Minimal pairs approach

OBJECTIVE: Simulation training for minimally invasive colorectal procedures is in developing stages. This study aims to assess the impact of simulation on procedural knowledge and simulated performance in laparoscopic low anterior resection (LLAR) and robotic right colectomy (RRC). DESIGN: LLAR and RRC simulation procedures were designed using human cadaveric models. Resident case experience and simulation selfassessments scores for operative ability and knowledge were collected before and after the simulation...

BACKGROUND AND OBJECTIVE: A notable paradigm shift has emerged in the choice of prostate biopsy approach, with a transition from transrectal biopsy (TRBx) to transperineal biopsy (TPBx) driven by the lower risk of severe urinary tract infections. The impact of this change on detection of clinically significant prostate cancer (csPCa) remains a subject of debate. Our aim was to compare the csPCa detection rate of TRBx and TPBx. METHODS: Patients who underwent magnetic resonance imaging (MRI)-targeted and systematic biopsies for clinically localized PCa at 15 European referral centers from 2016 to 2023 were included...

INTRODUCTION: Minimally invasive Pancreatoduodenectomy (MIPD), or the Whipple procedure, is increasingly utilized. No study has compared laparoscopic (LPD) and robotic (RPD) approaches, and the impact of the learning curve on oncologic, technical, and post-operative outcomes remains relatively understudied. METHODS: The National Cancer Database was queried for patients undergoing LPD or RPD from 2010 to 2020 with a diagnosis of pancreatic cancer. Outcomes were compared between approaches using propensity-score matching (PSM); the impact of annual center-level volume of MIPD was also assessed by dividing volume into quartiles...

Recent developments in synthetic biology, next-generation sequencing, and machine learning provide an unprecedented opportunity to rationally design new disease treatments based on measured responses to gene perturbations and drugs to reprogram cells. The main challenges to seizing this opportunity are the incomplete knowledge of the cellular network and the combinatorial explosion of possible interventions, both of which are insurmountable by experiments. To address these challenges, we develop a transfer learning approach to control cell behavior that is pre-trained on transcriptomic data associated with human cell fates, thereby generating a model of the network dynamics that can be transferred to specific reprogramming goals...

Bispecific antibodies (BsAbs) represent an emerging class of biologics that can recognize two different antigens or epitopes. T-cell engagers (TcEs) bind two targets in trans on the cell surface of the effector and target cell to induce proximal immune effects, opening exciting windows for immunotherapies. To date, the engineering of BsAbs has been mainly focused on tuning the molecular weight and valency. However, the effects of spatial factors on the biological functions of BsAbs have been less explored due to the lack of biochemical methods to precisely manipulate protein geometry...

BACKGROUND: Anatomical sectionectomy based on Takasaki's segmentation has shown advantages in hepatocellular carcinoma. However, whether this approach improves the survival of intrahepatic cholangiocarcinoma (ICC) remains unknown. METHODS: A series of 248 consecutive patients with solitary ICCs who underwent hepatectomy were studied retrospectively. The patients were classified into the groups of anatomical sectionectomy based on Takasaki's segmentation (TS group) and non-Takasaki's hepatectomy (NTH group)...

Objective
Performing PET denoising within the image space proves effective in reducing the variance in PET images. In recent years, deep learning has demonstrated superior denoising performance, but models trained on a specific noise level typically fail to generalize well on different noise levels, due to inherent distribution shifts between inputs. The distribution shift usually results in bias in the denoised images. Our goal is to tackle such a problem using a domain generalization technique.
Approach
We propose to utilize the domain generalization technique with a novel feature space continuous discriminator (CD) for adversarial training, using the fraction of events as a continuous domain label...

Histopathologic diagnosis and classification of cancer plays a critical role in guiding treatment. Advances in next-generation sequencing have ushered in new complementary molecular frameworks. However, existing approaches do not independently assess both site-of-origin (e.g. prostate) and lineage (e.g. adenocarcinoma) and have minimal validation in metastatic disease, where classification is more difficult. Utilizing gradient-boosted machine learning, we developed ATLAS, a pair of separate AI Tumor Lineage and Site-of-origin models from RNA expression data on 8249 tumor samples...

MOF-808, a metal-organic framework containing Zr6 O8 clusters, can serve as a secure anchoring point for stabilizing copper single-sites with redox activity, thus making it a promising candidate for catalytic applications. In this study, we target the incorporation of Cu-MOF-808 into a mixed-matrix membrane for the degradation of tyrosol, an emerging endocrine-disrupting compound commonly found in water sources, through Fenton reactions, developing innovative technologies for water treatment. We successfully demonstrate the effectiveness of this approach by preparing catalytic membranes with minimal metal leaching, which is one of the primary challenges in developing copper-based Fenton heterogeneous catalysts...

A polygenic risk score (PRS) combines the associations of multiple genetic variants that could be due to direct causal effects, indirect genetic effects, or other sources of familial confounding. We have developed new approaches to assess evidence for and against causation by using family data for pairs of relatives (Inference about Causation from Examination of FAmiliaL CONfounding [ICE FALCON]) or measures of family history (Inference about Causation from Examining Changes in Regression coefficients and Innovative STatistical AnaLyses [ICE CRISTAL])...

A unique assembly of a two-electron superatom, [Ag10 {S2 P(O i Pr)2 }8 ], as a primary building unit in the construction of a supramolecule [Ag10 {S2 P(O i Pr)2 }8 ]2 (μ-4,4'-bpy) through a 4,4'-bipyridine (4,4'-bpy) linker is reported. This approach is facilitated by an open site in the structure that allows for effective pairing. The assembled structure demonstrates a minimal solvatochromic shift across organic solvents with variable polarities, highlighting the influence of self-assembly on the photophysical properties of silver nanoclusters...

Undesired on- and off-target effects of CRISPR-Cas nucleases remain a challenge in genome editing. While the use of Cas9 nickases has been shown to minimize off-target mutagenesis, their use in therapeutic genome editing has been hampered by a lack of efficacy. To overcome this limitation, we and others have developed double nickase-based strategies to generate staggered DNA double-strand breaks to mediate gene disruption or gene correction with high efficiency. However, the impact of paired single-strand nicks on genome integrity has remained largely unexplored...

Recent developments in synthetic biology, next-generation sequencing, and machine learning provide an unprecedented opportunity to rationally design new disease treatments based on measured responses to gene perturbations and drugs to reprogram cells. The main challenges to seizing this opportunity are the incomplete knowledge of the cellular network and the combinatorial explosion of possible interventions, both of which are insurmountable by experiments. To address these challenges, we develop a transfer learning approach to control cell behavior that is pre-trained on transcriptomic data associated with human cell fates, thereby generating a model of the network dynamics that can be transferred to specific reprogramming goals...

Activity descriptors are a powerful tool for the design of catalysts that can efficiently utilize H2 with minimal energy losses. In this study, we develop the use of hydricity and H- self-exchange rates as thermodynamic and kinetic descriptors for the hydrogenation of ketones by molecular catalysts. Two complexes with known hydricity, HRh(dmpe)2 and HCo(dmpe)2 , were investigated for the catalytic hydrogenation of ketones under mild conditions (1.5 atm and 25 °C). The rhodium catalyst proved to be an efficient catalyst for a wide range of ketones, whereas the cobalt catalyst could only hydrogenate electron-deficient ketones...

This study explores a novel approach to address the challenges of delivering highly water-soluble drug molecules by employing hydrophobic ion-pairing (HIP) complexes within poly (lactic-co-glycolic acid) (PLGA) microspheres. The HIP complex, formed between doxycycline hyclate (DH) and docusate sodium (DS), renders the drug hydrophobic. The development of the microspheres was done using the QbD approach, namely, Box-Behnken Design (BBD). A comprehensive characterization of the HIP complex confirmed the successful conversion of DH...

Flexible endoscopes are ideal instruments for visualizing and diagnosing the inner surfaces of organs via a minimally invasive incision. Calibrating a flexible endoscope is a troublesome yet inevitable process in image-based tools tracking. Aiming to simplify the calibration process, we propose an electromagnetic (EM)-tracked calibration approach that does not require any predefined poses of the EM sensor. A three-stage calibration protocol was presented in an extensor. First, the orientation of the endoscope tube was derived by conducting a circular rotation of the endoscope around its axis utilizing a pair of tightly bearing stands...

Organisms must regulate their behavior flexibly in the face of environmental challenges. Failure can lead to a host of maladaptive behavioral traits associated with a range of neuropsychiatric disorders, including attention deficit hyperactivity disorder, autism, and substance use disorders. This maladaptive dysregulation of behavior is influenced by genetic and environmental factors. For example, environmental enrichment produces beneficial neurobehavioral effects in animal models of such disorders. The present study determined the effects of environmental enrichment on a range of measures related to behavioral regulation using a large cohort of male, outbred heterogeneous stock (HS) rats as subjects...

In the present work, a new form of descriptor using minimal moment vector (MMV) is introduced to compare protein sequences in the frequency domain under their component wise binary representations. From every sequence, 20 different binary component sequences are formed, each corresponding to 20 amino acids. Each such vector is now shifted from the time domain to the frequency domain by applying the Fast Fourier Transform (FFT). Next, the power spectrum calculated from the FFT values for each component sequence is so normalized that the sum of the components equals 1...

Large language models (LLMs) have been shown to have significant potential in few-shot learning across various fields, even with minimal training data. However, their ability to generalize to unseen tasks in more complex fields, such as biology and medicine has yet to be fully evaluated. LLMs can offer a promising alternative approach for biological inference, particularly in cases where structured data and sample size are limited, by extracting prior knowledge from text corpora. Here we report our proposed few-shot learning approach, which uses LLMs to predict the synergy of drug pairs in rare tissues that lack structured data and features...

The rise in infections caused by multidrug-resistant (MDR) bacteria has necessitated a variety of clinical approaches, including the use of antibiotic combinations. Here, we tested the hypothesis that drug-drug interactions vary in different media, and determined which in vitro models best predict drug interactions in the lungs. We systematically studied pair-wise antibiotic interactions in three different media, CAMHB, (a rich lab medium standard for antibiotic susceptibility testing), a urine mimetic medium (UMM), and a minimal medium of M9 salts supplemented with glucose and iron (M9Glu) with three Gram-negative ESKAPE pathogens, Acinetobacter baumannii (Ab), Klebsiella pneumoniae (Kp), and Pseudomonas aeruginosa (Pa)...