Title
Topic
-
‘Mechanomemory of Nucleoplasm and RNA Polymerase II After Chromatin Stretching by a Microinjected Magnetic Nanoparticle Force’
With this paper, professor of bioengineering Ning Wang, working with Ph.D. students Fazlur Rashid and Sadia Kabbo, demonstrates a process of “mechanomemory” in the chromatin of cells. “The mechanics of chromatin and nucleoplasm regulate gene transcription and nuclear function,” they write. “However, how the chromatin and nucleoplasm sense and respond to forces remains elusive.” Their results imply that “the viscoelastic behavior of the chromatin … provide[s] concrete evidence that the chromatin does not behave like a pure liquid, as concluded in one study, nor like a solid, as concluded in another study.” Find the full paper in Cell Reports.
-
‘Strategic Behavior of Large Language Models and the Role of Game Structure Versus Contextual Framing’
“This paper investigates the strategic behavior of large language models (LLMs) across various game-theoretic settings, scrutinizing the interplay between game structure and contextual framing in decision-making. We focus our analysis on three advanced LLMs—GPT-3.5, GPT-4, and LLaMa-2—and how they navigate both the intrinsic aspects of different games and the nuances of their surrounding contexts. Our results highlight discernible patterns in each model’s strategic approach.” Find the paper and full list of authors in Scientific Reports.
-
‘Lipid Nanoparticles Target Haematopoietic Stem Cells’
In this review, University Distinguished Professor of pharmaceutical sciences and chemical engineering Mansoor Amiji, with co-author Dimitrios Bitounis, discuss “a novel class of non-viral lipid nanoparticle (LNP)-based formulations for the in vivo delivery of genetic therapies to HSC [haematopoietic stem cells] in the bone marrow with the potential to treat blood disorders,” which have the potential to overcome clinical risks that “require removal of the patients own HSC, their curative modification, and transplantation back to the patient.”
-
‘Sweet and sensitive CE-MS method for quantitative characterization of native N-glycomes’
The Ivanov Lab has published a blog post detailing their “development of innovative sample preparation and nanoflow-based liquid phase separation techniques coupled with mass spectrometry for molecular (e.g., proteomic, glycomic) profiling of amount-limited biological and biomedically-relevant samples,” they write. “By minimizing the number of sample preparation steps and employing more efficient, low volume (nL-/pL-level)-based analytical techniques, we aim to detect, identify, structurally characterize, and quantify more molecular features (e.g., proteins and glycans) at lower sample amounts compared to conventional techniques.” Find the blog post and full list of authors in Springer Nature’s Chemistry Research Community.
-
‘Methods for assessing and removing non-specific photoimmunotherapy damage in patient-derived tumor cell culture models’
“Tumor-targeted, activatable photoimmunotherapy (taPIT) has been shown to selectively destroy tumor in a metastatic mouse model. However, the photoimmunoconjugate (PIC) used for taPIT includes a small fraction of non-covalently associated (free) benzoporphyrin derivative (BPD), which leads to non-specific killing in vitro. Here, we report a new treatment protocol for patient-derived primary tumor cell cultures ultrasensitive to BPD photodynamic therapy (BPD-PDT). … The modifications in the protocol suggested here improve in vitro taPIT experiments that lack in vivo mechanisms of free BPD clearance (i.e., lymph and blood flow).”Find the paper and full list of authors at Photochemistry and Photobiology.
-
Wegst presents primer on ‘Freeze casting’
“When solutions and slurries are directionally solidified, complex dynamics of solvent crystal growth and solvent templating determine the final hierarchical architecture of the freeze-cast material. With continuous X-ray tomoscopy, it is now possible to study in situ intricate and otherwise elusive ice crystal growth and solvent-templating phenomena. … The freeze casting process is attractive because the features of the final hierarchical material architecture … can be custom designed for a given application … [and] can be tailored for applications in, for example, biomedicine, environmental engineering, catalysis, power conversion, and energy generation and storage.Find the paper and full list of authors…
-
‘Experimentally Probing the Effect of Confinement Geometry on Lipid Diffusion’
“The lateral mobility of molecules within the cell membrane is ultimately governed by the local environment of the membrane. … Here, we prepare model lipid systems on substrates patterned with confined domains of varying geometries constructed with different materials to explore the influences of physical boundary conditions and specific molecular interactions on diffusion. We demonstrate a platform that is capable of significantly altering and steering the long-range diffusion of lipids by using simple oxide deposition approaches, enabling us to systematically explore how confinement size and shape impact diffusion.”Find the paper and authors list in the Journal of Physical Chemistry B.
-
‘Rapidly Changing Range Limits in a Warming World: Critical Data Limitations and Knowledge Gaps for Advancing Understanding of Mangrove Range Dynamics’
“Climate change is altering species’ range limits and transforming ecosystems. For example, warming temperatures are leading to the range expansion of tropical, cold-sensitive species at the expense of their cold-tolerant counterparts. In some temperate and subtropical coastal wetlands, warming winters are enabling mangrove forest encroachment into salt marsh, which is a major regime shift that has significant ecological and societal ramifications. Here, we synthesized existing data and expert knowledge to assess the distribution of mangroves near rapidly changing range limits in the southeastern USA.”Find the paper and full list of authors in Estuaries and Coasts.
-
‘Effects of Aerobic Exercise on Cognitive Function in Adults With Major Depressive Disorder: A Systematic Review and Meta-Analysis’
“Major Depressive Disorder (MDD) is a highly prevalent psychiatric disorder that impairs the cognitive function of individuals. Aerobic exercise stands out as a promising non-pharmacological intervention for enhancing cognitive function and promoting brain health. … Twelve randomized trials including 945 adults with MDD were included. Results indicated that aerobic exercise significantly improved overall cognitive function … and the sub-domains of memory … and executive function. … Significant benefits in cognitive function were found from moderate-to-vigorous (mixed) intensity … aerobic exercise conducted 3 times per week.”Find the paper and full list of authors in the International Journal of Clinical and Health Psychology.
-
‘Revisiting the Roles of Catalytic Residues in Human Ornithine Transcarbamylase’
“Human ornithine transcarbamylase (hOTC) is a mitochondrial transferase protein involved in the urea cycle and is crucial for the conversion of toxic ammonia to urea. Structural analysis coupled with kinetic studies of Escherichia coli, rat, bovine, and other transferase proteins has identified residues that play key roles in substrate recognition and conformational changes but has not provided direct evidence for all of the active residues involved. … Here, computational methods were used to predict the likely active residues of hOTC; the function of these residues was then probed with site-directed mutagenesis and biochemical characterization.”Find the paper and authors list in Biochemistry.
-
‘Framework for Department-Level Accountability To Diversify Engineering’
“Diverse teams are more innovative and creative. Nevertheless, science, technology, engineering and mathematics disciplines, including bioengineering, continue to fall short in increasing representation from persons from groups historically excluded because of their ethnicity or race. … In this Perspective, we present a framework for building, assessing and continuously improving strategic plans to improve recruitment and retention and to make departments more inclusive, including the collection of demographic data, the establishment and assessment of DEI plans, specific goal setting and assessment of achievements, with specific examples and guidelines.”Find the paper and full list of authors at Nature Reviews Bioengineering.
-
‘Geometric Origin of the Intrinsic Transverse Spin Transport in a Canted-Antiferromagnet/Heavy-Metal Heterostructure’
“We theoretically study the conditions under which an intrinsic spin Nernst effect—a transverse spin current induced by an applied temperature gradient—can occur in a canted-antiferromagnet insulator, such as LaFeO3 and other materials of the same family. … Our paper provides a general derivation of a symmetry-breaking-induced spin Nernst effect, which may open a path to engineering a finite spin Nernst effect in systems where it would otherwise not arise.” Find the paper and full list of authors at Physical Review B.
-
‘Synthesizing Tight Privacy and Accuracy Bounds via Weighted Model Counting’
“Programmatically generating tight differential privacy (DP) bounds is a hard problem. Two core challenges are (1) finding expressive, compact and efficient encodings of the distributions of DP algorithms and (2) state space explosion stemming from the multiple quantifiers and relational properties of the DP definition. We address the first challenge by developing a method for tight privacy and accuracy bound synthesis using weighted model counting on binary decision diagrams. … We address the second challenge by developing a framework for leveraging inherent symmetries in DP algorithms.” Find the paper and full list of authors at ArXiv.
-
‘The Joint Effect of Task Similarity and Overparameterization on Catastrophic Forgetting — An Analytical Model’
“In continual learning, catastrophic forgetting is affected by multiple aspects of the tasks. Previous works have analyzed separately how forgetting is affected by either task similarity or overparameterization. In contrast, our paper examines how task similarity and overparameterization jointly affect forgetting in an analyzable model. Specifically, we focus on two-task continual linear regression, where the second task is a random orthogonal transformation of an arbitrary first task (an abstraction of random permutation tasks). We derive an exact analytical expression for the expected forgetting — and uncover a nuanced pattern.” Find the paper and full list of authors at ArXiv.
-
‘Project-Based Activities to Introduce Hardware in a Software-Focused Course’
“This workshop introduces attendees to the low-level components used in the design of computer hardware, allowing them to experiment with the hardware-software interface. Attendees explore hands-on experiments that are designed for students unlikely to encounter hardware topics in their course of study. These experiments are offered in bridge courses of a graduate program enrolling students without a Computer Science background at Northeastern University (the Align MSCS Program). The workshop consists of 3 groupings of hardware experiments. In one grouping, attendees use breadboarding to construct digital circuits.” Find the paper and full list of authors in the SIGCSE 2024 proceedings.
-
‘Stability of P2P Networks Under Greedy Peering (Full Version)’
“Major cryptocurrency networks have relied on random peering choice rules for making connections in their peer-to-peer networks. Generally, these choices have good properties, particularly for open, permissionless networks. Random peering choices however do not take into account that some actors may choose to optimize who they connect to such that they are quicker to hear about information being propagated in the network. In this paper, we explore the dynamics of such greedy strategies.” Find the paper and full list of authors at ArXiv.
-
‘SunBlock: Cloudless Protection for IoT Systems’
“With an increasing number of Internet of Things (IoT) devices present in homes, there is a rise in the number of potential information leakage channels and their associated security threats and privacy risks. Despite a long history of attacks on IoT devices in unprotected home networks, the problem of accurate, rapid detection and prevention of such attacks remains open. … This paper investigates the potential for effective IoT threat detection locally, on a home router, using AI tools combined with classic rule-based traffic-filtering algorithms.” Find the paper and full list of authors at ArXiv.
-
‘A Survey on Hypergraph Mining: Patterns, Tools and Generators’
“Hypergraphs are a natural and powerful choice for modeling group interactions in the real world, which are often referred to as higher-order networks. For example, when modeling collaboration networks, where collaborations can involve not just two but three or more people, employing hypergraphs allows us to explore beyond pairwise (dyadic) patterns and capture groupwise (polyadic) patterns. … We provide comprehensive taxonomies for them, and we also provide in-depth discussions to provide insights into future research on hypergraph mining.” Find the paper and full list of authors at ArXiv.
-
‘RichWasm: Bringing Safe, Fine-Grained, Shared-Memory Interoperability Down to WebAssembly’
“Safe, shared-memory interoperability between languages with different type systems and memory-safety guarantees is an intricate problem as crossing language boundaries may result in memory-safety violations. In this paper, we present RichWasm, a novel richly typed intermediate language designed to serve as a compilation target for typed high-level languages with different memory-safety guarantees. RichWasm is based on WebAssembly and enables safe shared-memory interoperability by incorporating a variety of type features that support fine-grained memory ownership and sharing.” Find the paper and full list of authors at ArXiv.
-
‘Fine-Tuning Enhances Existing Mechanisms: A Case Study on Entity Tracking’
“Fine-tuning on generalized tasks such as instruction following, code generation, and mathematics has been shown to enhance language models’ performance on a range of tasks. Nevertheless, explanations of how such fine-tuning influences the internal computations in these models remain elusive. We study how fine-tuning affects the internal mechanisms implemented in language models. As a case study, we explore the property of entity tracking, a crucial facet of language comprehension, where models fine-tuned on mathematics have substantial performance gains.” Find the paper and full list of authors at ArXiv.
-
‘Measuring and Controlling Persona Drift in Language Model Dialogs’
“System-prompting is a standard tool for customizing language-model chatbots, enabling them to follow a specific instruction. An implicit assumption in the use of system prompts is that they will be stable, so the chatbot will continue to generate text according to the stipulated instructions for the duration of a conversation. We propose a quantitative benchmark to test this assumption, evaluating instruction stability via self-chats between two instructed chatbots. Testing popular models like LLaMA2-chat-70B and GPT-3.5, we reveal a significant instruction drift within eight rounds of conversations.” Find the paper and full list of authors at ArXiv.
-
‘Fully Dynamic Matching: (2-√2)-Approximation in Polylog Update Time’
“We study maximum matchings in fully dynamic graphs, … graphs that undergo both edge insertions and deletions. Our focus is on algorithms that estimate the size of maximum matching after each update while spending a small time. … We show that for any fixed ɛ > 0, a (2 — √2— ɛ) approximation can be maintained in poly(log n) time per update even in general graphs. Our techniques also lead to the same approximation for general graphs in two passes of the semi-streaming setting, removing a similar gap.” Find the paper and authors list in the 2024 Annual ACM-SIAM Symposium…
-
‘A Retrospective Study of One Decade of Artifact Evaluations’
“Reproducibility is a vital property of experimental and empirical research, without whichit is difficult to establish trust in derived conclusions. If results cannot be independently confirmed, they may be affected by observer bias or other confounding factors. As the full-scale reproduction of scientific results from a study takes significant time, which does not match well with the conference-focused publication in computer science, a lighter quality assurance mechanism for scientific work has been established. … After a decade of artifact evaluations, we analyze the impact they have had on published articles and artifacts.” Find the paper authors list at Software Engineering…
-
‘The Arrangement of Marks Impacts Afforded Messages: Ordering, Partitioning, Spacing and Coloring in Bar Charts’
“Data visualizations present a massive number of potential messages to an observer. … The message that a viewer tends to notice — the message that a visualization ‘affords’ — is strongly affected by how values are arranged in a chart, e.g., how the values are colored or positioned. … We present a set of empirical evaluations of how different messages … are afforded by variations in ordering, partitioning, spacing and coloring of values, within the ubiquitous case study of bar graphs.” Find the paper and full list of authors at Transactions on Visualization and Computer Graphics.