figures

Recent experiments searching for sub-GeV/$c^2$ dark matter have observed event excesses close to their respective energy thresholds. Although specific to the individual technologies, the measured excess event rates have been consistently reported at or below event energies of a few-hundred eV, or with charges of a few electron-hole pairs. In the present work, we operated a 1-gram silicon SuperCDMS-HVeV detector at three voltages across the crystal (0 V, 60 V and 100 V). The 0 V data show an excess of events in the tens of eV region. Despite this event excess, we demonstrate the ability to set a competitive exclusion limit on the spin-independent dark matter--nucleon elastic scattering cross section for dark matter masses of $\mathcal{O}(100)$ MeV/$c^2$, enabled by operation of the detector at 0 V potential and achievement of a very low $\mathcal{O}(10)$ eV threshold for nuclear recoils. Comparing the data acquired at 0 V, 60 V and 100 V potentials across the crystal, we investigated possible sources of the unexpected events observed at low energy. The data indicate that the dominant contribution to the excess is consistent with a hypothesized luminescence from the printed circuit boards used in the detector holder.

Low mass nuclear recoil dark matter and coherent-elastic-neutrino-nucleus-scattering (CENNS) searches confront similar challenges in choosing ultra-low threshold and large-mass detectors. We report experimental results from the first-of-its-kind 100 g single-crystal sapphire detector design with a diameter of 76 mm and thickness of 4 mm. The detector is designed to be sensitive for low-energy rare interactions with an intention to investigate the low mass region of dark matter phase-space and search for CENNS at the reactor site. Sapphire is a crystal of aluminum oxide (Al2O3) and has been found to be a good candidate for light mass spin-dependent dark matter search experiments due to its lower atomic mass compared to other detector materials such as germanium and silicon. Using the data collected from the test facility at Texas A&M University, we were able to resolve low energy lines from calibration sources and estimated that our newly developed sapphire detector has a baseline recoil energy resolution of 18 eV. These detectors are operated at 0 V with the phonon-assisted detection providing a quenching-free low-threshold operation., Comment: 9 pages, 6 figures

The SuperCDMS Collaboration is currently building SuperCDMS SNOLAB, a dark matter search focused on nucleon-coupled dark matter in the 1-5 GeV/c$^2$ mass range. Looking to the future, the Collaboration has developed a set of experience-based upgrade scenarios, as well as novel directions, to extend the search for dark matter using the SuperCDMS technology in the SNOLAB facility. The experienced-based scenarios are forecasted to probe many square decades of unexplored dark matter parameter space below 5 GeV/c$^2$, covering over 6 decades in mass: 1-100 eV/c$^2$ for dark photons and axion-like particles, 1-100 MeV/c$^2$ for dark-photon-coupled light dark matter, and 0.05-5 GeV/c$^2$ for nucleon-coupled dark matter. They will reach the neutrino fog in the 0.5-5 GeV/c$^2$ mass range and test a variety of benchmark models and sharp targets. The novel directions involve greater departures from current SuperCDMS technology but promise even greater reach in the long run, and their development must begin now for them to be available in a timely fashion. The experienced-based upgrade scenarios rely mainly on dramatic improvements in detector performance based on demonstrated scaling laws and reasonable extrapolations of current performance. Importantly, these improvements in detector performance obviate significant reductions in background levels beyond current expectations for the SuperCDMS SNOLAB experiment. Given that the dominant limiting backgrounds for SuperCDMS SNOLAB are cosmogenically created radioisotopes in the detectors, likely amenable only to isotopic purification and an underground detector life-cycle from before crystal growth to detector testing, the potential cost and time savings are enormous and the necessary improvements much easier to prototype., Comment: contribution to Snowmass 2021; v2 updated (assorted corrections and improvements to forecasts) October 2022; v3 updated (corrected SuperCDMS SNOLAB sensitivity curves in upgrade forecast plots in body of text) April 2023

In this paper, we present a re-analysis of SuperCDMS data using a profile likelihood approach to search for sub-GeV dark matter particles (DM) through two inelastic scattering channels: bremsstrahlung radiation and the Migdal effect. By considering possible inelastic scattering channels, experimental sensitivity can be extended to DM masses that would otherwise be undetectable through the DM-nucleon elastic scattering channel, given the energy threshold of current experiments. We exclude DM masses down to $220~\textrm{MeV}/c^2$ at $2.7 \times 10^{-30}~\textrm{cm}^2$ via the bremsstrahlung channel. The Migdal channel search excludes DM masses down to $30~\textrm{MeV}/c^2$ at $5.0 \times 10^{-30}~\textrm{cm}^2$., Comment: This paper is being withdrawn due to an error in data selection during the analysis. Although incorrect, the limits are roughly representative of the sensitivity. The new corrected version of the result will be uploaded once ready

We report the fabrication and performance of an annular, cryogenic, phonon-mediated veto detector that can host an inner target detector, allowing substantial reduction in radiogenic backgrounds for rare event search experiments. A germanium veto detector of mass $\sim$500 g with an outer diameter of 76 mm and an inner diameter of 28 mm was produced. A 25 mm diameter germanium inner target detector of mass $\sim$10 g was mounted inside the veto detector. The detector was designed using inputs from a GEANT4 based simulation, where it was modeled to be sandwiched between two germanium detectors. The simulation showed that the background rates (dominantly gamma interactions) could be reduced by $>$ 90$\%$, and that such an arrangement is sufficient for aggressive background reduction needed for neutrino and dark matter search experiments. During testing at the experimental site the veto detector prototype achieved a baseline resolution of 1.24 $\pm$ 0.02 keV while hosting a functional inner target detector. The baseline resolution of the inner target detector was 147 $\pm$ 2 eV. The detectors were operated at mK temperatures. The experimental results of an identical detector arrangement are in excellent agreement with the simulation., Comment: 8 pages and 9 figures

Two photo-neutron sources, $^{88}$Y$^{9}$Be and $^{124}$Sb$^{9}$Be, have been used to investigate the ionization yield of nuclear recoils in the CDMSlite germanium detectors by the SuperCDMS collaboration. This work evaluates the yield for nuclear recoil energies between 1 keV and 7 keV at a temperature of $\sim$ 50 mK. We use a Geant4 simulation to model the neutron spectrum assuming a charge yield model that is a generalization of the standard Lindhard model and consists of two energy dependent parameters. We perform a likelihood analysis using the simulated neutron spectrum, modeled background, and experimental data to obtain the best fit values of the yield model. The ionization yield between recoil energies of 1 keV and 7 keV is shown to be significantly lower than predicted by the standard Lindhard model for germanium. There is a general lack of agreement among different experiments using a variety of techniques studying the low-energy range of the nuclear recoil yield, which is most critical for interpretation of direct dark matter searches. This suggests complexity in the physical process that many direct detection experiments use to model their primary signal detection mechanism and highlights the need for further studies to clarify underlying systematic effects that have not been well understood up to this point.

Many low-threshold experiments observe sharply rising event rates of yet unknown origins below a few hundred eV, and larger than expected from known backgrounds. Due to the significant impact of this excess on the dark matter or neutrino sensitivity of these experiments, a collective effort has been started to share the knowledge about the individual observations. For this, the EXCESS Workshop was initiated. In its first iteration in June 2021, ten rare event search collaborations contributed to this initiative via talks and discussions. The contributing collaborations were CONNIE, CRESST, DAMIC, EDELWEISS, MINER, NEWS-G, NUCLEUS, RICOCHET, SENSEI and SuperCDMS. They presented data about their observed energy spectra and known backgrounds together with details about the respective measurements. In this paper, we summarize the presented information and give a comprehensive overview of the similarities and differences between the distinct measurements. The provided data is furthermore publicly available on the workshop's data repository together with a plotting tool for visualization., Comment: 44 pages, 20 figures; Editors: A. Fuss, M. Kaznacheeva, F. Reindl, F. Wagner; updated copyright statements and funding information

We report the first results of a search for leptophobic dark matter (DM) from the Coherent CAPTAIN-Mills (CCM) liquid argon (LAr) detector. An engineering run with 120 photomultiplier tubes (PMTs) and $17.9 \times 10^{20}$ protons-on-target (POT) was performed in Fall 2019 to study the characteristics of the CCM detector. The operation of this 10-ton detector was strictly light-based with a threshold of 50 keV and used coherent elastic scattering off argon nuclei to detect DM. Despite only 1.5 months of accumulated luminosity, contaminated LAr, and non-optimized shielding, CCM's first engineering run already achieved sensitivity to previously unexplored parameter space of light dark matter (LDM) models with a baryonic vector portal. With an expected background of 115,005 events, we observe 115,005+16.5 events which is compatible with background expectations. For a benchmark mediator-to-dark matter mass ratio of $m_{_{V_B}}/m_{\chi}=2.1$, DM masses within the range $9\,\text{MeV} \lesssim m_\chi \lesssim 50\,\text{MeV}$ have been excluded at 90% C.L. in the leptophobic model after applying the Feldman-Cousins test statistic. CCM's upgraded run with 200 PMTs, filtered LAr, improved shielding, and ten times more POT will be able to exclude the remaining thermal relic density parameter space of this model, as well as probe new parameter space of other leptophobic DM models.

This paper describes the operation of the Coherent CAPTAIN-Mills (CCM) detector located at the Lujan Neutron Science Center (LANSCE) at Los Alamos National Laboratory (LANL). CCM is a 10-ton liquid argon (LAr) detector located 20 meters from a high flux neutron/neutrino source and is designed to search for sterile neutrinos ($\nu_s$) and light dark matter (LDM). An engineering run was performed in Fall 2019 to study the characteristics of the CCM120 detector by searching for coherent scattering signals consistent with $\nu_s$'s and LDM resulting from $\pi^+$ and $\pi^0$ decays in the tungsten target. New parameter space in a leptophobic dark matter model was excluded for DM masses between $\sim2.0$ and 30 MeV. The lessons learned from this run have guided the development and construction of the new CCM200 detector that will begin operations in 2021 and significantly improve on these searches.

The Cryogenic Dark Matter Search low ionization threshold experiment (CDMSlite) achieved efficient detection of very small recoil energies in its germanium target, resulting in sensitivity to Lightly Ionizing Particles (LIPs) in a previously unexplored region of charge, mass, and velocity parameter space. We report first direct-detection limits calculated using the optimum interval method on the vertical intensity of cosmogenically-produced LIPs with an electric charge smaller than $e/(3\times10^5$), as well as the strongest limits for charge $\leq e/160$, with a minimum vertical intensity of $1.36\times10^{-7}$\,cm$^{-2}$s$^{-1}$sr$^{-1}$ at charge $e/160$. These results apply over a wide range of LIP masses (5\,MeV/$c^2$ to 100\,TeV/$c^2$) and cover a wide range of $\beta\gamma$ values (0.1 -- $10^6$), thus excluding non-relativistic LIPs with $\beta\gamma$ as small as 0.1 for the first time.

Large mass single-electron-resolution solid state detectors are desirable to search for low mass dark matter candidates and to measure coherent elastic neutrino nucleus scattering (CE$\nu$NS). Here, we present results from a novel 100 g phonon-mediated Si detector with a new interface architecture. This detector gives a baseline resolution of $\sim 1 e^{-}/h^{+}$ pair and a leakage current on the order of $10^{-16}$ A. This was achieved by removing the direct electrical contact between the Si crystal and the metallic electrode, and by increasing the phonon absorption efficiency of the sensors. The phonon signal amplification in the detector shows a linear increase while the signal to noise ratio improves with bias voltage, up to 240 V. This feature enables the detector to operate at a low energy threshold which is beneficial for dark matter and CE$\nu$NS like searches., Comment: 6 pages, 5 figures

An accurate assessment of the cardiovascular system and prediction of cardiovascular diseases (CVDs) are crucial. Measured cardiac blood flow data provide insights about patient-specific hemodynamics, where many specialized techniques have been developed for the visual exploration of such data sets to better understand the influence of morphological and hemodynamic conditions on CVDs. However, there is a lack of machine learning approaches techniques that allow a feature-based classification of heart-healthy people and patients with CVDs. In this work, we investigate the potential of morphological and hemodynamic characteristics, extracted from measured blood flow data in the aorta, for the classification of heart-healthy volunteers and patients with bicuspid aortic valve (BAV). Furthermore, we research if there are characteristic features to classify male and female as well as older heart-healthy volunteers and BAV patients. We propose a data analysis pipeline for the classification of the cardiac status, encompassing feature selection, model training and hyperparameter tuning. In our experiments, we use several feature selection methods and classification algorithms to train separate models for the healthy subgroups and BAV patients. We report on classification performance and investigate the predictive power of morphological and hemodynamic features with regard to the classification of the defined groups. Finally, we identify the key features for the best models., Comment: 29 pages, 7 figures

Time integrated spectroscopic measurements are carried out to characterize transient plasma stream produced in a coaxial pulsed plasma accelerator. This method allows the estimation of different plasma parameters and its evolution with time. It also provides information on the existence of different excited states from the spectral emissions of plasma. Using Argon as the discharge medium, the electron density estimated from Stark broadened line profiles gives a peak value $\sim 5 \times 10^{21} m^{-3}$ at a discharge voltage of 15 kV and the flow velocity of the plasma stream is measured to be $\sim (22 + 5)$ Km using Doppler shift method. Assuming p-LTE model, the electron excitation temperature is found to be $\sim 0.88$ eV using Boltzmann plot method. A temporal evolution of the plasma stream and its characteristic variation is studied from a time of $50 \mu s-300 \mu s$ in steps of $50 \mu s$ by adjusting delay time in the triggering. Analysis of different spectral lines shows the existence of some metastable states of Ar II having a long lifetime. The evolution of different Ar II transitions to metastable and non-metastable lower levels is observed for different time frame. The temporal evolution study shows a decrease in electron density from $1.96 \times 10^{21} m^{-3}$ to $1.23 \times 10^{20} m^{-3}$ at $300 \mu s$ after the initiation of plasma formation. A decrease in excitation temperature from 0.86 eV to 0.72 eV is observed till $250 \mu s$ and then again rises to 0.77 eV at $300 \mu s$

We present limits on spin-independent dark matter-nucleon interactions using a $10.6$ $\mathrm{g}$ Si athermal phonon detector with a baseline energy resolution of $\sigma_E=3.86 \pm 0.04$ $(\mathrm{stat.})^{+0.19}_{-0.00}$ $(\mathrm{syst.})$ $\mathrm{eV}$. This exclusion analysis sets the most stringent dark matter-nucleon scattering cross-section limits achieved by a cryogenic detector for dark matter particle masses from $93$ to $140$ $\mathrm{MeV}/c^2$, with a raw exposure of $9.9$ $\mathrm{g}\cdot\mathrm{d}$ acquired at an above-ground facility. This work illustrates the scientific potential of detectors with athermal phonon sensors with eV-scale energy resolution for future dark matter searches., Comment: 7 pages, 4 figures, this version includes ancillary files from official data release

We report the first demonstration of a phonon-mediated silicon detector technology that provides a primary phonon measurement in a low-voltage region, and a simultaneous indirect measurement of the ionization signal through Neganov-Trofimov-Luke amplification in a high voltage region, both in a monolithic crystal. We present characterization of charge and phonon transport between the two stages of the detector and the resulting background discrimination capability at low energies. This new detector technology has the potential to significantly enhance the sensitivity of dark matter and coherent neutrino scattering experiments beyond the capabilities of current technologies that have limited discrimination at low energies.

This article presents an analysis and the resulting limits on light dark matter inelastically scattering off of electrons, and on dark photon and axion-like particle absorption, using a second-generation SuperCDMS high-voltage eV-resolution detector. The 0.93 gram Si detector achieved a 3 eV phonon energy resolution; for a detector bias of 100 V, this corresponds to a charge resolution of 3% of a single electron-hole pair. The energy spectrum is reported from a blind analysis with 1.2 gram-days of exposure acquired in an above-ground laboratory. With charge carrier trapping and impact ionization effects incorporated into the dark matter signal models, the dark matter-electron cross section $\bar{\sigma}_{e}$ is constrained for dark matter masses from 0.5--$10^{4} $MeV$/c^{2}$; in the mass range from 1.2--50 eV$/c^{2}$ the dark photon kinetic mixing parameter $\varepsilon$ and the axioelectric coupling constant $g_{ae}$ are constrained. The minimum 90% confidence-level upper limits within the above mentioned mass ranges are $\bar{\sigma}_{e}\,=\,8.7\times10^{-34}$ cm$^{2}$, $\varepsilon\,=\,3.3\times10^{-14}$, and $g_{ae}\,=\,1.0\times10^{-9}$., Comment: 5 pages + title and references, 3 figures and 1 table